Starting phenix.real_space_refine on Thu Sep 26 15:37:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8b_10117/09_2024/6s8b_10117.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8b_10117/09_2024/6s8b_10117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8b_10117/09_2024/6s8b_10117.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8b_10117/09_2024/6s8b_10117.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8b_10117/09_2024/6s8b_10117.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8b_10117/09_2024/6s8b_10117.cif" } resolution = 2.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.723 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 3 7.51 5 Zn 1 6.06 5 P 98 5.49 5 S 103 5.16 5 C 39583 2.51 5 N 10243 2.21 5 O 12120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 287 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 62151 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1253 Classifications: {'peptide': 153} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 150} Chain: "B" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1261 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "C" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1261 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "D" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2274 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain: "E" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2274 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain: "F" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2274 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain: "G" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2273 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 274} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2468 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 8, 'TRANS': 295} Chain breaks: 1 Chain: "I" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2282 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 12, 'TRANS': 271} Chain: "J" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3889 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 469} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "U" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 933 Classifications: {'RNA': 44} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 18, 'rna3p_pyr': 19} Link IDs: {'rna2p': 7, 'rna3p': 36} Chain: "V" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1045 Classifications: {'RNA': 49} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 7, 'rna3p_pur': 17, 'rna3p_pyr': 13} Link IDs: {'rna2p': 19, 'rna3p': 29} Chain: "L" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "M" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "N" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "O" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "P" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "Q" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "R" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "S" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "T" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "W" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "X" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "l" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "m" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "n" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "o" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "p" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "q" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "r" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "s" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "t" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "w" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "x" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1378 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "K" Number of atoms: 8282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 8282 Classifications: {'peptide': 1009} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 973} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {' MN': 3, ' ZN': 1, 'ANP': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 57437 SG CYS K 464 65.143 99.839 40.875 1.00 51.25 S ATOM 57831 SG CYS K 515 60.911 99.070 40.929 1.00 57.32 S Time building chain proxies: 27.00, per 1000 atoms: 0.43 Number of scatterers: 62151 At special positions: 0 Unit cell: (150.592, 171.392, 248.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Mn 3 24.99 S 103 16.00 P 98 15.00 O 12120 8.00 N 10243 7.00 C 39583 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS R 63 " distance=2.03 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS Q 63 " distance=2.03 Simple disulfide: pdb=" SG CYS C 115 " - pdb=" SG CYS S 63 " distance=2.02 Simple disulfide: pdb=" SG CYS D 256 " - pdb=" SG CYS O 63 " distance=2.03 Simple disulfide: pdb=" SG CYS E 256 " - pdb=" SG CYS l 63 " distance=2.03 Simple disulfide: pdb=" SG CYS F 256 " - pdb=" SG CYS m 63 " distance=2.03 Simple disulfide: pdb=" SG CYS G 256 " - pdb=" SG CYS N 63 " distance=2.03 Simple disulfide: pdb=" SG CYS H 304 " - pdb=" SG CYS X 63 " distance=2.03 Simple disulfide: pdb=" SG CYS I 252 " - pdb=" SG CYS p 63 " distance=2.04 Simple disulfide: pdb=" SG CYS J 262 " - pdb=" SG CYS J 268 " distance=2.03 Simple disulfide: pdb=" SG CYS J 356 " - pdb=" SG CYS J 474 " distance=2.04 Simple disulfide: pdb=" SG CYS J 396 " - pdb=" SG CYS J 399 " distance=2.04 Simple disulfide: pdb=" SG CYS J 466 " - pdb=" SG CYS w 63 " distance=2.03 Simple disulfide: pdb=" SG CYS K 578 " - pdb=" SG CYS K 587 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.03 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K1101 " pdb="ZN ZN K1101 " - pdb=" SG CYS K 515 " pdb="ZN ZN K1101 " - pdb=" SG CYS K 464 " 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14250 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 0 sheets defined 29.9% alpha, 0.0% beta 29 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 14.44 Creating SS restraints... Processing helix chain 'A' and resid 4 through 21 removed outlier: 4.018A pdb=" N LYS A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 45 removed outlier: 4.017A pdb=" N VAL A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLU A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 56 removed outlier: 3.765A pdb=" N THR A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 71 removed outlier: 3.614A pdb=" N PHE A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 100 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 105 through 115 removed outlier: 3.531A pdb=" N CYS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 137 Proline residue: A 131 - end of helix removed outlier: 3.687A pdb=" N ALA A 135 " --> pdb=" O PRO A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 152 Processing helix chain 'B' and resid 4 through 21 removed outlier: 4.361A pdb=" N LYS B 8 " --> pdb=" O GLU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 45 removed outlier: 4.145A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLU B 39 " --> pdb=" O ARG B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 56 removed outlier: 3.521A pdb=" N THR B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 73 Processing helix chain 'B' and resid 81 through 101 Processing helix chain 'B' and resid 105 through 113 Processing helix chain 'B' and resid 116 through 129 removed outlier: 4.136A pdb=" N LEU B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 152 removed outlier: 3.940A pdb=" N ARG B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N THR B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TYR B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 21 removed outlier: 3.672A pdb=" N LYS C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 45 removed outlier: 3.638A pdb=" N LYS C 27 " --> pdb=" O HIS C 23 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 32 " --> pdb=" O GLN C 28 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLU C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.636A pdb=" N GLU C 58 " --> pdb=" O ILE C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 73 removed outlier: 3.974A pdb=" N PHE C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 101 removed outlier: 4.278A pdb=" N TYR C 87 " --> pdb=" O GLU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 115 Processing helix chain 'C' and resid 115 through 129 removed outlier: 3.763A pdb=" N ARG C 119 " --> pdb=" O CYS C 115 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 120 " --> pdb=" O GLU C 116 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 136 through 152 removed outlier: 3.594A pdb=" N TYR C 140 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 61 Processing helix chain 'D' and resid 64 through 73 Processing helix chain 'D' and resid 115 through 131 Processing helix chain 'D' and resid 136 through 148 Processing helix chain 'D' and resid 194 through 204 removed outlier: 4.834A pdb=" N GLU D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 257 removed outlier: 3.670A pdb=" N ILE D 252 " --> pdb=" O LYS D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 removed outlier: 3.697A pdb=" N LEU D 261 " --> pdb=" O LEU D 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 258 through 261' Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 281 through 285 Processing helix chain 'E' and resid 45 through 61 Processing helix chain 'E' and resid 64 through 72 Processing helix chain 'E' and resid 115 through 131 removed outlier: 3.567A pdb=" N GLN E 130 " --> pdb=" O ASP E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 148 Processing helix chain 'E' and resid 194 through 205 removed outlier: 3.641A pdb=" N GLU E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 256 Processing helix chain 'E' and resid 257 through 261 Processing helix chain 'E' and resid 269 through 273 Processing helix chain 'E' and resid 283 through 285 No H-bonds generated for 'chain 'E' and resid 283 through 285' Processing helix chain 'F' and resid 45 through 61 removed outlier: 3.742A pdb=" N LYS F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 72 Processing helix chain 'F' and resid 115 through 129 Processing helix chain 'F' and resid 136 through 149 removed outlier: 4.184A pdb=" N LYS F 149 " --> pdb=" O THR F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 206 removed outlier: 3.785A pdb=" N GLU F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 256 Processing helix chain 'F' and resid 257 through 261 Processing helix chain 'F' and resid 269 through 273 Processing helix chain 'F' and resid 281 through 286 removed outlier: 3.556A pdb=" N VAL F 285 " --> pdb=" O TRP F 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 61 Processing helix chain 'G' and resid 64 through 72 Processing helix chain 'G' and resid 115 through 130 removed outlier: 3.574A pdb=" N ILE G 128 " --> pdb=" O TYR G 124 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLN G 130 " --> pdb=" O ASP G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 149 removed outlier: 3.725A pdb=" N LYS G 140 " --> pdb=" O PHE G 136 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS G 149 " --> pdb=" O THR G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 206 removed outlier: 3.778A pdb=" N GLU G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 257 Processing helix chain 'G' and resid 269 through 273 Processing helix chain 'H' and resid 38 through 51 Processing helix chain 'H' and resid 59 through 68 removed outlier: 3.573A pdb=" N LEU H 67 " --> pdb=" O ASP H 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU H 68 " --> pdb=" O LEU H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 100 No H-bonds generated for 'chain 'H' and resid 98 through 100' Processing helix chain 'H' and resid 102 through 108 removed outlier: 3.640A pdb=" N GLU H 108 " --> pdb=" O PRO H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 124 Processing helix chain 'H' and resid 127 through 131 Processing helix chain 'H' and resid 225 through 232 removed outlier: 4.075A pdb=" N ASN H 232 " --> pdb=" O ASN H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 280 removed outlier: 4.024A pdb=" N ASP H 275 " --> pdb=" O ARG H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 296 Processing helix chain 'I' and resid 3 through 17 removed outlier: 4.829A pdb=" N LEU I 10 " --> pdb=" O LEU I 6 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLU I 11 " --> pdb=" O VAL I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 35 removed outlier: 3.686A pdb=" N ILE I 31 " --> pdb=" O SER I 27 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 40 Processing helix chain 'I' and resid 53 through 58 removed outlier: 3.579A pdb=" N ILE I 57 " --> pdb=" O LEU I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 88 Processing helix chain 'I' and resid 92 through 109 Processing helix chain 'I' and resid 133 through 138 Processing helix chain 'I' and resid 153 through 179 removed outlier: 7.703A pdb=" N GLU I 171 " --> pdb=" O GLY I 167 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N GLN I 172 " --> pdb=" O LYS I 168 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU I 173 " --> pdb=" O LEU I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 220 Processing helix chain 'I' and resid 247 through 261 removed outlier: 3.894A pdb=" N ILE I 251 " --> pdb=" O VAL I 247 " (cutoff:3.500A) Proline residue: I 256 - end of helix removed outlier: 3.612A pdb=" N LEU I 259 " --> pdb=" O MET I 255 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE I 260 " --> pdb=" O PRO I 256 