Starting phenix.real_space_refine on Tue Apr 7 14:51:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jhb_61477/04_2026/9jhb_61477.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jhb_61477/04_2026/9jhb_61477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jhb_61477/04_2026/9jhb_61477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jhb_61477/04_2026/9jhb_61477.map" model { file = "/net/cci-nas-00/data/ceres_data/9jhb_61477/04_2026/9jhb_61477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jhb_61477/04_2026/9jhb_61477.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 53 5.49 5 S 157 5.16 5 C 17762 2.51 5 N 5089 2.21 5 O 5477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28538 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1146 Classifications: {'RNA': 54} Modifications used: {'5*END': 1, 'rna2p_pur': 13, 'rna2p_pyr': 15, 'rna3p_pur': 15, 'rna3p_pyr': 11} Link IDs: {'rna2p': 28, 'rna3p': 25} Chain: "B" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 904 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "C" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2240 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "D" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2240 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "E" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 904 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "F" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 904 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "G" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 904 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "H" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 904 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "I" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 904 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "J" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 904 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "K" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2240 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "L" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2240 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "M" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2240 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "N" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2240 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "O" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2240 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "P" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2240 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "Q" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2240 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "R" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 904 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Time building chain proxies: 6.70, per 1000 atoms: 0.23 Number of scatterers: 28538 At special positions: 0 Unit cell: (128.74, 126.28, 236.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 157 16.00 P 53 15.00 O 5477 8.00 N 5089 7.00 C 17762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.52 Conformation dependent library (CDL) restraints added in 1.1 seconds 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6534 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 38 sheets defined 47.6% alpha, 19.8% beta 0 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 36 through 40 Processing helix chain 'B' and resid 40 through 47 Processing helix chain 'B' and resid 47 through 67 removed outlier: 4.056A pdb=" N VAL B 51 " --> pdb=" O ASN B 47 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N HIS B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N MET B 54 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 88 removed outlier: 3.595A pdb=" N GLY B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 117 removed outlier: 3.732A pdb=" N MET B 106 " --> pdb=" O GLN B 102 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 28 removed outlier: 3.596A pdb=" N GLY C 28 " --> pdb=" O PRO C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 59 Processing helix chain 'C' and resid 74 through 86 removed outlier: 3.518A pdb=" N ARG C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA C 82 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR C 83 " --> pdb=" O HIS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 113 removed outlier: 3.862A pdb=" N MET C 109 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN C 112 " --> pdb=" O TRP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 119 Processing helix chain 'C' and resid 162 through 168 removed outlier: 4.256A pdb=" N GLU C 166 " --> pdb=" O LYS C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 203 through 217 removed outlier: 3.759A pdb=" N ASN C 216 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 254 removed outlier: 3.521A pdb=" N LEU C 251 " --> pdb=" O PRO C 247 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP C 253 " --> pdb=" O HIS C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.599A pdb=" N GLY D 28 " --> pdb=" O PRO D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 59 Processing helix chain 'D' and resid 74 through 87 Processing helix chain 'D' and resid 98 through 113 removed outlier: 3.507A pdb=" N THR D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 119 Processing helix chain 'D' and resid 162 through 167 removed outlier: 4.199A pdb=" N GLU D 166 " --> pdb=" O LYS D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.723A pdb=" N LYS D 199 " --> pdb=" O PRO D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 217 removed outlier: 3.740A pdb=" N VAL D 215 " --> pdb=" O TRP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'E' and resid 9 through 29 removed outlier: 3.513A pdb=" N ALA E 19 " --> pdb=" O GLY E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 40 Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 47 through 68 removed outlier: 3.691A pdb=" N VAL E 51 " --> pdb=" O ASN E 47 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N HIS E 53 " --> pdb=" O GLY E 49 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N MET E 54 " --> pdb=" O GLN E 50 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 90 removed outlier: 3.750A pdb=" N GLY E 74 " --> pdb=" O PRO E 70 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 Processing helix chain 'F' and resid 9 through 29 removed outlier: 3.515A pdb=" N VAL F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F 21 " --> pdb=" O LEU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 40 Processing helix chain 'F' and resid 40 through 47 Processing helix chain 'F' and resid 47 through 67 removed outlier: 5.842A pdb=" N HIS F 53 " --> pdb=" O GLY F 49 