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG I 261 " --> pdb=" O ILE I 257 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 270 removed outlier: 3.559A pdb=" N VAL I 269 " --> pdb=" O ARG I 266 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 58 Processing helix chain 'J' and resid 63 through 71 Processing helix chain 'J' and resid 71 through 76 Processing helix chain 'J' and resid 109 through 113 removed outlier: 3.571A pdb=" N ARG J 113 " --> pdb=" O ASP J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 159 Processing helix chain 'J' and resid 161 through 166 Processing helix chain 'J' and resid 167 through 169 No H-bonds generated for 'chain 'J' and resid 167 through 169' Processing helix chain 'J' and resid 181 through 199 removed outlier: 3.992A pdb=" N LEU J 185 " --> pdb=" O ASP J 181 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR J 199 " --> pdb=" O ASN J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 242 Processing helix chain 'J' and resid 247 through 251 Processing helix chain 'J' and resid 264 through 277 removed outlier: 7.182A pdb=" N LYS J 270 " --> pdb=" O SER J 266 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE J 271 " --> pdb=" O ILE J 267 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP J 273 " --> pdb=" O LYS J 269 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU J 274 " --> pdb=" O LYS J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 283 through 300 Processing helix chain 'J' and resid 338 through 351 removed outlier: 4.240A pdb=" N TYR J 347 " --> pdb=" O LEU J 343 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS J 348 " --> pdb=" O ALA J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 364 through 375 Processing helix chain 'J' and resid 389 through 394 Processing helix chain 'J' and resid 417 through 424 Processing helix chain 'J' and resid 462 through 475 removed outlier: 3.790A pdb=" N CYS J 466 " --> pdb=" O LYS J 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 141 Processing helix chain 'L' and resid 155 through 167 removed outlier: 3.708A pdb=" N VAL L 159 " --> pdb=" O LYS L 155 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP L 162 " --> pdb=" O LYS L 158 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE L 167 " --> pdb=" O ILE L 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 146 removed outlier: 3.937A pdb=" N LYS M 139 " --> pdb=" O ASN M 135 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP M 143 " --> pdb=" O LYS M 139 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS M 144 " --> pdb=" O GLU M 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 165 removed outlier: 4.194A pdb=" N ILE M 163 " --> pdb=" O VAL M 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 145 removed outlier: 5.043A pdb=" N ASP N 143 " --> pdb=" O LYS N 139 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS N 144 " --> pdb=" O GLU N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 155 through 167 removed outlier: 3.704A pdb=" N VAL N 159 " --> pdb=" O LYS N 155 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS N 160 " --> pdb=" O ILE N 156 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLU N 161 " --> pdb=" O GLU N 157 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE N 167 " --> pdb=" O ILE N 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 146 removed outlier: 3.746A pdb=" N VAL O 134 " --> pdb=" O ASP O 130 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ASP O 143 " --> pdb=" O LYS O 139 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LYS O 144 " --> pdb=" O GLU O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 155 through 167 Processing helix chain 'P' and resid 131 through 141 Processing helix chain 'P' and resid 155 through 167 removed outlier: 3.727A pdb=" N ILE P 163 " --> pdb=" O VAL P 159 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS P 164 " --> pdb=" O LYS P 160 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU P 165 " --> pdb=" O GLU P 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 130 through 141 removed outlier: 3.666A pdb=" N VAL Q 134 " --> pdb=" O ASP Q 130 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN Q 136 " --> pdb=" O THR Q 132 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS Q 139 " --> pdb=" O ASN Q 135 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL Q 141 " --> pdb=" O ILE Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 155 through 167 removed outlier: 3.541A pdb=" N VAL Q 159 " --> pdb=" O LYS Q 155 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU Q 161 " --> pdb=" O GLU Q 157 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP Q 162 " --> pdb=" O LYS Q 158 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE Q 163 " --> pdb=" O VAL Q 159 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU Q 165 " --> pdb=" O GLU Q 161 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE Q 167 " --> pdb=" O ILE Q 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 141 removed outlier: 3.613A pdb=" N VAL R 134 " --> pdb=" O ASP R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 167 removed outlier: 3.733A pdb=" N GLU R 161 " --> pdb=" O GLU R 157 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU R 165 " --> pdb=" O GLU R 161 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE R 167 " --> pdb=" O ILE R 163 " (cutoff:3.500A) Processing helix chain 'S' and resid 131 through 141 removed outlier: 3.690A pdb=" N LYS S 139 " --> pdb=" O ASN S 135 " (cutoff:3.500A) Processing helix chain 'S' and resid 155 through 166 removed outlier: 3.798A pdb=" N VAL S 159 " --> pdb=" O LYS S 155 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU S 161 " --> pdb=" O GLU S 157 " (cutoff:3.500A) Processing helix chain 'T' and resid 130 through 139 removed outlier: 3.779A pdb=" N VAL T 134 " --> pdb=" O ASP T 130 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS T 139 " --> pdb=" O ASN T 135 " (cutoff:3.500A) Processing helix chain 'T' and resid 141 through 146 Processing helix chain 'T' and resid 155 through 167 removed outlier: 4.078A pdb=" N VAL T 159 " --> pdb=" O LYS T 155 " (cutoff:3.500A) Processing helix chain 'W' and resid 131 through 141 removed outlier: 3.576A pdb=" N ASN W 135 " --> pdb=" O ASP W 131 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASN W 136 " --> pdb=" O THR W 132 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE W 137 " --> pdb=" O ILE W 133 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL W 141 " --> pdb=" O ILE W 137 " (cutoff:3.500A) Processing helix chain 'W' and resid 157 through 167 removed outlier: 3.935A pdb=" N ILE W 163 " --> pdb=" O VAL W 159 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 141 removed outlier: 3.774A pdb=" N VAL X 134 " --> pdb=" O ASP X 130 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS X 139 " --> pdb=" O ASN X 135 " (cutoff:3.500A) Processing helix chain 'X' and resid 155 through 167 removed outlier: 3.683A pdb=" N VAL X 159 " --> pdb=" O LYS X 155 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE X 167 " --> pdb=" O ILE X 163 " (cutoff:3.500A) Processing helix chain 'l' and resid 130 through 145 removed outlier: 3.612A pdb=" N ASN l 135 " --> pdb=" O ASP l 131 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN l 136 " --> pdb=" O THR l 132 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP l 143 " --> pdb=" O LYS l 139 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS l 144 " --> pdb=" O GLU l 140 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE l 145 " --> pdb=" O VAL l 141 " (cutoff:3.500A) Processing helix chain 'l' and resid 155 through 164 removed outlier: 3.500A pdb=" N ASP l 162 " --> pdb=" O LYS l 158 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE l 163 " --> pdb=" O VAL l 159 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS l 164 " --> pdb=" O LYS l 160 " (cutoff:3.500A) Processing helix chain 'm' and resid 130 through 141 Processing helix chain 'm' and resid 155 through 167 removed outlier: 3.750A pdb=" N VAL m 159 " --> pdb=" O LYS m 155 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE m 167 " --> pdb=" O ILE m 163 " (cutoff:3.500A) Processing helix chain 'n' and resid 131 through 145 removed outlier: 4.186A pdb=" N ILE n 137 " --> pdb=" O ILE n 133 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS n 139 " --> pdb=" O ASN n 135 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASP n 143 " --> pdb=" O LYS n 139 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS n 144 " --> pdb=" O GLU n 140 " (cutoff:3.500A) Processing helix chain 'n' and resid 155 through 161 removed outlier: 3.747A pdb=" N VAL n 159 " --> pdb=" O LYS n 155 " (cutoff:3.500A) Processing helix chain 'o' and resid 130 through 141 removed outlier: 3.622A pdb=" N ASN o 135 " --> pdb=" O ASP o 131 " (cutoff:3.500A) Processing helix chain 'o' and resid 155 through 164 removed outlier: 3.734A pdb=" N VAL o 159 " --> pdb=" O LYS o 155 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP o 162 " --> pdb=" O LYS o 158 " (cutoff:3.500A) Processing helix chain 'p' and resid 130 through 143 removed outlier: 3.827A pdb=" N VAL p 134 " --> pdb=" O ASP p 130 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS p 139 " --> pdb=" O ASN p 135 " (cutoff:3.500A) Processing helix chain 'p' and resid 156 through 164 removed outlier: 4.018A pdb=" N ASP p 162 " --> pdb=" O LYS p 158 " (cutoff:3.500A) Processing helix chain 'q' and resid 130 through 142 removed outlier: 3.781A pdb=" N VAL q 134 " --> pdb=" O ASP q 130 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS q 139 " --> pdb=" O ASN q 135 " (cutoff:3.500A) Processing helix chain 'q' and resid 156 through 167 removed outlier: 3.722A pdb=" N ASP q 162 " --> pdb=" O LYS q 158 " (cutoff:3.500A) Processing helix chain 'r' and resid 130 through 145 removed outlier: 3.886A pdb=" N PHE r 142 " --> pdb=" O ILE r 138 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP r 143 " --> pdb=" O LYS r 139 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS r 144 " --> pdb=" O GLU r 140 " (cutoff:3.500A) Processing helix chain 'r' and resid 155 through 166 removed outlier: 4.176A pdb=" N VAL r 159 " --> pdb=" O LYS r 155 " (cutoff:3.500A) Processing helix chain 's' and resid 131 through 141 removed outlier: 4.117A pdb=" N LYS s 139 " --> pdb=" O ASN s 135 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL s 141 " --> pdb=" O ILE s 137 " (cutoff:3.500A) Processing helix chain 's' and resid 141 through 146 Processing helix chain 's' and resid 156 through 167 removed outlier: 3.567A pdb=" N LYS s 160 " --> pdb=" O ILE s 156 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP s 162 " --> pdb=" O LYS s 158 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU s 165 " --> pdb=" O GLU s 161 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE s 167 " --> pdb=" O ILE s 163 " (cutoff:3.500A) Processing helix chain 't' and resid 130 through 141 removed outlier: 3.678A pdb=" N VAL t 134 " --> pdb=" O ASP t 130 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS t 139 " --> pdb=" O ASN t 135 " (cutoff:3.500A) Processing helix chain 't' and resid 157 through 162 removed outlier: 3.850A pdb=" N ASP t 162 " --> pdb=" O LYS t 158 " (cutoff:3.500A) Processing helix chain 't' and resid 162 through 167 removed outlier: 3.782A pdb=" N PHE t 167 " --> pdb=" O ILE t 163 " (cutoff:3.500A) Processing helix chain 'w' and resid 130 through 141 removed outlier: 3.812A pdb=" N VAL w 134 " --> pdb=" O ASP w 130 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS w 139 " --> pdb=" O ASN w 135 " (cutoff:3.500A) Processing helix chain 'w' and resid 157 through 162 Processing helix chain 'x' and resid 130 through 141 removed outlier: 3.525A pdb=" N VAL x 134 " --> pdb=" O ASP x 130 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS x 139 " --> pdb=" O ASN x 135 " (cutoff:3.500A) Processing helix chain 'x' and resid 155 through 164 removed outlier: 3.642A pdb=" N VAL x 159 " --> pdb=" O LYS x 155 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE x 163 " --> pdb=" O VAL x 159 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS x 164 " --> pdb=" O LYS x 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 19 removed outlier: 3.798A pdb=" N LEU K 19 " --> pdb=" O ILE K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 77 removed outlier: 3.848A pdb=" N LEU K 75 " --> pdb=" O ASN K 71 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER K 77 " --> pdb=" O ASP K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 83 Processing helix chain 'K' and resid 84 through 91 Processing helix chain 'K' and resid 120 through 129 removed outlier: 4.347A pdb=" N ASP K 125 " --> pdb=" O LYS K 121 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ASN K 126 " --> pdb=" O SER K 122 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU K 127 " --> pdb=" O LYS K 123 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 152 removed outlier: 4.007A pdb=" N LEU K 152 " --> pdb=" O GLN K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 157 removed outlier: 4.204A pdb=" N LEU K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 196 removed outlier: 3.779A pdb=" N ALA K 183 " --> pdb=" O ASP K 179 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN K 189 " --> pdb=" O ALA K 185 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP K 190 " --> pdb=" O ALA K 186 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS K 196 " --> pdb=" O LEU K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 216 Processing helix chain 'K' and resid 220 through 245 removed outlier: 3.679A pdb=" N LEU K 234 " --> pdb=" O VAL K 230 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE K 238 " --> pdb=" O LEU K 234 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP K 240 " --> pdb=" O TYR K 236 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 260 through 273 removed outlier: 3.591A pdb=" N LYS K 271 " --> pdb=" O GLU K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 290 removed outlier: 3.854A pdb=" N LEU K 285 " --> pdb=" O GLU K 281 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS K 288 " --> pdb=" O GLU K 284 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR K 289 " --> pdb=" O LEU K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 301 removed outlier: 3.554A pdb=" N LEU K 300 " --> pdb=" O LEU K 296 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 361 removed outlier: 3.580A pdb=" N TRP K 347 " --> pdb=" O TYR K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 366 through 377 Processing helix chain 'K' and resid 409 through 412 Processing helix chain 'K' and resid 413 through 429 Processing helix chain 'K' and resid 435 through 439 Processing helix chain 'K' and resid 441 through 447 Processing helix chain 'K' and resid 496 through 505 removed outlier: 4.020A pdb=" N SER K 500 " --> pdb=" O LYS K 496 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET K 504 " --> pdb=" O SER K 500 " (cutoff:3.500A) Processing helix chain 'K' and resid 512 through 524 Processing helix chain 'K' and resid 528 through 534 removed outlier: 3.852A pdb=" N GLY K 534 " --> pdb=" O ILE K 530 " (cutoff:3.500A) Processing helix chain 'K' and resid 538 through 549 removed outlier: 3.849A pdb=" N SER K 548 " --> pdb=" O ASN K 544 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG K 549 " --> pdb=" O GLU K 545 " (cutoff:3.500A) Processing helix chain 'K' and resid 557 through 562 removed outlier: 3.621A pdb=" N ILE K 561 " --> pdb=" O SER K 557 " (cutoff:3.500A) Processing helix chain 'K' and resid 563 through 573 removed outlier: 3.820A pdb=" N GLU K 572 " --> pdb=" O GLU K 568 " (cutoff:3.500A) Processing helix chain 'K' and resid 600 through 604 removed outlier: 3.713A pdb=" N ASN K 604 " --> pdb=" O PHE K 601 " (cutoff:3.500A) Processing helix chain 'K' and resid 624 through 636 removed outlier: 3.549A pdb=" N SER K 630 " --> pdb=" O ARG K 626 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG K 634 " --> pdb=" O SER K 630 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 659 Processing helix chain 'K' and resid 672 through 680 removed outlier: 3.673A pdb=" N ASN K 677 " --> pdb=" O ASP K 674 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ILE K 678 " --> pdb=" O TYR K 675 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N SER K 679 " --> pdb=" O ALA K 676 " (cutoff:3.500A) Processing helix chain 'K' and resid 681 through 694 removed outlier: 4.276A pdb=" N LEU K 688 " --> pdb=" O GLU K 684 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU K 691 " --> pdb=" O LYS K 687 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL K 694 " --> pdb=" O GLU K 690 " (cutoff:3.500A) Processing helix chain 'K' and resid 695 through 697 No H-bonds generated for 'chain 'K' and resid 695 through 697' Processing helix chain 'K' and resid 700 through 709 removed outlier: 3.533A pdb=" N LYS K 706 " --> pdb=" O VAL K 702 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR K 707 " --> pdb=" O ASP K 703 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL K 708 " --> pdb=" O TYR K 704 " (cutoff:3.500A) Processing helix chain 'K' and resid 721 through 724 Processing helix chain 'K' and resid 725 through 734 removed outlier: 4.241A pdb=" N GLU K 729 " --> pdb=" O ILE K 725 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS K 732 " --> pdb=" O ASN K 728 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET K 734 " --> pdb=" O VAL K 730 " (cutoff:3.500A) Processing helix chain 'K' and resid 746 through 761 removed outlier: 3.652A pdb=" N SER K 751 " --> pdb=" O GLU K 747 " (cutoff:3.500A) Processing helix chain 'K' and resid 767 through 792 Processing helix chain 'K' and resid 812 through 826 removed outlier: 3.597A pdb=" N ALA K 825 " --> pdb=" O ARG K 821 " (cutoff:3.500A) Processing helix chain 'K' and resid 869 through 887 removed outlier: 3.717A pdb=" N LEU K 881 " --> pdb=" O SER K 877 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU K 886 " --> pdb=" O GLU K 882 " (cutoff:3.500A) Processing helix chain 'K' and resid 929 through 935 removed outlier: 3.596A pdb=" N PHE K 932 " --> pdb=" O VAL K 929 " (cutoff:3.500A) Processing helix chain 'K' and resid 936 through 951 removed outlier: 3.690A pdb=" N ASP K 940 " --> pdb=" O ALA K 936 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG K 948 " --> pdb=" O GLU K 944 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP K 950 " --> pdb=" O LYS K 946 " (cutoff:3.500A) Processing helix chain 'K' and resid 957 through 972 removed outlier: 3.609A pdb=" N TYR K 962 " --> pdb=" O LEU K 958 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLU K 963 " --> pdb=" O LEU K 959 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LYS K 964 " --> pdb=" O TYR K 960 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR K 965 " --> pdb=" O ASP K 961 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N HIS K 967 " --> pdb=" O GLU K 963 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU K 968 " --> pdb=" O LYS K 964 " (cutoff:3.500A) Processing helix chain 'K' and resid 974 through 988 Processing helix chain 'K' and resid 1000 through 1004 removed outlier: 3.560A pdb=" N LEU K1003 " --> pdb=" O ASP K1000 " (cutoff:3.500A) Processing helix chain 'K' and resid 1020 through 1035 1277 hydrogen bonds defined for protein. 3735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 13.77 Time building geometry restraints manager: 15.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 16782 1.33 - 1.46: 14997 1.46 - 1.58: 31346 1.58 - 1.71: 160 1.71 - 1.84: 150 Bond restraints: 63435 Sorted by residual: bond pdb=" N3B ANP K1102 " pdb=" PG ANP K1102 " ideal model delta sigma weight residual 1.795 1.623 0.172 2.00e-02 2.50e+03 7.36e+01 bond pdb=" O3A ANP K1103 " pdb=" PB ANP K1103 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" O3A ANP K1102 " pdb=" PB ANP K1102 " ideal model delta sigma weight residual 1.700 1.563 0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" N3B ANP K1103 " pdb=" PG ANP K1103 " ideal model delta sigma weight residual 1.795 1.686 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" O5' ANP K1103 " pdb=" PA ANP K1103 " ideal model delta sigma weight residual 1.655 1.564 0.091 2.00e-02 2.50e+03 2.07e+01 ... (remaining 63430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 85730 3.62 - 7.23: 504 7.23 - 10.85: 22 10.85 - 14.46: 2 14.46 - 18.08: 1 Bond angle restraints: 86259 Sorted by residual: angle pdb=" N VAL M 154 " pdb=" CA VAL M 154 " pdb=" C VAL M 154 " ideal model delta sigma weight residual 112.80 104.17 8.63 1.15e+00 7.56e-01 5.64e+01 angle pdb=" N VAL D 285 " pdb=" CA VAL D 285 " pdb=" C VAL D 285 " ideal model delta sigma weight residual 113.71 107.86 5.85 9.50e-01 1.11e+00 3.80e+01 angle pdb=" PB ANP K1103 " pdb=" N3B ANP K1103 " pdb=" PG ANP K1103 " ideal model delta sigma weight residual 126.95 108.87 18.08 3.00e+00 1.11e-01 3.63e+01 angle pdb=" N ILE J 271 " pdb=" CA ILE J 271 " pdb=" C ILE J 271 " ideal model delta sigma weight residual 111.90 107.05 4.85 8.10e-01 1.52e+00 3.59e+01 angle pdb=" N ILE K 208 " pdb=" CA ILE K 208 " pdb=" C ILE K 208 " ideal model delta sigma weight residual 111.00 116.97 -5.97 1.09e+00 8.42e-01 3.00e+01 ... (remaining 86254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 38171 35.40 - 70.79: 792 70.79 - 106.19: 88 106.19 - 141.59: 3 141.59 - 176.98: 5 Dihedral angle restraints: 39059 sinusoidal: 16972 harmonic: 22087 Sorted by residual: dihedral pdb=" CB CYS J 262 " pdb=" SG CYS J 262 " pdb=" SG CYS J 268 " pdb=" CB CYS J 268 " ideal model delta sinusoidal sigma weight residual 93.00 -177.85 -89.15 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CA CYS J 302 " pdb=" C CYS J 302 " pdb=" N ILE J 303 " pdb=" CA ILE J 303 " ideal model delta harmonic sigma weight residual 180.00 -132.54 -47.46 0 5.00e+00 4.00e-02 9.01e+01 dihedral pdb=" O4' U V 3 " pdb=" C1' U V 3 " pdb=" N1 U V 3 " pdb=" C2 U V 3 " ideal model delta sinusoidal sigma weight residual -160.00 15.34 -175.34 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 39056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 9254 0.092 - 0.185: 823 0.185 - 0.277: 9 0.277 - 0.370: 0 0.370 - 0.462: 1 Chirality restraints: 10087 Sorted by residual: chirality pdb=" C3' ANP K1102 " pdb=" C2' ANP K1102 " pdb=" C4' ANP K1102 " pdb=" O3' ANP K1102 " both_signs ideal model delta sigma weight residual False -2.36 -2.82 0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" C3' ANP K1103 " pdb=" C2' ANP K1103 " pdb=" C4' ANP K1103 " pdb=" O3' ANP K1103 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C1' A V 21 " pdb=" O4' A V 21 " pdb=" C2' A V 21 " pdb=" N9 A V 21 " both_signs ideal model delta sigma weight residual False 2.44 2.21 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 10084 not shown) Planarity restraints: 10532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 19 " 0.060 2.00e-02 2.50e+03 2.66e-02 1.95e+01 pdb=" N9 A V 19 " -0.060 2.00e-02 2.50e+03 pdb=" C8 A V 19 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A V 19 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 19 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A V 19 " 0.010 2.00e-02 2.50e+03 pdb=" N6 A V 19 " 0.016 2.00e-02 2.50e+03 pdb=" N1 A V 19 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A V 19 " -0.006 2.00e-02 2.50e+03 pdb=" N3 A V 19 " -0.009 2.00e-02 2.50e+03 pdb=" C4 A V 19 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A V 13 " -0.051 2.00e-02 2.50e+03 2.18e-02 1.31e+01 pdb=" N9 A V 13 " 0.044 2.00e-02 2.50e+03 pdb=" C8 A V 13 " 0.006 2.00e-02 2.50e+03 pdb=" N7 A V 13 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A V 13 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A V 13 " -0.009 2.00e-02 2.50e+03 pdb=" N6 A V 13 " -0.013 2.00e-02 2.50e+03 pdb=" N1 A V 13 " -0.006 2.00e-02 2.50e+03 pdb=" C2 A V 13 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A V 13 " 0.009 2.00e-02 2.50e+03 pdb=" C4 A V 13 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS J 364 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.72e+00 pdb=" C LYS J 364 " 0.054 2.00e-02 2.50e+03 pdb=" O LYS J 364 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR J 365 " -0.018 2.00e-02 2.50e+03 ... (remaining 10529 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 160 2.34 - 2.98: 33985 2.98 - 3.62: 95334 3.62 - 4.26: 155009 4.26 - 4.90: 247881 Nonbonded interactions: 532369 Sorted by model distance: nonbonded pdb=" O2A ANP K1103 " pdb="MN MN K1105 " model vdw 1.698 2.320 nonbonded pdb=" O1G ANP K1103 " pdb="MN MN K1104 " model vdw 1.728 2.320 nonbonded pdb=" O2B ANP K1103 " pdb="MN MN K1104 " model vdw 1.733 2.320 nonbonded pdb=" O1A ANP K1103 " pdb="MN MN K1104 " model vdw 1.900 2.320 nonbonded pdb=" O3A ANP K1102 " pdb="MN MN K1106 " model vdw 1.996 2.320 ... (remaining 532364 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 3 through 155) selection = (chain 'C' and resid 3 through 155) } ncs_group { reference = (chain 'D' and (resid 2 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB )) or resid 159 through 286)) selection = (chain 'E' and (resid 2 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB )) or resid 159 through 286)) selection = (chain 'F' and (resid 2 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB )) or resid 159 through 286)) selection = chain 'G' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'w' selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 46.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.900 Check model and map are aligned: 0.360 Set scattering table: 0.440 Process input model: 119.810 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 181.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.172 63435 Z= 0.393 Angle : 0.790 18.080 86259 Z= 0.435 Chirality : 0.051 0.462 10087 Planarity : 0.004 0.045 10532 Dihedral : 15.092 176.983 24767 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.45 % Allowed : 15.00 % Favored : 84.56 % Rotamer: Outliers : 0.19 % Allowed : 6.06 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (0.08), residues: 7409 helix: -2.64 (0.09), residues: 2048 sheet: -1.91 (0.12), residues: 1555 loop : -3.86 (0.08), residues: 3806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 158 HIS 0.008 0.001 HIS D 19 PHE 0.023 0.002 PHE D 136 TYR 0.032 0.002 TYR B 42 ARG 0.017 0.001 ARG K 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1583 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1570 time to evaluate : 5.728 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: D 8 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6732 (mm-30) REVERT: G 286 ILE cc_start: 0.6244 (OUTLIER) cc_final: 0.5868 (tt) REVERT: J 226 ASP cc_start: 0.7215 (p0) cc_final: 0.7007 (p0) REVERT: O 136 ASN cc_start: 0.7624 (p0) cc_final: 0.7287 (p0) REVERT: S 30 ILE cc_start: 0.7714 (mp) cc_final: 0.7307 (tt) REVERT: S 104 ASP cc_start: 0.7658 (t70) cc_final: 0.7445 (p0) REVERT: T 13 THR cc_start: 0.6639 (p) cc_final: 0.6318 (p) REVERT: W 116 ASP cc_start: 0.6961 (t0) cc_final: 0.6652 (t0) REVERT: X 121 MET cc_start: 0.5656 (ptt) cc_final: 0.5394 (pmt) REVERT: l 102 ILE cc_start: 0.7593 (mm) cc_final: 0.7326 (mm) REVERT: p 52 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7804 (mmmt) REVERT: s 95 LEU cc_start: 0.8334 (mt) cc_final: 0.8085 (mt) REVERT: s 121 MET cc_start: 0.6459 (mmp) cc_final: 0.5255 (mmp) REVERT: s 172 LEU cc_start: 0.7308 (pp) cc_final: 0.7093 (pp) REVERT: x 98 LYS cc_start: 0.8071 (ptmt) cc_final: 0.7552 (tptm) REVERT: K 121 LYS cc_start: 0.4615 (tttp) cc_final: 0.4371 (mptt) REVERT: K 158 TRP cc_start: 0.3648 (m100) cc_final: 0.2640 (m100) REVERT: K 187 MET cc_start: 0.6630 (ppp) cc_final: 0.6287 (tmm) REVERT: K 240 TRP cc_start: 0.7894 (t60) cc_final: 0.7013 (t60) REVERT: K 759 LEU cc_start: 0.8918 (pp) cc_final: 0.8703 (pp) REVERT: K 1013 TYR cc_start: 0.6526 (t80) cc_final: 0.6215 (t80) outliers start: 13 outliers final: 6 residues processed: 1579 average time/residue: 1.3039 time to fit residues: 2726.6723 Evaluate side-chains 1013 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1006 time to evaluate : 5.