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N MET F 54 " --> pdb=" O GLN F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 89 removed outlier: 4.098A pdb=" N GLY F 74 " --> pdb=" O PRO F 70 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 117 removed outlier: 3.564A pdb=" N LEU F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 29 removed outlier: 3.768A pdb=" N ALA G 19 " --> pdb=" O GLY G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 40 Processing helix chain 'G' and resid 40 through 47 Processing helix chain 'G' and resid 47 through 67 removed outlier: 3.654A pdb=" N VAL G 51 " --> pdb=" O ASN G 47 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N HIS G 53 " --> pdb=" O GLY G 49 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N MET G 54 " --> pdb=" O GLN G 50 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN G 61 " --> pdb=" O LYS G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 89 removed outlier: 3.848A pdb=" N GLY G 74 " --> pdb=" O PRO G 70 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE G 86 " --> pdb=" O MET G 82 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN G 89 " --> pdb=" O GLU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 117 removed outlier: 3.541A pdb=" N LYS G 114 " --> pdb=" O TYR G 110 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA G 115 " --> pdb=" O HIS G 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 29 removed outlier: 3.711A pdb=" N GLY H 15 " --> pdb=" O PRO H 11 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP H 27 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 47 through 50 removed outlier: 3.787A pdb=" N GLN H 50 " --> pdb=" O ASN H 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 47 through 50' Processing helix chain 'H' and resid 51 through 68 removed outlier: 3.602A pdb=" N SER H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 90 removed outlier: 3.849A pdb=" N GLY H 74 " --> pdb=" O PRO H 70 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE H 90 " --> pdb=" O ILE H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 117 Processing helix chain 'I' and resid 9 through 29 Processing helix chain 'I' and resid 36 through 40 Processing helix chain 'I' and resid 40 through 47 Processing helix chain 'I' and resid 48 through 68 removed outlier: 4.134A pdb=" N HIS I 53 " --> pdb=" O GLY I 49 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N MET I 54 " --> pdb=" O GLN I 50 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS I 68 " --> pdb=" O ALA I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 90 removed outlier: 3.874A pdb=" N GLY I 74 " --> pdb=" O PRO I 70 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER I 75 " --> pdb=" O GLU I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 117 removed outlier: 3.502A pdb=" N ALA I 115 " --> pdb=" O HIS I 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 29 removed outlier: 3.551A pdb=" N ALA J 19 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 40 Processing helix chain 'J' and resid 40 through 47 Processing helix chain 'J' and resid 47 through 68 removed outlier: 3.941A pdb=" N HIS J 53 " --> pdb=" O GLY J 49 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N MET J 54 " --> pdb=" O GLN J 50 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 90 removed outlier: 3.918A pdb=" N GLY J 74 " --> pdb=" O PRO J 70 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 117 Processing helix chain 'K' and resid 24 through 28 removed outlier: 4.046A pdb=" N GLY K 28 " --> pdb=" O PRO K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 59 removed outlier: 3.648A pdb=" N LEU K 47 " --> pdb=" O THR K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 86 removed outlier: 3.745A pdb=" N ARG K 81 " --> pdb=" O GLU K 77 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA K 82 " --> pdb=" O THR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 113 Processing helix chain 'K' and resid 113 through 119 Processing helix chain 'K' and resid 161 through 167 removed outlier: 3.711A pdb=" N ALA K 165 " --> pdb=" O THR K 161 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU K 166 " --> pdb=" O LYS K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 193 through 201 removed outlier: 4.478A pdb=" N LYS K 199 " --> pdb=" O PRO K 195 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR K 200 " --> pdb=" O LEU K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 216 removed outlier: 3.563A pdb=" N VAL K 215 " --> pdb=" O TRP K 211 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN K 216 " --> pdb=" O ASP K 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 217 through 221 removed outlier: 3.906A pdb=" N HIS K 220 " --> pdb=" O MET K 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 254 Processing helix chain 'K' and resid 269 through 271 No H-bonds generated for 'chain 'K' and resid 269 through 271' Processing helix chain 'L' and resid 43 through 59 Processing helix chain 'L' and resid 74 through 87 removed outlier: 3.642A pdb=" N ARG L 81 " --> pdb=" O GLU L 77 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA L 82 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR L 83 " --> pdb=" O HIS L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 112 Processing helix chain 'L' and resid 113 through 119 Processing helix chain 'L' and resid 161 through 167 removed outlier: 4.411A pdb=" N ALA L 165 " --> pdb=" O THR L 161 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU L 166 " --> pdb=" O LYS L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 193 through 201 removed outlier: 3.508A pdb=" N GLU L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS L 199 " --> pdb=" O PRO L 195 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR L 200 " --> pdb=" O LEU L 196 " (cutoff:3.500A) Processing helix chain 'L' and resid 203 through 217 Processing helix chain 'L' and resid 218 through 221 Processing helix chain 'L' and resid 248 through 253 Processing helix chain 'L' and resid 269 through 271 No H-bonds generated for 'chain 'L' and resid 269 through 271' Processing helix chain 'M' and resid 43 through 59 Processing helix chain 'M' and resid 74 through 87 Processing helix chain 'M' and resid 98 through 113 removed outlier: 3.657A pdb=" N ARG M 104 " --> pdb=" O GLU M 100 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL M 105 " --> pdb=" O ASP M 101 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR M 106 " --> pdb=" O ALA M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 119 Processing helix chain 'M' and resid 161 through 167 removed outlier: 3.950A pdb=" N ALA M 165 " --> pdb=" O THR M 161 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU M 166 " --> pdb=" O LYS M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 201 removed outlier: 3.631A pdb=" N THR M 200 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 217 removed outlier: 3.564A pdb=" N LEU M 209 " --> pdb=" O GLU M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 218 through 221 Processing helix chain 'M' and resid 247 through 254 removed outlier: 3.610A pdb=" N LEU M 251 " --> pdb=" O PRO M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 269 through 271 No H-bonds generated for 'chain 'M' and resid 269 through 271' Processing helix chain 'N' and resid 43 through 59 removed outlier: 3.537A pdb=" N LYS N 50 " --> pdb=" O CYS N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 87 removed outlier: 3.682A pdb=" N ARG N 81 " --> pdb=" O GLU N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 112 removed outlier: 3.709A pdb=" N ARG N 104 " --> pdb=" O GLU N 100 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET N 109 " --> pdb=" O VAL N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 113 through 120 Processing helix chain 'N' and resid 161 through 167 removed outlier: 3.655A pdb=" N ALA N 165 " --> pdb=" O THR N 161 " (cutoff:3.500A) Processing helix chain 'N' and resid 193 through 201 removed outlier: 3.771A pdb=" N LYS N 199 " --> pdb=" O PRO N 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 203 through 217 Processing helix chain 'N' and resid 218 through 221 removed outlier: 3.707A pdb=" N ASP N 221 " --> pdb=" O PHE N 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 218 through 221' Processing helix chain 'N' and resid 248 through 253 Processing helix chain 'N' and resid 269 through 271 No H-bonds generated for 'chain 'N' and resid 269 through 271' Processing helix chain 'O' and resid 43 through 59 Processing helix chain 'O' and resid 74 through 87 Processing helix chain 'O' and resid 98 through 113 removed outlier: 3.677A pdb=" N ARG O 104 " --> pdb=" O GLU O 100 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR O 106 " --> pdb=" O ALA O 102 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET O 109 " --> pdb=" O VAL O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 119 removed outlier: 3.609A pdb=" N ARG O 117 " --> pdb=" O PHE O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 161 through 167 Processing helix chain 'O' and resid 193 through 198 removed outlier: 3.594A pdb=" N GLU O 198 " --> pdb=" O ALA O 194 " (cutoff:3.500A) Processing helix chain 'O' and resid 203 through 217 removed outlier: 3.540A pdb=" N VAL O 215 " --> pdb=" O TRP O 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 218 through 221 Processing helix chain 'O' and resid 247 through 253 Processing helix chain 'O' and resid 269 through 271 No H-bonds generated for 'chain 'O' and resid 269 through 271' Processing helix chain 'P' and resid 24 through 28 removed outlier: 3.856A pdb=" N GLY P 28 " --> pdb=" O PRO P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 59 Processing helix chain 'P' and resid 74 through 86 removed outlier: 4.391A pdb=" N ALA P 82 " --> pdb=" O THR P 78 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR P 83 " --> pdb=" O HIS P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 113 Processing helix chain 'P' and resid 113 through 120 Processing helix chain 'P' and resid 162 through 167 removed outlier: 4.155A pdb=" N GLU P 166 " --> pdb=" O LYS P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 193 through 201 removed outlier: 3.783A pdb=" N GLU P 198 " --> pdb=" O ALA P 194 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS P 199 " --> pdb=" O PRO P 195 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR P 200 " --> pdb=" O LEU P 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 203 through 216 Processing helix chain 'P' and resid 247 through 254 removed outlier: 3.627A pdb=" N LEU P 254 " --> pdb=" O LYS P 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 28 removed outlier: 3.919A pdb=" N GLY Q 28 " --> pdb=" O PRO Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 59 Processing helix chain 'Q' and resid 74 through 87 removed outlier: 3.849A pdb=" N ARG Q 81 " --> pdb=" O GLU Q 77 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA Q 82 " --> pdb=" O THR Q 78 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR Q 83 " --> pdb=" O HIS Q 79 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 113 removed outlier: 3.922A pdb=" N MET Q 109 " --> pdb=" O VAL Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 113 through 120 Processing helix chain 'Q' and resid 161 through 168 removed outlier: 3.790A pdb=" N ALA Q 165 " --> pdb=" O THR Q 161 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU Q 166 " --> pdb=" O LYS Q 162 " (cutoff:3.500A) Processing helix chain 'Q' and resid 193 through 201 removed outlier: 4.005A pdb=" N LYS Q 199 " --> pdb=" O PRO Q 195 " (cutoff:3.500A) Processing helix chain 'Q' and resid 203 through 216 removed outlier: 3.822A pdb=" N ASP Q 212 " --> pdb=" O THR Q 208 " (cutoff:3.500A) Processing helix chain 'Q' and resid 247 through 253 Processing helix chain 'Q' and resid 269 through 273 Processing helix chain 'R' and resid 9 through 29 Processing helix chain 'R' and resid 36 through 40 Processing helix chain 'R' and resid 40 through 47 removed outlier: 3.726A pdb=" N ALA R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 68 removed outlier: 4.622A pdb=" N HIS R 53 " --> pdb=" O GLY R 49 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N MET R 54 " --> pdb=" O GLN R 50 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS R 68 " --> pdb=" O ALA R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 89 removed outlier: 3.872A pdb=" N GLY R 74 " --> pdb=" O PRO R 70 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER R 75 " --> pdb=" O GLU R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 117 removed outlier: 3.618A pdb=" N ALA R 115 " --> pdb=" O HIS R 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AA2, first strand: chain 'C' and resid 41 through 42 removed outlier: 6.637A pdb=" N TYR C 183 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLU C 17 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU C 185 " --> pdb=" O ASP C 15 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASP C 15 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL C 187 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU C 13 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS C 189 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL C 11 " --> pdb=" O HIS C 189 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE C 191 " --> pdb=" O GLU C 9 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU C 9 " --> pdb=" O PHE C 191 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP C 15 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N SER C 231 " --> pdb=" O ASP C 15 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLU C 17 " --> pdb=" O MET