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain M residue 128 ILE Chi-restraints excluded: chain S residue 137 ILE Chi-restraints excluded: chain K residue 212 ASP Chi-restraints excluded: chain K residue 448 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 628 optimal weight: 6.9990 chunk 563 optimal weight: 0.2980 chunk 312 optimal weight: 9.9990 chunk 192 optimal weight: 2.9990 chunk 380 optimal weight: 0.8980 chunk 301 optimal weight: 5.9990 chunk 583 optimal weight: 2.9990 chunk 225 optimal weight: 0.5980 chunk 354 optimal weight: 4.9990 chunk 434 optimal weight: 5.9990 chunk 675 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 75 ASN B 84 ASN C 60 ASN C 84 ASN C 128 ASN D 17 HIS D 141 ASN D 153 ASN D 178 ASN ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN F 166 ASN F 178 ASN G 13 HIS G 19 HIS G 133 ASN G 141 ASN H 32 GLN H 79 ASN H 130 GLN H 133 ASN H 182 ASN H 298 ASN I 19 ASN I 61 ASN I 74 ASN I 87 ASN I 97 ASN I 227 HIS J 23 HIS J 46 ASN J 158 ASN J 337 ASN J 345 ASN ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN L 174 GLN M 150 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN P 29 HIS P 119 ASN R 135 ASN S 77 GLN W 53 ASN X 29 HIS X 39 HIS X 40 ASN X 135 ASN l 40 ASN l 174 GLN m 4 GLN m 101 ASN m 174 GLN o 135 ASN p 40 ASN p 135 ASN p 174 GLN q 147 ASN s 77 GLN s 91 ASN t 4 GLN t 29 HIS t 79 GLN ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 76 GLN w 135 ASN x 32 ASN ** x 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 259 GLN K 387 ASN K 392 GLN K 604 ASN K 695 ASN K 845 ASN ** K 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 63435 Z= 0.269 Angle : 0.756 19.398 86259 Z= 0.393 Chirality : 0.050 0.278 10087 Planarity : 0.005 0.067 10532 Dihedral : 12.415 179.958 9631 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.23 % Favored : 86.64 % Rotamer: Outliers : 3.41 % Allowed : 16.38 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.08), residues: 7409 helix: -1.65 (0.10), residues: 2130 sheet: -1.60 (0.12), residues: 1576 loop : -3.44 (0.08), residues: 3703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 985 HIS 0.008 0.001 HIS O 39 PHE 0.018 0.002 PHE D 136 TYR 0.025 0.002 TYR O 112 ARG 0.008 0.001 ARG H 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1429 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1197 time to evaluate : 5.416 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: B 106 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7932 (tt0) REVERT: C 83 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: D 107 TYR cc_start: 0.8120 (m-80) cc_final: 0.7914 (m-80) REVERT: D 195 ASP cc_start: 0.6630 (m-30) cc_final: 0.6200 (m-30) REVERT: F 75 ASP cc_start: 0.7529 (p0) cc_final: 0.7309 (p0) REVERT: G 136 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7340 (p90) REVERT: H 144 LYS cc_start: 0.7608 (mmtm) cc_final: 0.6885 (mtmp) REVERT: H 163 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7956 (mmmm) REVERT: J 226 ASP cc_start: 0.7118 (p0) cc_final: 0.6906 (p0) REVERT: J 465 ARG cc_start: 0.7537 (tmm-80) cc_final: 0.6899 (tmm-80) REVERT: N 94 TYR cc_start: 0.6664 (t80) cc_final: 0.6355 (t80) REVERT: P 144 LYS cc_start: 0.7017 (mptt) cc_final: 0.6047 (tppt) REVERT: Q 69 ILE cc_start: 0.8045 (pp) cc_final: 0.7680 (pt) REVERT: R 52 LYS cc_start: 0.6432 (mppt) cc_final: 0.5650 (mtmt) REVERT: S 88 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7482 (mm) REVERT: T 13 THR cc_start: 0.6485 (p) cc_final: 0.6246 (p) REVERT: W 105 ASP cc_start: 0.6506 (OUTLIER) cc_final: 0.6246 (t0) REVERT: W 169 TYR cc_start: 0.7300 (p90) cc_final: 0.7064 (p90) REVERT: X 121 MET cc_start: 0.5578 (ptt) cc_final: 0.5266 (pmt) REVERT: l 102 ILE cc_start: 0.7470 (mm) cc_final: 0.7176 (mm) REVERT: n 172 LEU cc_start: 0.4478 (mt) cc_final: 0.4250 (mt) REVERT: p 52 LYS cc_start: 0.7913 (ttmm) cc_final: 0.7653 (mmmt) REVERT: s 95 LEU cc_start: 0.8409 (mt) cc_final: 0.8124 (mt) REVERT: s 110 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8301 (tp) REVERT: s 121 MET cc_start: 0.6588 (mmp) cc_final: 0.5277 (mmp) REVERT: s 163 ILE cc_start: 0.7846 (mp) cc_final: 0.7613 (mp) REVERT: s 172 LEU cc_start: 0.7331 (pp) cc_final: 0.7067 (pp) REVERT: t 166 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7739 (tt) REVERT: w 105 ASP cc_start: 0.4727 (t0) cc_final: 0.4476 (OUTLIER) REVERT: K 150 PHE cc_start: 0.6336 (t80) cc_final: 0.5938 (t80) REVERT: K 187 MET cc_start: 0.6250 (ppp) cc_final: 0.5980 (tmm) REVERT: K 216 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7746 (mttm) REVERT: K 328 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7314 (pptt) REVERT: K 408 SER cc_start: 0.7601 (m) cc_final: 0.7261 (t) REVERT: K 528 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7934 (mpp) REVERT: K 692 TYR cc_start: 0.8258 (t80) cc_final: 0.8034 (t80) REVERT: K 831 LYS cc_start: 0.8616 (tttt) cc_final: 0.8401 (tttt) REVERT: K 1002 LYS cc_start: 0.7812 (mmtm) cc_final: 0.7595 (mmtm) outliers start: 232 outliers final: 73 residues processed: 1326 average time/residue: 1.1853 time to fit residues: 2121.0577 Evaluate side-chains 1079 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 996 time to evaluate : 5.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain J residue 399 CYS Chi-restraints excluded: chain J residue 459 ILE Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 16 ILE Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain Q residue 148 ILE Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 137 ILE Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 108 ILE Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 34 ASP Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 105 ASP Chi-restraints excluded: chain W residue 172 LEU Chi-restraints excluded: chain l residue 98 LYS Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain m residue 6 GLU Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 134 VAL Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 132 THR Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 110 ILE Chi-restraints excluded: chain t residue 166 LEU Chi-restraints excluded: chain w residue 104 ASP Chi-restraints excluded: chain w residue 108 ILE Chi-restraints excluded: chain w residue 141 VAL Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 148 ILE Chi-restraints excluded: chain K residue 216 LYS Chi-restraints excluded: chain K residue 328 LYS Chi-restraints excluded: chain K residue 528 MET Chi-restraints excluded: chain K residue 531 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 375 optimal weight: 0.7980 chunk 209 optimal weight: 2.9990 chunk 562 optimal weight: 7.9990 chunk 460 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 676 optimal weight: 0.9990 chunk 731 optimal weight: 8.9990 chunk 602 optimal weight: 3.9990 chunk 671 optimal weight: 8.9990 chunk 230 optimal weight: 6.9990 chunk 542 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN B 84 ASN C 60 ASN E 19 HIS F 260 ASN G 133 ASN H 79 ASN H 90 ASN H 130 GLN H 135 GLN I 61 ASN ** J 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** M 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN P 135 ASN Q 136 ASN ** R 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 HIS ** l 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 4 GLN m 14 ASN m 40 ASN o 4 GLN t 101 ASN ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 150 GLN ** x 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 259 GLN ** K 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 63435 Z= 0.313 Angle : 0.741 19.606 86259 Z= 0.384 Chirality : 0.049 0.226 10087 Planarity : 0.005 0.073 10532 Dihedral : 12.081 179.872 9622 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.05 % Favored : 86.81 % Rotamer: Outliers : 4.13 % Allowed : 19.00 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.09), residues: 7409 helix: -1.28 (0.11), residues: 2130 sheet: -1.48 (0.13), residues: 1598 loop : -3.27 (0.09), residues: 3681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 411 HIS 0.006 0.001 HIS O 39 PHE 0.021 0.002 PHE D 136 TYR 0.029 0.002 TYR O 112 ARG 0.009 0.001 ARG H 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1377 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1096 time to evaluate : 5.431 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: E 99 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8650 (mp) REVERT: G 136 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7472 (p90) REVERT: H 144 LYS cc_start: 0.7541 (mmtm) cc_final: 0.6864 (mtmp) REVERT: H 163 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7939 (mmmm) REVERT: J 226 ASP cc_start: 0.7165 (p0) cc_final: 0.6949 (p0) REVERT: J 418 MET cc_start: 0.8392 (mmt) cc_final: 0.8170 (mmt) REVERT: J 426 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: J 465 ARG cc_start: 0.7612 (tmm-80) cc_final: 0.7189 (tmm-80) REVERT: P 86 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7353 (mm) REVERT: P 144 LYS cc_start: 0.6984 (mptt) cc_final: 0.6043 (tppt) REVERT: R 120 SER cc_start: 0.6739 (t) cc_final: 0.6533 (p) REVERT: S 110 ILE cc_start: 0.8187 (pp) cc_final: 0.7951 (pt) REVERT: W 105 ASP cc_start: 0.6424 (OUTLIER) cc_final: 0.6148 (t0) REVERT: X 121 MET cc_start: 0.5250 (ptt) cc_final: 0.4849 (pmt) REVERT: l 102 ILE cc_start: 0.7468 (mm) cc_final: 0.7149 (mm) REVERT: m 14 ASN cc_start: 0.5165 (OUTLIER) cc_final: 0.4657 (m-40) REVERT: o 121 MET cc_start: 0.7891 (pmm) cc_final: 0.7608 (ptp) REVERT: p 52 LYS cc_start: 0.7792 (ttmm) cc_final: 0.7283 (pptt) REVERT: r 55 ARG cc_start: 0.4427 (OUTLIER) cc_final: 0.4058 (tpp-160) REVERT: s 88 LEU cc_start: 0.8229 (mt) cc_final: 0.8010 (mt) REVERT: s 95 LEU cc_start: 0.8441 (mt) cc_final: 0.8218 (mt) REVERT: s 110 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8357 (tp) REVERT: s 121 MET cc_start: 0.6687 (mmp) cc_final: 0.5420 (mmp) REVERT: s 164 LYS cc_start: 0.6903 (tmtt) cc_final: 0.6568 (tptp) REVERT: s 172 LEU cc_start: 0.7429 (pp) cc_final: 0.7103 (pp) REVERT: x 65 TYR cc_start: 0.8140 (p90) cc_final: 0.7495 (p90) REVERT: x 98 LYS cc_start: 0.8148 (ptmt) cc_final: 0.7625 (tptm) REVERT: K 14 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7378 (ttmm) REVERT: K 121 LYS cc_start: 0.4612 (tttp) cc_final: 0.4301 (mptt) REVERT: K 158 TRP cc_start: 0.3678 (m100) cc_final: 0.2558 (m100) REVERT: K 187 MET cc_start: 0.6245 (ppp) cc_final: 0.6016 (tmm) REVERT: K 216 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7776 (mttm) REVERT: K 408 SER cc_start: 0.7624 (m) cc_final: 0.7329 (t) REVERT: K 528 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7934 (mpp) REVERT: K 659 GLU cc_start: 0.8118 (tt0) cc_final: 0.7710 (tt0) REVERT: K 846 ASN cc_start: 0.6782 (m-40) cc_final: 0.6534 (m-40) outliers start: 281 outliers final: 116 residues processed: 1273 average time/residue: 1.1816 time to fit residues: 2041.5969 Evaluate side-chains 1081 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 953 time to evaluate : 5.