C 229 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N MET C 229 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 120 through 122 Processing sheet with id=AA4, first strand: chain 'C' and resid 153 through 154 Processing sheet with id=AA5, first strand: chain 'C' and resid 255 through 259 removed outlier: 3.558A pdb=" N SER C 258 " --> pdb=" O ALA C 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 41 through 42 Processing sheet with id=AA7, first strand: chain 'D' and resid 136 through 138 removed outlier: 6.889A pdb=" N TYR D 183 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLU D 17 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU D 185 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP D 15 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL D 187 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU D 13 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N HIS D 189 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL D 11 " --> pdb=" O HIS D 189 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE D 191 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLU D 9 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP D 15 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N SER D 231 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLU D 17 " --> pdb=" O MET D 229 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N MET D 229 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU D 234 " --> pdb=" O MET D 289 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.639A pdb=" N ALA D 121 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL D 132 " --> pdb=" O ALA D 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 255 through 258 Processing sheet with id=AB1, first strand: chain 'K' and resid 39 through 42 removed outlier: 4.845A pdb=" N GLY K 40 " --> pdb=" O SER K 143 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU K 185 " --> pdb=" O VAL K 144 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N TYR K 183 " --> pdb=" O PRO K 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 136 through 138 removed outlier: 6.956A pdb=" N GLU K 9 " --> pdb=" O VAL K 236 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL K 236 " --> pdb=" O GLU K 9 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL K 11 " --> pdb=" O LEU K 234 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU K 234 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU K 13 " --> pdb=" O ARG K 232 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU K 228 " --> pdb=" O GLU K 17 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 255 through 259 Processing sheet with id=AB4, first strand: chain 'L' and resid 41 through 42 removed outlier: 3.538A pdb=" N VAL L 152 " --> pdb=" O LYS L 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 136 through 138 removed outlier: 6.598A pdb=" N ASP L 15 " --> pdb=" O SER L 231 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N SER L 231 " --> pdb=" O ASP L 15 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N GLU L 17 " --> pdb=" O MET L 229 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N MET L 229 " --> pdb=" O GLU L 17 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU L 234 " --> pdb=" O MET L 289 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 120 through 122 Processing sheet with id=AB7, first strand: chain 'L' and resid 255 through 259 removed outlier: 3.561A pdb=" N LYS L 256 " --> pdb=" O THR L 276 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER L 258 " --> pdb=" O ALA L 274 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 41 through 42 Processing sheet with id=AB9, first strand: chain 'M' and resid 136 through 138 removed outlier: 3.514A pdb=" N GLY M 184 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASP M 15 " --> pdb=" O SER M 231 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N SER M 231 " --> pdb=" O ASP M 15 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLU M 17 " --> pdb=" O MET M 229 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N MET M 229 " --> pdb=" O GLU M 17 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 120 through 122 Processing sheet with id=AC2, first strand: chain 'M' and resid 255 through 259 removed outlier: 3.622A pdb=" N SER M 258 " --> pdb=" O ALA M 274 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 41 through 42 Processing sheet with id=AC4, first strand: chain 'N' and resid 41 through 42 removed outlier: 3.505A pdb=" N LYS N 233 " --> pdb=" O LEU N 13 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP N 15 " --> pdb=" O SER N 231 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N SER N 231 " --> pdb=" O ASP N 15 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N GLU N 17 " --> pdb=" O MET N 229 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N MET N 229 " --> pdb=" O GLU N 17 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 121 through 122 Processing sheet with id=AC6, first strand: chain 'N' and resid 153 through 154 Processing sheet with id=AC7, first strand: chain 'N' and resid 255 through 259 Processing sheet with id=AC8, first strand: chain 'O' and resid 41 through 42 Processing sheet with id=AC9, first strand: chain 'O' and resid 136 through 138 removed outlier: 6.914A pdb=" N ARG O 7 " --> pdb=" O LYS O 238 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LYS O 238 " --> pdb=" O ARG O 7 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU O 9 " --> pdb=" O VAL O 236 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N VAL O 236 " --> pdb=" O GLU O 9 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL O 11 " --> pdb=" O LEU O 234 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU O 234 " --> pdb=" O VAL O 11 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU O 13 " --> pdb=" O ARG O 232 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 23 through 24 removed outlier: 3.825A pdb=" N MET O 30 " --> pdb=" O ASP O 24 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 120 through 122 Processing sheet with id=AD3, first strand: chain 'O' and resid 255 through 259 Processing sheet with id=AD4, first strand: chain 'P' and resid 136 through 138 removed outlier: 3.612A pdb=" N ALA P 188 " --> pdb=" O LEU P 12 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLU P 17 " --> pdb=" O TYR P 183 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TYR P 183 " --> pdb=" O GLU P 17 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY P 19 " --> pdb=" O VAL P 181 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 136 through 138 removed outlier: 3.612A pdb=" N ALA P 188 " --> pdb=" O LEU P 12 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLU P 9 " --> pdb=" O VAL P 236 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL P 236 " --> pdb=" O GLU P 9 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL P 11 " --> pdb=" O LEU P 234 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU P 234 " --> pdb=" O VAL P 11 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU P 13 " --> pdb=" O ARG P 232 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 41 through 42 Processing sheet with id=AD7, first strand: chain 'P' and resid 255 through 259 Processing sheet with id=AD8, first strand: chain 'Q' and resid 41 through 42 removed outlier: 4.801A pdb=" N HIS Q 189 " --> pdb=" O ALA Q 139 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA Q 141 " --> pdb=" O VAL Q 187 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL Q 187 " --> pdb=" O ALA Q 141 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER Q 143 " --> pdb=" O LEU Q 185 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU Q 185 " --> pdb=" O SER Q 143 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL Q 152 " --> pdb=" O LYS Q 178 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 41 through 42 removed outlier: 4.801A pdb=" N HIS Q 189 " --> pdb=" O ALA Q 139 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA Q 141 " --> pdb=" O VAL Q 187 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL Q 187 " --> pdb=" O ALA Q 141 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER Q 143 " --> pdb=" O LEU Q 185 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU Q 185 " --> pdb=" O SER Q 143 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR Q 183 " --> pdb=" O GLU Q 17 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N GLU Q 17 " --> pdb=" O TYR Q 183 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU Q 185 " --> pdb=" O ASP Q 15 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP Q 15 " --> pdb=" O LEU Q 185 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL Q 187 " --> pdb=" O LEU Q 13 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU Q 13 " --> pdb=" O VAL Q 187 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS Q 189 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL Q 11 " --> pdb=" O HIS Q 189 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE Q 191 " --> pdb=" O GLU Q 9 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU Q 9 " --> pdb=" O PHE Q 191 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLU Q 9 " --> pdb=" O VAL Q 236 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL Q 236 " --> pdb=" O GLU Q 9 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL Q 11 " --> pdb=" O LEU Q 234 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU Q 234 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU Q 13 " --> pdb=" O ARG Q 232 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LEU Q 234 " --> pdb=" O MET Q 289 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 121 through 122 Processing sheet with id=AE2, first strand: chain 'Q' and resid 255 through 257 1297 hydrogen bonds defined for protein. 3738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 6.33 Time building geometry restraints manager: 3.38 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: 7698 1.33 - 1.45: 5139 1.45 - 1.57: 16001 1.57 - 1.69: 106 1.69 - 1.81: 278 Bond restraints: 29222 Sorted by residual: bond pdb=" C1' U A 39 " pdb=" N1 U A 39 " ideal model delta sigma weight residual 1.470 1.498 -0.028 1.50e-02 4.44e+03 3.42e+00 bond pdb=" C ASN M 20 " pdb=" N PRO M 21 " ideal model delta sigma weight residual 1.336 1.321 0.015 1.20e-02 6.94e+03 1.51e+00 bond pdb=" CA TYR L 186 " pdb=" CB TYR L 186 " ideal model delta sigma weight residual 1.532 1.511 0.021 1.82e-02 3.02e+03 1.29e+00 bond pdb=" CB VAL N 45 " pdb=" CG1 VAL N 45 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 bond pdb=" CA PHE N 218 " pdb=" CB PHE N 218 " ideal model delta sigma weight residual 1.532 1.515 0.017 1.78e-02 3.16e+03 9.36e-01 ... (remaining 29217 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 39297 1.94 - 3.88: 390 3.88 - 5.82: 34 5.82 - 7.76: 0 7.76 - 9.69: 2 Bond angle restraints: 39723 Sorted by residual: angle pdb=" C1' U A 39 " pdb=" N1 U A 39 " pdb=" C6 U A 39 " ideal model delta sigma weight residual 121.20 111.51 9.69 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C1' U A 39 " pdb=" N1 U A 39 " pdb=" C2 U A 39 " ideal model delta sigma weight residual 117.70 126.36 -8.66 3.00e+00 1.11e-01 8.33e+00 angle pdb=" C VAL K 127 " pdb=" N ASN K 128 " pdb=" CA ASN K 128 " ideal model delta sigma weight residual 121.56 125.43 -3.87 1.56e+00 4.11e-01 6.16e+00 angle pdb=" C2' U A 39 " pdb=" C1' U A 39 " pdb=" N1 U A 39 " ideal model delta sigma weight residual 114.00 117.72 -3.72 1.50e+00 4.44e-01 6.14e+00 angle pdb=" C VAL Q 127 " pdb=" N ASN Q 128 " pdb=" CA ASN Q 128 " ideal model delta sigma weight residual 121.56 125.29 -3.73 1.56e+00 4.11e-01 5.71e+00 ... (remaining 39718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 17580 35.28 - 70.56: 276 70.56 - 105.84: 29 105.84 - 141.13: 3 141.13 - 176.41: 3 Dihedral angle restraints: 17891 sinusoidal: 7802 harmonic: 10089 Sorted by residual: dihedral pdb=" O4' C A 13 " pdb=" C1' C A 13 " pdb=" N1 C A 13 " pdb=" C2 C A 13 " ideal model delta sinusoidal sigma weight residual 200.00 62.04 137.96 1 1.50e+01 4.44e-03 7.44e+01 dihedral pdb=" O4' U A 42 " pdb=" C1' U A 42 " pdb=" N1 U A 42 " pdb=" C2 U A 42 " ideal model delta sinusoidal sigma weight residual 232.00 55.59 176.41 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C A 43 " pdb=" C1' C A 43 " pdb=" N1 C A 43 " pdb=" C2 C A 43 " ideal model delta sinusoidal sigma weight residual 232.00 55.72 176.28 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 17888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2996 0.035 - 0.070: 920 0.070 - 0.104: 371 0.104 - 0.139: 120 0.139 - 0.174: 3 Chirality restraints: 4410 Sorted by residual: chirality pdb=" C1' C A 13 " pdb=" O4' C A 13 " pdb=" C2' C A 13 " pdb=" N1 C A 13 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" C1' G A 29 " pdb=" O4' G A 29 " pdb=" C2' G A 29 " pdb=" N9 G A 29 " both_signs ideal model delta sigma weight residual False 2.44 2.27 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA VAL Q 181 " pdb=" N VAL Q 181 " pdb=" C VAL Q 181 " pdb=" CB VAL Q 181 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 4407 not shown) Planarity restraints: 5013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU N 91 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO N 92 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO N 92 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO N 92 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU Q 95 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO Q 96 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO Q 96 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO Q 96 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU L 95 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO L 96 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " 0.021 5.00e-02 4.00e+02 ... (remaining 5010 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 852 2.69 - 3.25: 29097 3.25 - 3.80: 48089 3.80 - 4.35: 65570 4.35 - 4.90: 104300 Nonbonded interactions: 247908 Sorted by model distance: nonbonded pdb=" O ASP P 107 " pdb=" OG1 THR P 111 " model vdw 2.142 3.040 nonbonded pdb=" OG SER O 143 " pdb=" O GLU O 145 " model vdw 2.144 3.040 nonbonded pdb=" OP1 G A 36 " pdb=" NH2 ARG N 52 " model vdw 2.149 3.120 nonbonded pdb=" OG SER E 43 " pdb=" O ASP Q 26 " model vdw 2.153 3.040 nonbonded pdb=" O2' C A 38 " pdb=" OD1 ASN N 29 " model vdw 2.156 3.040 ... (remaining 247903 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 'B' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'R' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.650 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.004 0.046 29222 Z= 0.183 Angle : 0.487 9.695 39723 Z= 0.256 Chirality : 0.042 0.174 4410 Planarity : 0.004 0.040 5013 Dihedral : 12.508 176.407 11357 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.97 % Favored : 95.00 % Rotamer: Outliers : 2.12 % Allowed : 3.73 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.14), residues: 3418 helix: 1.13 (0.14), residues: 1319 sheet: -0.38 (0.23), residues: 540 loop : -0.66 (0.16), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 232 TYR 0.017 0.001 TYR N 8 PHE 0.015 0.001 PHE K 10 TRP 0.008 0.001 TRP Q 211 HIS 0.004 0.001 HIS O 39 Details of bonding type rmsd covalent geometry : bond 0.00372 (29222) covalent geometry : angle 0.48707 (39723) hydrogen bonds : bond 0.27449 ( 1272) hydrogen bonds : angle 8.55138 ( 3738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 870 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 23 LYS cc_start: 0.8741 (tptt) cc_final: 0.8365 (mmtt) REVERT: B 106 MET cc_start: 0.7347 (mmm) cc_final: 0.7007 (mmm) REVERT: C 217 MET cc_start: 0.8334 (ptt) cc_final: 0.8080 (ptt) REVERT: D 83 TYR cc_start: 0.7267 (m-80) cc_final: 0.6685 (m-80) REVERT: D 186 TYR cc_start: 0.6094 (m-80) cc_final: 0.5819 (m-10) REVERT: D 214 LEU cc_start: 0.8242 (mt) cc_final: 0.7997 (mt) REVERT: G 17 LEU cc_start: 0.8841 (tp) cc_final: 0.8290 (tp) REVERT: G 45 SER cc_start: 0.8876 (m) cc_final: 0.8640 (m) REVERT: H 99 SER cc_start: 0.8943 (m) cc_final: 0.8712 (p) REVERT: I 13 LEU cc_start: 0.9170 (mt) cc_final: 0.8849 (mt) REVERT: J 66 LEU cc_start: 0.4334 (mt) cc_final: 0.2588 (mt) REVERT: J 79 TYR cc_start: 0.7940 (m-10) cc_final: 0.7196 (m-10) REVERT: J 97 MET cc_start: 0.7523 (mtm) cc_final: 0.7031 (mtm) REVERT: K 43 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.8023 (p) REVERT: K 144 VAL cc_start: 0.7642 (m) cc_final: 0.7324 (p) REVERT: M 127 VAL cc_start: 0.9296 (OUTLIER) cc_final: 0.8945 (t) REVERT: M 150 GLN cc_start: 0.7929 (mt0) cc_final: 0.7539 (mt0) REVERT: N 157 MET cc_start: 0.8100 (mtp) cc_final: 0.7327 (mmt) REVERT: O 207 LEU cc_start: 0.9117 (tp) cc_final: 0.8189 (tp) REVERT: O 217 MET cc_start: 0.7887 (ptt) cc_final: 0.7657 (ptt) REVERT: P 45 VAL cc_start: 0.8604 (t) cc_final: 0.8205 (t) REVERT: P 124 THR cc_start: 0.8329 (p) cc_final: 0.8101 (t) REVERT: P 186 TYR cc_start: 0.7918 (m-80) cc_final: 0.7718 (m-80) REVERT: Q 9 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7701 (tp30) REVERT: Q 49 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8055 (tpp-160) REVERT: Q 75 LEU cc_start: 0.8871 (mt) cc_final: 0.8580 (mp) REVERT: Q 186 TYR cc_start: 0.8604 (m-80) cc_final: 0.8399 (m-80) REVERT: Q 191 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8243 (m-80) REVERT: R 21 LEU cc_start: 0.8660 (mt) cc_final: 0.8446 (mt) REVERT: R 52 PHE cc_start: 0.7705 (m-80) cc_final: 0.7444 (m-10) REVERT: R 116 LEU cc_start: 0.7504 (mt) cc_final: 0.6664 (tp) outliers start: 62 outliers final: 20 residues processed: 913 average time/residue: 0.2104 time to fit residues: 296.7453 Evaluate side-chains 525 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 500 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 191 PHE Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain P residue 122 VAL Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 216 ASN Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 49 ARG Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 191 PHE Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 216 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN B 102 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS C 240 GLN E 47 ASN E 112 GLN F 78 HIS G 47 ASN G 84 GLN H 84 GLN I 58 ASN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN K 240 GLN K 249 HIS L 70 GLN L 240 GLN N 70 GLN O 131 GLN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 131 GLN ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 78 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.077470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.053638 restraints weight = 124611.420| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 4.26 r_work: 0.2974 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29222 Z= 0.199 Angle : 0.676 12.471 39723 Z= 0.352 Chirality : 0.046 0.235 4410 Planarity : 0.005 0.052 5013 Dihedral : 14.084 178.903 4653 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.12 % Allowed : 12.68 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.14), residues: 3418 helix: 1.18 (0.13), residues: 1432 sheet: -0.23 (0.23), residues: 540 loop : -0.74 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 72 TYR 0.019 0.002 TYR B 110 PHE 0.034 0.002 PHE R 93 TRP 0.033 0.002 TRP N 211 HIS 0.012 0.001 HIS B 53 Details of bonding type rmsd covalent geometry : bond 0.00432 (29222) covalent geometry : angle 0.67641 (39723) hydrogen bonds : bond 0.05207 ( 1272) hydrogen bonds : angle 5.77925 ( 3738) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 528 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 LEU cc_start: 0.9270 (mt) cc_final: 0.8886 (tp) REVERT: B 23 LYS cc_start: 0.8117 (tptt) cc_final: 0.7648 (tptt) REVERT: B 54 MET cc_start: 0.9477 (OUTLIER) cc_final: 0.9134 (tpp) REVERT: B 80 GLU cc_start: 0.9259 (pp20) cc_final: 0.8991 (pp20) REVERT: B 101 GLU cc_start: 0.9353 (mm-30) cc_final: 0.9000 (mp0) REVERT: B 110 TYR cc_start: 0.9244 (m-80) cc_final: 0.8219 (m-80) REVERT: C 30 MET cc_start: 0.9135 (mtp) cc_final: 0.8553 (mtm) REVERT: C 36 GLU cc_start: 0.8445 (mp0) cc_final: 0.8143 (mp0) REVERT: C 68 TYR cc_start: 0.8537 (t80) cc_final: 0.8323 (t80) REVERT: C 175 MET cc_start: 0.8771 (mtm) cc_final: 0.8460 (mtm) REVERT: D 30 MET cc_start: 0.9200 (tpt) cc_final: 0.8989 (tpp) REVERT: D 137 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8315 (mm110) REVERT: D 186 TYR cc_start: 0.6587 (m-80) cc_final: 