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain J residue 399 CYS Chi-restraints excluded: chain J residue 426 GLU Chi-restraints excluded: chain J residue 437 ILE Chi-restraints excluded: chain J residue 459 ILE Chi-restraints excluded: chain J residue 467 ILE Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 16 ILE Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 99 LYS Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 4 GLN Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 137 ILE Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 79 GLN Chi-restraints excluded: chain T residue 108 ILE Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain W residue 105 ASP Chi-restraints excluded: chain W residue 172 LEU Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 98 LYS Chi-restraints excluded: chain l residue 137 ILE Chi-restraints excluded: chain m residue 14 ASN Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain n residue 120 SER Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 132 THR Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain p residue 141 VAL Chi-restraints excluded: chain q residue 85 THR Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 132 THR Chi-restraints excluded: chain q residue 166 LEU Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain r residue 36 ARG Chi-restraints excluded: chain r residue 55 ARG Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain r residue 166 LEU Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 110 ILE Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain w residue 24 ILE Chi-restraints excluded: chain w residue 104 ASP Chi-restraints excluded: chain w residue 105 ASP Chi-restraints excluded: chain w residue 108 ILE Chi-restraints excluded: chain w residue 141 VAL Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 17 THR Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 148 ILE Chi-restraints excluded: chain K residue 14 LYS Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 216 LYS Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 396 THR Chi-restraints excluded: chain K residue 469 VAL Chi-restraints excluded: chain K residue 528 MET Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 744 VAL Chi-restraints excluded: chain K residue 758 ILE Chi-restraints excluded: chain K residue 862 ILE Chi-restraints excluded: chain K residue 987 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 668 optimal weight: 9.9990 chunk 508 optimal weight: 5.9990 chunk 351 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 323 optimal weight: 5.9990 chunk 454 optimal weight: 0.9990 chunk 679 optimal weight: 3.9990 chunk 719 optimal weight: 0.9990 chunk 354 optimal weight: 0.9990 chunk 643 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN B 75 ASN B 84 ASN B 106 GLN C 60 ASN D 178 ASN E 185 ASN G 133 ASN H 91 HIS H 130 GLN H 135 GLN H 279 ASN I 61 ASN J 452 HIS L 4 GLN M 150 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN ** Q 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 136 ASN l 79 GLN m 4 GLN o 4 GLN s 39 HIS ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 39 HIS ** x 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 HIS K 259 GLN K 599 GLN ** K 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 63435 Z= 0.222 Angle : 0.707 25.682 86259 Z= 0.364 Chirality : 0.048 0.208 10087 Planarity : 0.004 0.076 10532 Dihedral : 11.850 179.682 9622 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.27 % Favored : 87.61 % Rotamer: Outliers : 4.60 % Allowed : 20.31 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.09), residues: 7409 helix: -0.99 (0.11), residues: 2132 sheet: -1.31 (0.13), residues: 1632 loop : -3.15 (0.09), residues: 3645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 411 HIS 0.004 0.001 HIS K 994 PHE 0.018 0.001 PHE H 229 TYR 0.030 0.001 TYR O 112 ARG 0.010 0.000 ARG H 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1418 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 1105 time to evaluate : 6.108 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: E 99 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8657 (mp) REVERT: F 29 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7462 (mt-10) REVERT: F 152 LYS cc_start: 0.7857 (pttm) cc_final: 0.7620 (ptpt) REVERT: G 136 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7395 (p90) REVERT: H 144 LYS cc_start: 0.7496 (mmtm) cc_final: 0.6824 (mtmp) REVERT: J 226 ASP cc_start: 0.7139 (p0) cc_final: 0.6925 (p0) REVERT: M 173 GLU cc_start: 0.5823 (mm-30) cc_final: 0.5613 (mm-30) REVERT: N 65 TYR cc_start: 0.8200 (p90) cc_final: 0.7965 (p90) REVERT: O 136 ASN cc_start: 0.7791 (p0) cc_final: 0.7277 (p0) REVERT: P 77 GLN cc_start: 0.5872 (OUTLIER) cc_final: 0.5664 (mm-40) REVERT: P 144 LYS cc_start: 0.6842 (mptt) cc_final: 0.5990 (tppt) REVERT: S 110 ILE cc_start: 0.8142 (pp) cc_final: 0.7904 (pt) REVERT: T 131 ASP cc_start: 0.6907 (t0) cc_final: 0.6529 (m-30) REVERT: W 105 ASP cc_start: 0.6370 (OUTLIER) cc_final: 0.6112 (t0) REVERT: X 98 LYS cc_start: 0.4869 (OUTLIER) cc_final: 0.4535 (ptpp) REVERT: X 121 MET cc_start: 0.5123 (ptt) cc_final: 0.4693 (pmt) REVERT: l 94 TYR cc_start: 0.8010 (t80) cc_final: 0.6763 (t80) REVERT: l 102 ILE cc_start: 0.7359 (mm) cc_final: 0.7089 (mm) REVERT: n 86 LEU cc_start: 0.7160 (tm) cc_final: 0.6677 (tp) REVERT: n 172 LEU cc_start: 0.4435 (mt) cc_final: 0.4180 (mt) REVERT: o 74 THR cc_start: 0.8199 (m) cc_final: 0.7839 (p) REVERT: r 102 ILE cc_start: 0.6972 (OUTLIER) cc_final: 0.6716 (mm) REVERT: s 110 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8320 (tp) REVERT: s 121 MET cc_start: 0.6622 (mmp) cc_final: 0.5423 (mmp) REVERT: x 65 TYR cc_start: 0.8121 (p90) cc_final: 0.7585 (p90) REVERT: x 98 LYS cc_start: 0.8197 (ptmt) cc_final: 0.7639 (tptm) REVERT: K 14 LYS cc_start: 0.7882 (mtmm) cc_final: 0.7432 (ttmm) REVERT: K 110 GLN cc_start: 0.7698 (tp-100) cc_final: 0.7282 (tp40) REVERT: K 121 LYS cc_start: 0.4709 (tttp) cc_final: 0.4406 (mptt) REVERT: K 158 TRP cc_start: 0.3572 (m100) cc_final: 0.2463 (m100) REVERT: K 187 MET cc_start: 0.6220 (ppp) cc_final: 0.5971 (tmm) REVERT: K 216 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7736 (mttm) REVERT: K 328 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7398 (pptt) REVERT: K 408 SER cc_start: 0.7552 (OUTLIER) cc_final: 0.7274 (t) REVERT: K 419 ARG cc_start: 0.7777 (mtp-110) cc_final: 0.7511 (mtp85) REVERT: K 910 TYR cc_start: 0.7439 (t80) cc_final: 0.6980 (t80) outliers start: 313 outliers final: 130 residues processed: 1315 average time/residue: 1.1856 time to fit residues: 2118.0618 Evaluate side-chains 1094 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 954 time to evaluate : 5.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain J residue 399 CYS Chi-restraints excluded: chain J residue 437 ILE Chi-restraints excluded: chain J residue 459 ILE Chi-restraints excluded: chain J residue 467 ILE Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 16 ILE Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 143 ASP Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain P residue 99 LYS Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 4 GLN Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 61 ASP Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 137 ILE Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 108 ILE Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain W residue 105 ASP Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 98 LYS Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain l residue 98 LYS Chi-restraints excluded: chain l residue 137 ILE Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain n residue 120 SER Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 136 ASN Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain p residue 166 LEU Chi-restraints excluded: chain q residue 74 THR Chi-restraints excluded: chain q residue 85 THR Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 132 THR Chi-restraints excluded: chain r residue 102 ILE Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain r residue 166 LEU Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 43 VAL Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 69 ILE Chi-restraints excluded: chain s residue 110 ILE Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain s residue 166 LEU Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain w residue 24 ILE Chi-restraints excluded: chain w residue 57 VAL Chi-restraints excluded: chain w residue 108 ILE Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 17 THR Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 148 ILE Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 216 LYS Chi-restraints excluded: chain K residue 328 LYS Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 469 VAL Chi-restraints excluded: chain K residue 631 VAL Chi-restraints excluded: chain K residue 709 LEU Chi-restraints excluded: chain K residue 744 VAL Chi-restraints excluded: chain K residue 783 LEU Chi-restraints excluded: chain K residue 815 ASP Chi-restraints excluded: chain K residue 819 GLU Chi-restraints excluded: chain K residue 925 ILE Chi-restraints excluded: chain K residue 987 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 598 optimal weight: 3.9990 chunk 408 optimal weight: 0.0040 chunk 10 optimal weight: 3.9990 chunk 535 optimal weight: 8.9990 chunk 296 optimal weight: 6.9990 chunk 613 optimal weight: 9.9990 chunk 497 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 367 optimal weight: 10.0000 chunk 645 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 overall best weight: 4.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN B 84 ASN C 60 ASN E 130 GLN F 260 ASN G 133 ASN H 66 ASN H 91 HIS H 130 GLN H 135 GLN J 126 ASN N 76 GLN N 77 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN ** O 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 91 ASN ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 53 ASN T 76 GLN ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 136 ASN T 150 GLN l 32 ASN ** l 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 4 GLN o 4 GLN q 147 ASN ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 259 GLN ** K 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1024 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 63435 Z= 0.497 Angle : 0.803 24.671 86259 Z= 0.412 Chirality : 0.052 0.293 10087 Planarity : 0.005 0.071 10532 Dihedral : 11.900 178.665 9622 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.58 % Favored : 86.31 % Rotamer: Outliers : 5.04 % Allowed : 21.74 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -3.17 (0.09), residues: 7409 helix: -1.14 (0.11), residues: 2148 sheet: -1.34 (0.13), residues: 1629 loop : -3.15 (0.09), residues: 3632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 411 HIS 0.006 0.001 HIS K 865 PHE 0.026 0.002 PHE D 136 TYR 0.034 0.002 TYR P 94 ARG 0.010 0.001 ARG m 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1342 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 343 poor density : 999 time to evaluate : 5.548 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: D 100 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7302 (pp20) REVERT: D 210 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7385 (mtm180) REVERT: D 218 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8324 (mtmm) REVERT: E 99 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8641 (mp) REVERT: G 136 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7637 (p90) REVERT: H 144 LYS cc_start: 0.7630 (mmtm) cc_final: 0.6930 (mtmp) REVERT: H 163 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.7979 (mmmm) REVERT: J 426 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: O 136 ASN cc_start: 0.7935 (p0) cc_final: 0.7610 (p0) REVERT: R 102 ILE cc_start: 0.5997 (OUTLIER) cc_final: 0.5653 (pp) REVERT: S 110 ILE cc_start: 0.8210 (pp) cc_final: 0.7993 (pt) REVERT: S 160 LYS cc_start: 0.4475 (OUTLIER) cc_final: 0.2867 (ptpp) REVERT: W 13 THR cc_start: 0.7211 (p) cc_final: 0.6969 (t) REVERT: W 105 ASP cc_start: 0.6426 (OUTLIER) cc_final: 0.6166 (t0) REVERT: X 98 LYS cc_start: 0.4922 (OUTLIER) cc_final: 0.4598 (ptpp) REVERT: X 121 MET cc_start: 0.4801 (ptt) cc_final: 0.4456 (pmt) REVERT: l 102 ILE cc_start: 0.7583 (mm) cc_final: 0.7378 (mm) REVERT: o 82 ASP cc_start: 0.6590 (p0) cc_final: 0.6130 (p0) REVERT: p 131 ASP cc_start: 0.7572 (p0) cc_final: 0.7369 (p0) REVERT: p 135 ASN cc_start: 0.7298 (m-40) cc_final: 0.6959 (t0) REVERT: r 102 ILE cc_start: 0.7199 (OUTLIER) cc_final: 0.6960 (mm) REVERT: s 110 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8415 (tp) REVERT: s 121 MET cc_start: 0.6390 (mmp) cc_final: 0.5113 (mmp) REVERT: t 98 LYS cc_start: 0.7133 (mppt) cc_final: 0.6268 (tptp) REVERT: x 65 TYR cc_start: 0.8140 (p90) cc_final: 0.7711 (p90) REVERT: x 98 LYS cc_start: 0.8080 (ptmt) cc_final: 0.7548 (tptm) REVERT: K 14 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7633 (ttmm) REVERT: K 110 GLN cc_start: 0.7782 (tp-100) cc_final: 0.7347 (tp40) REVERT: K 121 LYS cc_start: 0.4744 (tttp) cc_final: 0.4433 (mptt) REVERT: K 158 TRP cc_start: 0.3671 (m100) cc_final: 0.2476 (m100) REVERT: K 187 MET cc_start: 0.6252 (OUTLIER) cc_final: 0.6031 (tmm) REVERT: K 216 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7868 (mttm) REVERT: K 408 SER cc_start: 0.7613 (OUTLIER) cc_final: 0.7324 (t) REVERT: K 499 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7288 (mpp-170) outliers start: 343 outliers final: 184 residues processed: 1229 average time/residue: 1.1651 time to fit residues: 1950.8513 Evaluate side-chains 1110 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 908 time to evaluate : 5.