0.6136 (m-10) REVERT: E 54 MET cc_start: 0.8895 (mtm) cc_final: 0.8462 (ptp) REVERT: F 50 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8334 (mp10) REVERT: G 47 ASN cc_start: 0.9084 (m-40) cc_final: 0.8806 (m-40) REVERT: G 109 TYR cc_start: 0.8384 (t80) cc_final: 0.8169 (t80) REVERT: H 10 ARG cc_start: 0.8279 (ttp80) cc_final: 0.8029 (mmm-85) REVERT: H 17 LEU cc_start: 0.8986 (tp) cc_final: 0.8700 (tp) REVERT: H 38 ASP cc_start: 0.8691 (t0) cc_final: 0.8177 (m-30) REVERT: H 40 TYR cc_start: 0.6420 (m-80) cc_final: 0.6175 (m-80) REVERT: H 51 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.8024 (m) REVERT: H 80 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8854 (pt0) REVERT: H 83 MET cc_start: 0.8541 (mmm) cc_final: 0.8237 (mmt) REVERT: H 102 GLN cc_start: 0.8135 (mt0) cc_final: 0.7934 (mt0) REVERT: I 12 TYR cc_start: 0.8541 (t80) cc_final: 0.7942 (t80) REVERT: I 18 PHE cc_start: 0.9515 (t80) cc_final: 0.9191 (t80) REVERT: I 66 LEU cc_start: 0.7656 (tp) cc_final: 0.7434 (tp) REVERT: I 110 TYR cc_start: 0.9101 (m-80) cc_final: 0.8598 (m-80) REVERT: J 52 PHE cc_start: 0.9402 (m-10) cc_final: 0.9160 (m-10) REVERT: J 79 TYR cc_start: 0.8135 (m-10) cc_final: 0.7746 (m-10) REVERT: J 82 MET cc_start: 0.9190 (ptp) cc_final: 0.8788 (ptp) REVERT: K 150 GLN cc_start: 0.8126 (mm110) cc_final: 0.7694 (mm110) REVERT: K 179 HIS cc_start: 0.8138 (OUTLIER) cc_final: 0.7904 (m90) REVERT: L 229 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8611 (mtp) REVERT: M 221 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8517 (t0) REVERT: N 157 MET cc_start: 0.8012 (mtp) cc_final: 0.7117 (mmt) REVERT: N 177 ARG cc_start: 0.7642 (mtm-85) cc_final: 0.7408 (mtt-85) REVERT: O 30 MET cc_start: 0.9304 (mtp) cc_final: 0.9057 (mmt) REVERT: O 207 LEU cc_start: 0.9357 (tp) cc_final: 0.8710 (tp) REVERT: O 217 MET cc_start: 0.8837 (ptt) cc_final: 0.8573 (ptp) REVERT: O 221 ASP cc_start: 0.8610 (t70) cc_final: 0.8399 (t0) REVERT: O 289 MET cc_start: 0.8501 (mtt) cc_final: 0.8175 (mtt) REVERT: P 33 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.6948 (mm) REVERT: P 175 MET cc_start: 0.7155 (ppp) cc_final: 0.6551 (ptt) REVERT: Q 9 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8073 (tp30) REVERT: Q 75 LEU cc_start: 0.9581 (mt) cc_final: 0.9366 (mp) REVERT: Q 127 VAL cc_start: 0.9569 (OUTLIER) cc_final: 0.9283 (p) REVERT: Q 131 GLN cc_start: 0.8728 (pt0) cc_final: 0.8458 (pm20) REVERT: Q 186 TYR cc_start: 0.9298 (m-80) cc_final: 0.8972 (m-80) REVERT: R 52 PHE cc_start: 0.7671 (m-80) cc_final: 0.7087 (m-80) REVERT: R 65 LYS cc_start: 0.8512 (mtmt) cc_final: 0.8218 (pttt) REVERT: R 80 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8652 (mm-30) outliers start: 91 outliers final: 42 residues processed: 586 average time/residue: 0.2077 time to fit residues: 189.9242 Evaluate side-chains 484 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 434 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 100 ASP Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain K residue 179 HIS Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 191 PHE Chi-restraints excluded: chain L residue 229 MET Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 221 ASP Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 191 PHE Chi-restraints excluded: chain Q residue 216 ASN Chi-restraints excluded: chain R residue 99 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 213 optimal weight: 0.8980 chunk 262 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 chunk 289 optimal weight: 4.9990 chunk 332 optimal weight: 0.0050 chunk 145 optimal weight: 30.0000 chunk 100 optimal weight: 20.0000 chunk 335 optimal weight: 5.9990 chunk 334 optimal weight: 9.9990 chunk 320 optimal weight: 5.9990 overall best weight: 2.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN C 18 ASN C 54 HIS F 78 HIS ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 ASN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 220 HIS K 240 GLN K 249 HIS M 150 GLN M 240 GLN N 70 GLN O 112 ASN P 112 ASN ** Q 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.080649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.056966 restraints weight = 122300.083| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 4.22 r_work: 0.2968 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29222 Z= 0.180 Angle : 0.634 12.159 39723 Z= 0.326 Chirality : 0.045 0.302 4410 Planarity : 0.004 0.042 5013 Dihedral : 13.954 179.852 4639 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.01 % Allowed : 12.50 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.14), residues: 3418 helix: 1.14 (0.13), residues: 1432 sheet: -0.02 (0.23), residues: 540 loop : -0.73 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 72 TYR 0.019 0.002 TYR M 183 PHE 0.029 0.002 PHE J 93 TRP 0.049 0.002 TRP N 211 HIS 0.012 0.001 HIS F 78 Details of bonding type rmsd covalent geometry : bond 0.00391 (29222) covalent geometry : angle 0.63364 (39723) hydrogen bonds : bond 0.04373 ( 1272) hydrogen bonds : angle 5.39805 ( 3738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 471 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 LEU cc_start: 0.9346 (mt) cc_final: 0.8918 (tp) REVERT: B 54 MET cc_start: 0.9570 (OUTLIER) cc_final: 0.9062 (tpp) REVERT: B 101 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8959 (mp0) REVERT: B 106 MET cc_start: 0.9395 (mmm) cc_final: 0.8795 (mmm) REVERT: B 110 TYR cc_start: 0.9466 (m-80) cc_final: 0.8332 (m-80) REVERT: C 30 MET cc_start: 0.9141 (mtp) cc_final: 0.8492 (mtm) REVERT: C 36 GLU cc_start: 0.8626 (mp0) cc_final: 0.8364 (mp0) REVERT: C 123 MET cc_start: 0.8731 (mtm) cc_final: 0.8413 (mtm) REVERT: C 131 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8590 (tt0) REVERT: D 89 LYS cc_start: 0.9131 (mttt) cc_final: 0.8922 (tmtt) REVERT: D 186 TYR cc_start: 0.6501 (m-80) cc_final: 0.6202 (m-80) REVERT: D 229 MET cc_start: 0.5750 (mmm) cc_final: 0.4703 (mmt) REVERT: F 66 LEU cc_start: 0.9287 (tp) cc_final: 0.9067 (mt) REVERT: G 47 ASN cc_start: 0.9126 (m-40) cc_final: 0.8769 (m-40) REVERT: G 83 MET cc_start: 0.8653 (tpp) cc_final: 0.8438 (mmt) REVERT: H 10 ARG cc_start: 0.8269 (ttp80) cc_final: 0.8027 (mmm-85) REVERT: H 39 ARG cc_start: 0.8521 (mpt180) cc_final: 0.8316 (mpt180) REVERT: H 40 TYR cc_start: 0.6678 (m-80) cc_final: 0.6425 (m-80) REVERT: H 51 VAL cc_start: 0.8338 (OUTLIER) cc_final: 0.8053 (m) REVERT: H 80 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8832 (pt0) REVERT: H 102 GLN cc_start: 0.8371 (mt0) cc_final: 0.8104 (mt0) REVERT: H 107 ILE cc_start: 0.9146 (mm) cc_final: 0.8840 (mm) REVERT: I 10 ARG cc_start: 0.8411 (ttp-170) cc_final: 0.8044 (mtp-110) REVERT: I 12 TYR cc_start: 0.8287 (t80) cc_final: 0.7481 (t80) REVERT: I 16 ARG cc_start: 0.9265 (mtp180) cc_final: 0.9049 (mtm-85) REVERT: I 66 LEU cc_start: 