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 265 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 262 CYS Chi-restraints excluded: chain J residue 266 SER Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain J residue 399 CYS Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 426 GLU Chi-restraints excluded: chain J residue 437 ILE Chi-restraints excluded: chain J residue 459 ILE Chi-restraints excluded: chain J residue 467 ILE Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 16 ILE Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 99 LYS Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 4 GLN Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 137 ILE Chi-restraints excluded: chain S residue 160 LYS Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 79 GLN Chi-restraints excluded: chain T residue 108 ILE Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain T residue 168 SER Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 105 ASP Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 98 LYS Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 87 LYS Chi-restraints excluded: chain l residue 98 LYS Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 172 LEU Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 83 PHE Chi-restraints excluded: chain o residue 136 ASN Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain p residue 42 LEU Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain p residue 85 THR Chi-restraints excluded: chain p residue 166 LEU Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 74 THR Chi-restraints excluded: chain q residue 85 THR Chi-restraints excluded: chain q residue 97 ARG Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 132 THR Chi-restraints excluded: chain r residue 30 ILE Chi-restraints excluded: chain r residue 36 ARG Chi-restraints excluded: chain r residue 51 GLU Chi-restraints excluded: chain r residue 102 ILE Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain r residue 165 GLU Chi-restraints excluded: chain r residue 166 LEU Chi-restraints excluded: chain s residue 43 VAL Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 110 ILE Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain s residue 166 LEU Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain t residue 99 LYS Chi-restraints excluded: chain w residue 24 ILE Chi-restraints excluded: chain w residue 57 VAL Chi-restraints excluded: chain w residue 164 LYS Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 17 THR Chi-restraints excluded: chain x residue 38 ILE Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 148 ILE Chi-restraints excluded: chain K residue 14 LYS Chi-restraints excluded: chain K residue 108 ASN Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 187 MET Chi-restraints excluded: chain K residue 216 LYS Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 396 THR Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 469 VAL Chi-restraints excluded: chain K residue 499 ARG Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 631 VAL Chi-restraints excluded: chain K residue 709 LEU Chi-restraints excluded: chain K residue 744 VAL Chi-restraints excluded: chain K residue 758 ILE Chi-restraints excluded: chain K residue 855 VAL Chi-restraints excluded: chain K residue 929 VAL Chi-restraints excluded: chain K residue 987 LYS Chi-restraints excluded: chain K residue 1015 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 241 optimal weight: 1.9990 chunk 647 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 422 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 719 optimal weight: 0.8980 chunk 597 optimal weight: 5.9990 chunk 333 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 238 optimal weight: 0.8980 chunk 377 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN B 84 ASN C 60 ASN E 130 GLN G 133 ASN H 91 HIS H 130 GLN L 4 GLN M 150 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN ** O 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 91 ASN ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 GLN ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 136 ASN l 79 GLN m 4 GLN m 40 ASN ** m 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 135 ASN o 4 GLN q 147 ASN ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 259 GLN K 599 GLN K 686 ASN ** K 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 63435 Z= 0.240 Angle : 0.722 24.027 86259 Z= 0.371 Chirality : 0.048 0.209 10087 Planarity : 0.004 0.075 10532 Dihedral : 11.772 179.677 9622 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.21 % Favored : 87.69 % Rotamer: Outliers : 4.02 % Allowed : 23.74 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -2.91 (0.09), residues: 7409 helix: -0.89 (0.11), residues: 2139 sheet: -1.00 (0.14), residues: 1439 loop : -3.02 (0.09), residues: 3831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP K 411 HIS 0.004 0.001 HIS F 13 PHE 0.019 0.001 PHE N 83 TYR 0.033 0.002 TYR O 112 ARG 0.010 0.000 ARG m 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1308 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1035 time to evaluate : 5.444 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: D 100 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7314 (pp20) REVERT: E 99 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8643 (mp) REVERT: G 136 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7538 (p90) REVERT: H 144 LYS cc_start: 0.7501 (mmtm) cc_final: 0.6852 (mtmp) REVERT: M 16 ILE cc_start: 0.3064 (OUTLIER) cc_final: 0.1819 (mm) REVERT: M 79 GLN cc_start: 0.4942 (OUTLIER) cc_final: 0.4654 (mm-40) REVERT: P 144 LYS cc_start: 0.6927 (mptt) cc_final: 0.5996 (tppt) REVERT: R 51 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6765 (pm20) REVERT: S 110 ILE cc_start: 0.8223 (pp) cc_final: 0.8012 (pt) REVERT: T 131 ASP cc_start: 0.7043 (t0) cc_final: 0.6721 (m-30) REVERT: W 13 THR cc_start: 0.7070 (p) cc_final: 0.6862 (t) REVERT: W 105 ASP cc_start: 0.6374 (OUTLIER) cc_final: 0.6173 (t0) REVERT: X 98 LYS cc_start: 0.4901 (OUTLIER) cc_final: 0.4652 (ptpp) REVERT: X 121 MET cc_start: 0.4753 (ptt) cc_final: 0.4551 (pmt) REVERT: l 102 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.7191 (mm) REVERT: m 14 ASN cc_start: 0.5056 (OUTLIER) cc_final: 0.4404 (m-40) REVERT: n 42 LEU cc_start: 0.7990 (tp) cc_final: 0.7580 (tp) REVERT: o 74 THR cc_start: 0.8269 (m) cc_final: 0.7932 (p) REVERT: r 102 ILE cc_start: 0.7038 (OUTLIER) cc_final: 0.6788 (mm) REVERT: s 110 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8402 (tp) REVERT: s 121 MET cc_start: 0.6335 (mmp) cc_final: 0.5061 (mmp) REVERT: x 65 TYR cc_start: 0.8100 (p90) cc_final: 0.7688 (p90) REVERT: x 98 LYS cc_start: 0.8085 (ptmt) cc_final: 0.7503 (tptm) REVERT: K 14 LYS cc_start: 0.7964 (mtmm) cc_final: 0.7647 (ttmm) REVERT: K 110 GLN cc_start: 0.7698 (tp-100) cc_final: 0.7416 (tp40) REVERT: K 121 LYS cc_start: 0.4722 (tttp) cc_final: 0.4438 (mptt) REVERT: K 158 TRP cc_start: 0.3571 (m100) cc_final: 0.2416 (m100) REVERT: K 179 ASP cc_start: 0.7758 (m-30) cc_final: 0.7335 (m-30) REVERT: K 216 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7768 (mttm) REVERT: K 287 THR cc_start: 0.7920 (OUTLIER) cc_final: 0.7677 (m) REVERT: K 408 SER cc_start: 0.7582 (OUTLIER) cc_final: 0.7278 (t) REVERT: K 599 GLN cc_start: 0.8050 (tt0) cc_final: 0.7759 (tp-100) REVERT: K 988 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7214 (ttt-90) outliers start: 273 outliers final: 147 residues processed: 1216 average time/residue: 1.2957 time to fit residues: 2160.6537 Evaluate side-chains 1108 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 945 time to evaluate : 5.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 262 CYS Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 362 THR Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain J residue 399 CYS Chi-restraints excluded: chain J residue 437 ILE Chi-restraints excluded: chain J residue 459 ILE Chi-restraints excluded: chain J residue 467 ILE Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 16 ILE Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 143 ASP Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 99 LYS Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 135 ASN Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain Q residue 172 LEU Chi-restraints excluded: chain R residue 39 HIS Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 79 GLN Chi-restraints excluded: chain T residue 108 ILE Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain W residue 105 ASP Chi-restraints excluded: chain W residue 108 ILE Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 98 LYS Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 98 LYS Chi-restraints excluded: chain l residue 102 ILE Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain m residue 3 THR Chi-restraints excluded: chain m residue 14 ASN Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 93 LEU Chi-restraints excluded: chain n residue 120 SER Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 83 PHE Chi-restraints excluded: chain o residue 136 ASN Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain p residue 42 LEU Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 74 THR Chi-restraints excluded: chain q residue 85 THR Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 134 VAL Chi-restraints excluded: chain q residue 153 LYS Chi-restraints excluded: chain r residue 51 GLU Chi-restraints excluded: chain r residue 102 ILE Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain r residue 166 LEU Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 43 VAL Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 110 ILE Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain s residue 166 LEU Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain w residue 24 ILE Chi-restraints excluded: chain w residue 57 VAL Chi-restraints excluded: chain w residue 164 LYS Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 17 THR Chi-restraints excluded: chain x residue 45 THR Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 148 ILE Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 216 LYS Chi-restraints excluded: chain K residue 287 THR Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 396 THR Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 469 VAL Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 631 VAL Chi-restraints excluded: chain K residue 744 VAL Chi-restraints excluded: chain K residue 783 LEU Chi-restraints excluded: chain K residue 883 GLU Chi-restraints excluded: chain K residue 987 LYS Chi-restraints excluded: chain K residue 988 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 694 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 410 optimal weight: 20.0000 chunk 525 optimal weight: 0.9990 chunk 407 optimal weight: 0.9980 chunk 605 optimal weight: 5.9990 chunk 401 optimal weight: 30.0000 chunk 717 optimal weight: 7.9990 chunk 448 optimal weight: 0.7980 chunk 437 optimal weight: 10.0000 chunk 331 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN B 84 ASN C 60 ASN D 178 ASN G 133 ASN H 91 HIS H 130 GLN H 135 GLN L 135 ASN M 150 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN ** O 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 GLN S 91 ASN ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 GLN ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 136 ASN l 79 GLN m 4 GLN ** m 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 76 GLN o 4 GLN ** p 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 147 ASN ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 259 GLN ** K 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 63435 Z= 0.311 Angle : 0.746 22.591 86259 Z= 0.384 Chirality : 0.049 0.253 10087 Planarity : 0.004 0.073 10532 Dihedral : 11.724 179.475 9620 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.73 % Favored : 87.18 % Rotamer: Outliers : 4.03 % Allowed : 24.64 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.91 (0.09), residues: 7409 helix: -0.89 (0.11), residues: 2145 sheet: -1.20 (0.13), residues: 1599 loop : -3.00 (0.09), residues: 3665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP K 411 HIS 0.010 0.001 HIS R 39 PHE 0.021 0.002 PHE D 136 TYR 0.033 0.002 TYR O 112 ARG 0.009 0.001 ARG H 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1243 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 969 time to evaluate : 5.522 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: D 100 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7279 (pp20) REVERT: E 99 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8656 (mp) REVERT: G 136 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7569 (p90) REVERT: G 222 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6980 (mt-10) REVERT: H 144 LYS cc_start: 0.7512 (mmtm) cc_final: 0.6862 (mtmp) REVERT: H 163 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7878 (mmmm) REVERT: M 79 GLN cc_start: 0.5005 (OUTLIER) cc_final: 0.4679 (mm-40) REVERT: P 144 LYS cc_start: 0.6968 (mptt) cc_final: 0.6049 (tppt) REVERT: R 51 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6738 (pm20) REVERT: R 102 ILE cc_start: 0.5717 (OUTLIER) cc_final: 0.5476 (pp) REVERT: S 121 MET cc_start: 0.6587 (mmm) cc_final: 0.6327 (mmm) REVERT: S 160 LYS cc_start: 0.4604 (OUTLIER) cc_final: 0.2935 (ptpp) REVERT: W 13 THR cc_start: 0.7089 (p) cc_final: 0.6869 (t) REVERT: W 105 ASP cc_start: 0.6411 (OUTLIER) cc_final: 0.6167 (t0) REVERT: l 102 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.7254 (mm) REVERT: m 14 ASN cc_start: 0.4968 (OUTLIER) cc_final: 0.4298 (m-40) REVERT: n 42 LEU cc_start: 0.8028 (tp) cc_final: 0.7671 (tp) REVERT: o 74 THR cc_start: 0.8279 (m) cc_final: 0.7945 (p) REVERT: p 135 ASN cc_start: 0.7203 (m-40) cc_final: 0.6952 (t0) REVERT: q 53 ASN cc_start: 0.5920 (t0) cc_final: 0.5678 (p0) REVERT: r 102 ILE cc_start: 0.7036 (OUTLIER) cc_final: 0.6793 (mm) REVERT: s 110 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8419 (tp) REVERT: s 121 MET cc_start: 0.6353 (mmp) cc_final: 0.5062 (mmp) REVERT: w 115 PRO cc_start: 0.7109 (Cg_exo) cc_final: 0.6775 (Cg_endo) REVERT: x 65 TYR cc_start: 0.8104 (p90) cc_final: 0.7679 (p90) REVERT: x 98 LYS cc_start: 0.8076 (ptmt) cc_final: 0.7522 (tptm) REVERT: K 14 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7620 (ttmm) REVERT: K 110 GLN cc_start: 0.7736 (tp-100) cc_final: 0.7464 (tp40) REVERT: K 121 LYS cc_start: 0.4715 (tttp) cc_final: 0.4439 (mptt) REVERT: K 158 TRP cc_start: 0.3557 (m100) cc_final: 0.2346 (m100) REVERT: K 216 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7809 (mttm) REVERT: K 287 THR cc_start: 0.7881 (OUTLIER) cc_final: 0.7651 (m) REVERT: K 408 SER cc_start: 0.7588 (OUTLIER) cc_final: 0.7294 (t) REVERT: K 599 GLN cc_start: 0.8063 (tt0) cc_final: 0.7770 (tp-100) REVERT: K 835 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.6509 (ptp) outliers start: 274 outliers final: 168 residues processed: 1155 average time/residue: 1.1862 time to fit residues: 1861.2639 Evaluate side-chains 1112 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 925 time to evaluate : 5.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 262 ARG Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 222 GLU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 265 GLU Chi-restraints excluded: chain H residue 302 SER Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 262 CYS Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 362 THR Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain J residue 399 CYS Chi-restraints excluded: chain J residue 437 ILE Chi-restraints excluded: chain J residue 459 ILE Chi-restraints excluded: chain J residue 464 VAL Chi-restraints excluded: chain J residue 467 ILE Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 140 GLU Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 16 ILE Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 143 ASP Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 99 LYS Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain Q residue 108 ILE Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 137 ILE Chi-restraints excluded: chain S residue 160 LYS Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 76 GLN Chi-restraints excluded: chain T residue 108 ILE Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain T residue 168 SER Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 105 ASP Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 98 LYS Chi-restraints excluded: chain l residue 102 ILE Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain l residue 140 GLU Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain m residue 3 THR Chi-restraints excluded: chain m residue 14 ASN Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 70 LEU Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 83 PHE Chi-restraints excluded: chain o residue 136 ASN Chi-restraints excluded: chain p residue 42 LEU Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain p residue 166 LEU Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 85 THR Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 134 VAL Chi-restraints excluded: chain q residue 153 LYS Chi-restraints excluded: chain r residue 102 ILE Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 141 VAL Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 31 THR Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 110 ILE Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain s residue 166 LEU Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain w residue 24 ILE Chi-restraints excluded: chain w residue 57 VAL Chi-restraints excluded: chain w residue 164 LYS Chi-restraints excluded: chain x residue 8 VAL Chi-restraints excluded: chain x residue 17 THR Chi-restraints excluded: chain x residue 45 THR Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 148 ILE Chi-restraints excluded: chain K residue 14 LYS Chi-restraints excluded: chain K residue 89 LYS Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 216 LYS Chi-restraints excluded: chain K residue 287 THR Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 396 THR Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 469 VAL Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 631 VAL Chi-restraints excluded: chain K residue 726 TYR Chi-restraints excluded: chain K residue 744 VAL Chi-restraints excluded: chain K residue 754 TYR Chi-restraints excluded: chain K residue 783 LEU Chi-restraints excluded: chain K residue 835 MET Chi-restraints excluded: chain K residue 987 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 443 optimal weight: 0.9980 chunk 286 optimal weight: 4.9990 chunk 428 optimal weight: 20.0000 chunk 216 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 455 optimal weight: 5.9990 chunk 488 optimal weight: 0.6980 chunk 354 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 563 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN B 84 ASN G 133 ASN H 91 HIS H 130 GLN M 150 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN ** Q 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 91 ASN ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 GLN T 136 ASN m 4 GLN o 4 GLN p 4 GLN q 147 ASN ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 259 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 63435 Z= 0.209 Angle : 0.728 21.110 86259 Z= 0.373 Chirality : 0.048 0.230 10087 Planarity : 0.004 0.075 10532 Dihedral : 11.636 179.600 9620 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.90 % Favored : 88.03 % Rotamer: Outliers : 3.62 % Allowed : 25.61 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.71 (0.09), residues: 7409 helix: -0.72 (0.11), residues: 2144 sheet: -0.86 (0.14), residues: 1434 loop : -2.91 (0.09), residues: 3831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP K 411 HIS 0.005 0.001 HIS O 39 PHE 0.022 0.001 PHE N 83 TYR 0.032 0.001 TYR O 112 ARG 0.009 0.000 ARG H 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1018 time to evaluate : 5.381 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: D 100 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7328 (pp20) REVERT: D 216 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.6279 (ttm-80) REVERT: E 99 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8634 (mp) REVERT: G 136 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7490 (p90) REVERT: H 111 TYR cc_start: 0.7661 (t80) cc_final: 0.7211 (t80) REVERT: H 144 LYS cc_start: 0.7481 (mmtm) cc_final: 0.6809 (mtmp) REVERT: M 16 ILE cc_start: 0.3084 (OUTLIER) cc_final: 0.1847 (mm) REVERT: M 79 GLN cc_start: 0.4838 (OUTLIER) cc_final: 0.4597 (mm-40) REVERT: P 144 LYS cc_start: 0.6806 (mptt) cc_final: 0.6013 (tppt) REVERT: Q 124 LYS cc_start: 0.5972 (mptt) cc_final: 0.5542 (mptp) REVERT: R 51 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6660 (pm20) REVERT: R 102 ILE cc_start: 0.5495 (OUTLIER) cc_final: 0.5265 (pp) REVERT: S 121 MET cc_start: 0.6569 (mmm) cc_final: 0.6348 (mmm) REVERT: S 160 LYS cc_start: 0.4710 (OUTLIER) cc_final: 0.3013 (ptpp) REVERT: T 76 GLN cc_start: 0.1559 (OUTLIER) cc_final: 0.1172 (mm110) REVERT: X 4 GLN cc_start: 0.2837 (OUTLIER) cc_final: 0.2577 (tm-30) REVERT: l 102 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.7102 (mm) REVERT: n 42 LEU cc_start: 0.7890 (tp) cc_final: 0.7554 (tp) REVERT: o 16 ILE cc_start: 0.3215 (OUTLIER) cc_final: 0.2396 (mp) REVERT: o 74 THR cc_start: 0.8294 (m) cc_final: 0.7958 (p) REVERT: o 121 MET cc_start: 0.7757 (ptp) cc_final: 0.7359 (ptt) REVERT: q 53 ASN cc_start: 0.6005 (t0) cc_final: 0.5709 (p0) REVERT: r 102 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6657 (mm) REVERT: s 5 ARG cc_start: 0.6653 (mpp80) cc_final: 0.6289 (mpt-90) REVERT: s 121 MET cc_start: 0.6329 (mmp) cc_final: 0.5080 (mmp) REVERT: w 115 PRO cc_start: 0.7105 (Cg_exo) cc_final: 0.6765 (Cg_endo) REVERT: x 65 TYR cc_start: 0.8096 (p90) cc_final: 0.7735 (p90) REVERT: x 98 LYS cc_start: 0.8084 (ptmt) cc_final: 0.7523 (tptm) REVERT: K 14 LYS cc_start: 0.7920 (mtmm) cc_final: 0.7636 (ttmm) REVERT: K 121 LYS cc_start: 0.4744 (tttp) cc_final: 0.4467 (mptt) REVERT: K 156 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7914 (tp) REVERT: K 158 TRP cc_start: 0.3507 (m100) cc_final: 0.2306 (m100) REVERT: K 216 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7752 (mttm) REVERT: K 272 GLU cc_start: 0.7966 (tp30) cc_final: 0.7641 (tm-30) REVERT: K 328 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7319 (ptmm) REVERT: K 408 SER cc_start: 0.7588 (OUTLIER) cc_final: 0.7306 (t) REVERT: K 599 GLN cc_start: 0.7971 (tt0) cc_final: 0.7662 (tp-100) REVERT: K 714 GLU cc_start: -0.0587 (OUTLIER) cc_final: -0.1048 (pm20) REVERT: K 835 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.6270 (ptp) outliers start: 246 outliers final: 149 residues processed: 1181 average time/residue: 1.1668 time to fit residues: 1899.6232 Evaluate side-chains 1080 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 911 time to evaluate : 5.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 265 GLU Chi-restraints excluded: chain H residue 302 SER Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 262 CYS Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 362 THR Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain J residue 399 CYS Chi-restraints excluded: chain J residue 437 ILE Chi-restraints excluded: chain J residue 459 ILE Chi-restraints excluded: chain J residue 467 ILE Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 162 ASP Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 143 ASP Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 99 LYS Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 108 ILE Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain Q residue 172 LEU Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 137 ILE Chi-restraints excluded: chain S residue 160 LYS Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 76 GLN Chi-restraints excluded: chain T residue 108 ILE Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain T residue 168 SER Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 108 ILE Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 4 GLN Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 98 LYS Chi-restraints excluded: chain l residue 102 ILE Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain l residue 140 GLU Chi-restraints excluded: chain m residue 24 ILE Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 70 LEU Chi-restraints excluded: chain n residue 120 SER Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 17 THR Chi-restraints excluded: chain o residue 83 PHE Chi-restraints excluded: chain o residue 136 ASN Chi-restraints excluded: chain p residue 42 LEU Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 20 VAL Chi-restraints excluded: chain q residue 85 THR Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 132 THR Chi-restraints excluded: chain q residue 134 VAL Chi-restraints excluded: chain q residue 153 LYS Chi-restraints excluded: chain r residue 102 ILE Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 166 LEU Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 31 THR Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain w residue 24 ILE Chi-restraints excluded: chain w residue 57 VAL Chi-restraints excluded: chain w residue 164 LYS Chi-restraints excluded: chain x residue 17 THR Chi-restraints excluded: chain x residue 45 THR Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 148 ILE Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 216 LYS Chi-restraints excluded: chain K residue 328 LYS Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 396 THR Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 469 VAL Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 714 GLU Chi-restraints excluded: chain K residue 726 TYR Chi-restraints excluded: chain K residue 744 VAL Chi-restraints excluded: chain K residue 783 LEU Chi-restraints excluded: chain K residue 835 MET Chi-restraints excluded: chain K residue 883 GLU Chi-restraints excluded: chain K residue 987 LYS Chi-restraints excluded: chain K residue 1015 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 652 optimal weight: 8.9990 chunk 686 optimal weight: 0.9980 chunk 626 optimal weight: 6.9990 chunk 668 optimal weight: 8.9990 chunk 402 optimal weight: 4.9990 chunk 291 optimal weight: 0.8980 chunk 524 optimal weight: 5.9990 chunk 205 optimal weight: 0.6980 chunk 603 optimal weight: 8.9990 chunk 632 optimal weight: 0.0000 chunk 665 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN B 84 ASN C 60 ASN F 260 ASN G 133 ASN H 91 HIS H 130 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN ** Q 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 136 ASN ** R 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 91 ASN ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 GLN T 136 ASN m 4 GLN o 4 GLN ** p 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 147 ASN ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 63435 Z= 0.244 Angle : 0.744 18.258 86259 Z= 0.381 Chirality : 0.049 0.221 10087 Planarity : 0.004 0.078 10532 Dihedral : 11.552 179.744 9620 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.16 % Favored : 87.79 % Rotamer: Outliers : 3.44 % Allowed : 26.22 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.66 (0.09), residues: 7409 helix: -0.71 (0.11), residues: 2148 sheet: -0.81 (0.14), residues: 1416 loop : -2.87 (0.09), residues: 3845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP K 411 HIS 0.006 0.001 HIS R 39 PHE 0.026 0.001 PHE t 83 TYR 0.033 0.002 TYR H 119 ARG 0.009 0.000 ARG m 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1192 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 958 time to evaluate : 5.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7284 (pp20) REVERT: D 216 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.6228 (ttm-80) REVERT: E 99 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8642 (mp) REVERT: G 136 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7501 (p90) REVERT: H 111 TYR cc_start: 0.7771 (t80) cc_final: 0.7445 (t80) REVERT: H 144 LYS cc_start: 0.7448 (mmtm) cc_final: 0.6818 (mtmp) REVERT: M 79 GLN cc_start: 0.4783 (OUTLIER) cc_final: 0.4510 (mm-40) REVERT: O 97 ARG cc_start: 0.7565 (mmm-85) cc_final: 0.7326 (mtt90) REVERT: P 144 LYS cc_start: 0.6778 (mptt) cc_final: 0.6042 (tppt) REVERT: R 102 ILE cc_start: 0.5554 (OUTLIER) cc_final: 0.5303 (pp) REVERT: S 110 ILE cc_start: 0.8173 (pp) cc_final: 0.7891 (pt) REVERT: S 121 MET cc_start: 0.6580 (mmm) cc_final: 0.6287 (mmm) REVERT: S 160 LYS cc_start: 0.4617 (OUTLIER) cc_final: 0.2921 (ptpp) REVERT: T 76 GLN cc_start: 0.2029 (OUTLIER) cc_final: 0.1613 (mm110) REVERT: X 4 GLN cc_start: 0.3012 (OUTLIER) cc_final: 0.2762 (tm-30) REVERT: X 121 MET cc_start: 0.6019 (pmt) cc_final: 0.5319 (ppp) REVERT: l 102 ILE cc_start: 0.7457 (OUTLIER) cc_final: 0.7236 (mm) REVERT: n 42 LEU cc_start: 0.7926 (tp) cc_final: 0.7508 (tp) REVERT: o 16 ILE cc_start: 0.3235 (OUTLIER) cc_final: 0.1991 (mp) REVERT: o 74 THR cc_start: 0.8316 (m) cc_final: 0.7978 (p) REVERT: q 53 ASN cc_start: 0.6072 (t0) cc_final: 0.5780 (p0) REVERT: s 121 MET cc_start: 0.6307 (mmp) cc_final: 0.5053 (mmp) REVERT: s 164 LYS cc_start: 0.7029 (tmtt) cc_final: 0.6497 (tptp) REVERT: w 115 PRO cc_start: 0.7129 (Cg_exo) cc_final: 0.6791 (Cg_endo) REVERT: x 65 TYR cc_start: 0.8132 (p90) cc_final: 0.7760 (p90) REVERT: x 98 LYS cc_start: 0.8090 (ptmt) cc_final: 0.7562 (tptm) REVERT: K 14 LYS cc_start: 0.7914 (mtmm) cc_final: 0.7632 (ttmm) REVERT: K 121 LYS cc_start: 0.4749 (tttp) cc_final: 0.4479 (mptt) REVERT: K 156 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7919 (tp) REVERT: K 158 TRP cc_start: 0.3555 (m100) cc_final: 0.2335 (m100) REVERT: K 179 ASP cc_start: 0.7831 (t70) cc_final: 0.7253 (t70) REVERT: K 216 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7780 (mttm) REVERT: K 272 GLU cc_start: 0.8073 (tp30) cc_final: 0.7665 (tm-30) REVERT: K 328 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7396 (ptmm) REVERT: K 408 SER cc_start: 0.7584 (OUTLIER) cc_final: 0.7313 (t) REVERT: K 599 GLN cc_start: 0.7907 (tt0) cc_final: 0.7468 (tp40) REVERT: K 659 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: K 714 GLU cc_start: -0.0572 (OUTLIER) cc_final: -0.0988 (pm20) outliers start: 234 outliers final: 155 residues processed: 1119 average time/residue: 1.1921 time to fit residues: 1818.9944 Evaluate side-chains 1058 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 886 time to evaluate : 5.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 265 GLU Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 262 CYS Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 362 THR Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain J residue 399 CYS Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 437 ILE Chi-restraints excluded: chain J residue 459 ILE Chi-restraints excluded: chain J residue 467 ILE Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 140 GLU Chi-restraints excluded: chain M residue 162 ASP Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 143 ASP Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 99 LYS Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain Q residue 172 LEU Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 137 ILE Chi-restraints excluded: chain S residue 160 LYS Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 76 GLN Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain T residue 168 SER Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 108 ILE Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 4 GLN Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 98 LYS Chi-restraints excluded: chain l residue 102 ILE Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain l residue 140 GLU Chi-restraints excluded: chain m residue 3 THR Chi-restraints excluded: chain m residue 24 ILE Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 70 LEU Chi-restraints excluded: chain n residue 120 SER Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 16 ILE Chi-restraints excluded: chain o residue 83 PHE Chi-restraints excluded: chain o residue 136 ASN Chi-restraints excluded: chain p residue 42 LEU Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 20 VAL Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 85 THR Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 132 THR Chi-restraints excluded: chain q residue 134 VAL Chi-restraints excluded: chain q residue 153 LYS Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 166 LEU Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 31 THR Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain w residue 24 ILE Chi-restraints excluded: chain w residue 57 VAL Chi-restraints excluded: chain x residue 17 THR Chi-restraints excluded: chain x residue 45 THR Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 148 ILE Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 216 LYS Chi-restraints excluded: chain K residue 328 LYS Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 396 THR Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 469 VAL Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 631 VAL Chi-restraints excluded: chain K residue 659 GLU Chi-restraints excluded: chain K residue 714 GLU Chi-restraints excluded: chain K residue 726 TYR Chi-restraints excluded: chain K residue 744 VAL Chi-restraints excluded: chain K residue 925 ILE Chi-restraints excluded: chain K residue 987 LYS Chi-restraints excluded: chain K residue 1015 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 438 optimal weight: 6.9990 chunk 706 optimal weight: 5.9990 chunk 431 optimal weight: 20.0000 chunk 335 optimal weight: 7.9990 chunk 491 optimal weight: 5.9990 chunk 741 optimal weight: 4.9990 chunk 682 optimal weight: 6.9990 chunk 590 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 455 optimal weight: 6.9990 chunk 361 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN B 75 ASN B 84 ASN G 133 ASN H 91 HIS H 130 GLN J 157 HIS J 220 HIS J 440 ASN ** O 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 91 ASN ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 GLN T 136 ASN T 150 GLN X 39 HIS ** l 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 4 GLN m 40 ASN ** m 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 4 GLN o 77 GLN o 119 ASN ** p 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 147 ASN ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 40 ASN ** K 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.095 63435 Z= 0.631 Angle : 0.902 17.757 86259 Z= 0.462 Chirality : 0.056 0.256 10087 Planarity : 0.005 0.082 10532 Dihedral : 11.811 178.304 9620 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.63 % Favored : 86.27 % Rotamer: Outliers : 3.31 % Allowed : 27.09 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.09), residues: 7409 helix: -1.12 (0.11), residues: 2154 sheet: -1.20 (0.13), residues: 1607 loop : -2.99 (0.09), residues: 3648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP K 411 HIS 0.015 0.002 HIS J 157 PHE 0.029 0.003 PHE D 136 TYR 0.042 0.003 TYR P 94 ARG 0.011 0.001 ARG O 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14818 Ramachandran restraints generated. 7409 Oldfield, 0 Emsley, 7409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1135 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 910 time to evaluate : 5.431 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: C 116 GLU cc_start: 0.7309 (pm20) cc_final: 0.7097 (pp20) REVERT: D 100 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7292 (pp20) REVERT: E 99 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8668 (mp) REVERT: G 136 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7661 (p90) REVERT: H 17 GLN cc_start: 0.7739 (pp30) cc_final: 0.7308 (pp30) REVERT: H 144 LYS cc_start: 0.7689 (mmtm) cc_final: 0.6983 (mtmp) REVERT: R 51 GLU cc_start: 0.6989 (pt0) cc_final: 0.6700 (pm20) REVERT: S 110 ILE cc_start: 0.8197 (pp) cc_final: 0.7912 (pt) REVERT: S 121 MET cc_start: 0.6659 (mmm) cc_final: 0.6367 (mmm) REVERT: S 160 LYS cc_start: 0.4564 (OUTLIER) cc_final: 0.2761 (ptpp) REVERT: T 76 GLN cc_start: 0.2470 (OUTLIER) cc_final: 0.1635 (mm110) REVERT: X 4 GLN cc_start: 0.2920 (OUTLIER) cc_final: 0.2681 (tm-30) REVERT: n 42 LEU cc_start: 0.8106 (tp) cc_final: 0.7658 (tp) REVERT: p 131 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7128 (p0) REVERT: q 151 LYS cc_start: 0.6986 (mmpt) cc_final: 0.6334 (mmpt) REVERT: q 153 LYS cc_start: 0.1585 (mttt) cc_final: 0.1280 (pttp) REVERT: s 121 MET cc_start: 0.6276 (mmp) cc_final: 0.5113 (mmp) REVERT: s 164 LYS cc_start: 0.7153 (tmtt) cc_final: 0.6489 (tptp) REVERT: w 115 PRO cc_start: 0.7180 (Cg_exo) cc_final: 0.6855 (Cg_endo) REVERT: x 65 TYR cc_start: 0.8144 (p90) cc_final: 0.7772 (p90) REVERT: x 98 LYS cc_start: 0.8080 (ptmt) cc_final: 0.7514 (tptm) REVERT: K 14 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7523 (ttmm) REVERT: K 121 LYS cc_start: 0.4762 (tttp) cc_final: 0.4478 (mptt) REVERT: K 179 ASP cc_start: 0.7890 (t70) cc_final: 0.7534 (t70) REVERT: K 216 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7900 (mttm) REVERT: K 528 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8037 (mpp) REVERT: K 659 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8130 (tm-30) outliers start: 225 outliers final: 152 residues processed: 1061 average time/residue: 1.2053 time to fit residues: 1739.7591 Evaluate side-chains 1013 residues out of total 6803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 850 time to evaluate : 5.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 265 GLU Chi-restraints excluded: chain H residue 302 SER Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 262 CYS Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 362 THR Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain J residue 399 CYS Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 437 ILE Chi-restraints excluded: chain J residue 459 ILE Chi-restraints excluded: chain J residue 467 ILE Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 140 GLU Chi-restraints excluded: chain M residue 162 ASP Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 143 ASP Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 172 LEU Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 137 ILE Chi-restraints excluded: chain S residue 160 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 76 GLN Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain T residue 150 GLN Chi-restraints excluded: chain T residue 168 SER Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 4 GLN Chi-restraints excluded: chain X residue 16 ILE Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain l residue 12 ILE Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 98 LYS Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain l residue 140 GLU Chi-restraints excluded: chain m residue 3 THR Chi-restraints excluded: chain m residue 24 ILE Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 41 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 70 LEU Chi-restraints excluded: chain n residue 95 LEU Chi-restraints excluded: chain n residue 120 SER Chi-restraints excluded: chain n residue 148 ILE Chi-restraints excluded: chain o residue 83 PHE Chi-restraints excluded: chain o residue 119 ASN Chi-restraints excluded: chain o residue 136 ASN Chi-restraints excluded: chain p residue 42 LEU Chi-restraints excluded: chain p residue 45 THR Chi-restraints excluded: chain p residue 131 ASP Chi-restraints excluded: chain q residue 20 VAL Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 85 THR Chi-restraints excluded: chain q residue 123 THR Chi-restraints excluded: chain q residue 132 THR Chi-restraints excluded: chain r residue 69 ILE Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 165 GLU Chi-restraints excluded: chain r residue 166 LEU Chi-restraints excluded: chain s residue 8 VAL Chi-restraints excluded: chain s residue 31 THR Chi-restraints excluded: chain s residue 49 VAL Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 141 VAL Chi-restraints excluded: chain s residue 166 LEU Chi-restraints excluded: chain t residue 8 VAL Chi-restraints excluded: chain w residue 24 ILE Chi-restraints excluded: chain x residue 17 THR Chi-restraints excluded: chain x residue 45 THR Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain x residue 108 ILE Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 148 ILE Chi-restraints excluded: chain K residue 14 LYS Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 216 LYS Chi-restraints excluded: chain K residue 384 THR Chi-restraints excluded: chain K residue 396 THR Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 469 VAL Chi-restraints excluded: chain K residue 528 MET Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 631 VAL Chi-restraints excluded: chain K residue 659 GLU Chi-restraints excluded: chain K residue 666 LEU Chi-restraints excluded: chain K residue 726 TYR Chi-restraints excluded: chain K residue 744 VAL Chi-restraints excluded: chain K residue 883 GLU Chi-restraints excluded: chain K residue 925 ILE Chi-restraints excluded: chain K residue 987 LYS Chi-restraints excluded: chain K residue 1015 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 468 optimal weight: 0.5980 chunk 628 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 544 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 591 optimal weight: 9.9990 chunk 247 optimal weight: 0.9980 chunk 607 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN B 75 ASN ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 133 ASN H 130 GLN J 220 HIS ** Q 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 ASN ** S 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 91 ASN ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 GLN T 136 ASN T 150 GLN m 4 GLN m 40 ASN p 4 GLN p 32 ASN q 147 ASN t 91 ASN ** t 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.188271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.115084 restraints weight = 84784.620| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.57 r_work: 0.3291 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 63435 Z= 0.228 Angle : 0.773 16.607 86259 Z= 0.396 Chirality : 0.049 0.216 10087 Planarity : 0.005 0.092 10532 Dihedral : 11.690 179.461 9620 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.11 % Favored : 87.83 % Rotamer: Outliers : 2.63 % Allowed : 28.09 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.72 (0.09), residues: 7409 helix: -0.81 (0.11), residues: 2149 sheet: -0.84 (0.14), residues: 1410 loop : -2.88 (0.09), residues: 3850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP K 411 HIS 0.009 0.001 HIS R 39 PHE 0.020 0.001 PHE D 136 TYR 0.036 0.002 TYR r 112 ARG 0.021 0.001 ARG o 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31777.42 seconds wall clock time: 541 minutes 34.18 seconds (32494.18 seconds total)