0.7514 (tp) cc_final: 0.7311 (tp) REVERT: I 80 GLU cc_start: 0.9212 (pp20) cc_final: 0.8954 (pp20) REVERT: I 81 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8980 (pt) REVERT: I 110 TYR cc_start: 0.9047 (m-80) cc_final: 0.8629 (m-80) REVERT: I 113 ARG cc_start: 0.9657 (ptt90) cc_final: 0.9358 (ptt90) REVERT: J 7 ARG cc_start: 0.7042 (ttm-80) cc_final: 0.6775 (ttm-80) REVERT: J 79 TYR cc_start: 0.8150 (m-10) cc_final: 0.7768 (m-10) REVERT: J 82 MET cc_start: 0.9100 (ptp) cc_final: 0.8765 (ptp) REVERT: J 86 ILE cc_start: 0.8886 (mt) cc_final: 0.8613 (tt) REVERT: J 97 MET cc_start: 0.6607 (mtm) cc_final: 0.6304 (mmm) REVERT: J 101 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8808 (mt-10) REVERT: J 102 GLN cc_start: 0.8954 (mt0) cc_final: 0.8553 (mm-40) REVERT: K 150 GLN cc_start: 0.8206 (mm110) cc_final: 0.7667 (mm110) REVERT: K 179 HIS cc_start: 0.8018 (OUTLIER) cc_final: 0.7778 (m90) REVERT: L 229 MET cc_start: 0.8865 (mtp) cc_final: 0.8583 (mtp) REVERT: M 131 GLN cc_start: 0.9052 (pt0) cc_final: 0.8536 (pt0) REVERT: N 109 MET cc_start: 0.9091 (mmm) cc_final: 0.8819 (mmm) REVERT: N 157 MET cc_start: 0.8052 (mtp) cc_final: 0.7280 (mmt) REVERT: N 186 TYR cc_start: 0.9373 (m-80) cc_final: 0.9167 (m-80) REVERT: O 30 MET cc_start: 0.9282 (mtp) cc_final: 0.9005 (mmt) REVERT: O 207 LEU cc_start: 0.9477 (tp) cc_final: 0.8777 (tp) REVERT: O 211 TRP cc_start: 0.7824 (m-10) cc_final: 0.7535 (m-90) REVERT: P 33 ILE cc_start: 0.7391 (OUTLIER) cc_final: 0.6943 (mm) REVERT: Q 75 LEU cc_start: 0.9586 (mt) cc_final: 0.9366 (mp) REVERT: Q 127 VAL cc_start: 0.9609 (OUTLIER) cc_final: 0.9364 (p) REVERT: R 52 PHE cc_start: 0.7520 (m-80) cc_final: 0.7243 (m-80) REVERT: R 58 ASN cc_start: 0.8889 (m-40) cc_final: 0.8428 (p0) REVERT: R 65 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8300 (pttt) REVERT: R 80 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8708 (mm-30) outliers start: 88 outliers final: 51 residues processed: 525 average time/residue: 0.2005 time to fit residues: 166.6701 Evaluate side-chains 460 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 402 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 105 PHE Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 179 HIS Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 191 PHE Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 105 VAL Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain Q residue 138 MET Chi-restraints excluded: chain Q residue 191 PHE Chi-restraints excluded: chain Q residue 216 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 92 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 243 optimal weight: 0.5980 chunk 266 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 256 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 325 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 ASN ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 HIS ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 HIS K 150 GLN L 70 GLN L 220 HIS ** M 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 70 GLN N 172 ASN ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 240 GLN R 50 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.080263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.056659 restraints weight = 121560.180| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 4.15 r_work: 0.2941 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 29222 Z= 0.226 Angle : 0.653 13.673 39723 Z= 0.334 Chirality : 0.045 0.277 4410 Planarity : 0.004 0.042 5013 Dihedral : 13.925 179.022 4634 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.56 % Allowed : 13.39 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 3418 helix: 1.09 (0.14), residues: 1432 sheet: 0.05 (0.23), residues: 540 loop : -0.74 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 67 TYR 0.022 0.002 TYR M 183 PHE 0.023 0.002 PHE I 18 TRP 0.025 0.002 TRP N 211 HIS 0.028 0.001 HIS I 62 Details of bonding type rmsd covalent geometry : bond 0.00491 (29222) covalent geometry : angle 0.65285 (39723) hydrogen bonds : bond 0.04171 ( 1272) hydrogen bonds : angle 5.34639 ( 3738) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 416 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 LEU cc_start: 0.9407 (mt) cc_final: 0.8902 (tp) REVERT: B 54 MET cc_start: 0.9515 (OUTLIER) cc_final: 0.8944 (mmm) REVERT: B 101 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8917 (mp0) REVERT: B 102 GLN cc_start: 0.9510 (mt0) cc_final: 0.9094 (mm-40) REVERT: B 106 MET cc_start: 0.9533 (mmm) cc_final: 0.8694 (mmm) REVERT: B 110 TYR cc_start: 0.9523 (m-80) cc_final: 0.8462 (m-80) REVERT: C 30 MET cc_start: 0.9137 (mtp) cc_final: 0.8498 (mtm) REVERT: C 131 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8534 (tt0) REVERT: C 238 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8198 (tttp) REVERT: D 89 LYS cc_start: 0.9138 (mttt) cc_final: 0.8914 (tmtt) REVERT: D 90 PRO cc_start: 0.6946 (Cg_endo) cc_final: 0.6589 (Cg_exo) REVERT: D 186 TYR cc_start: 0.6514 (m-80) cc_final: 0.6119 (m-80) REVERT: D 229 MET cc_start: 0.5998 (mmm) cc_final: 0.5252 (mmm) REVERT: E 54 MET cc_start: 0.8873 (mtm) cc_final: 0.8574 (mtm) REVERT: F 66 LEU cc_start: 0.9237 (tp) cc_final: 0.9014 (mt) REVERT: F 97 MET cc_start: 0.8852 (mtp) cc_final: 0.8615 (mtp) REVERT: F 102 GLN cc_start: 0.8774 (mt0) cc_final: 0.8278 (mt0) REVERT: G 47 ASN cc_start: 0.9163 (m-40) cc_final: 0.8813 (m-40) REVERT: G 72 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6748 (mtm-85) REVERT: G 102 GLN cc_start: 0.8709 (mt0) cc_final: 0.8434 (mt0) REVERT: G 106 MET cc_start: 0.8834 (mmp) cc_final: 0.8148 (mmt) REVERT: H 10 ARG cc_start: 0.8192 (ttp80) cc_final: 0.7863 (mmm-85) REVERT: H 38 ASP cc_start: 0.8748 (t70) cc_final: 0.8416 (t70) REVERT: H 39 ARG cc_start: 0.8658 (mpt180) cc_final: 0.8407 (mpt180) REVERT: H 40 TYR cc_start: 0.6801 (m-80) cc_final: 0.6590 (m-80) REVERT: H 51 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8237 (m) REVERT: H 80 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8785 (pt0) REVERT: H 102 GLN cc_start: 0.8329 (mt0) cc_final: 0.8082 (mt0) REVERT: I 10 ARG cc_start: 0.8507 (ttp-170) cc_final: 0.8246 (mtm110) REVERT: I 12 TYR cc_start: 0.8356 (t80) cc_final: 0.7497 (t80) REVERT: I 16 ARG cc_start: 0.9316 (mtp180) cc_final: 0.9076 (mtm-85) REVERT: I 80 GLU cc_start: 0.9233 (pp20) cc_final: 0.8927 (pp20) REVERT: I 81 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.8993 (pt) REVERT: I 100 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7499 (t70) REVERT: I 113 ARG cc_start: 0.9564 (ptt90) cc_final: 0.9029 (ptt-90) REVERT: J 10 ARG cc_start: 0.8922 (tmm-80) cc_final: 0.8327 (tpp80) REVERT: J 62 HIS cc_start: 0.9039 (m-70) cc_final: 0.8773 (m-70) REVERT: J 82 MET cc_start: 0.9025 (ptp) cc_final: 0.8814 (ptp) REVERT: J 83 MET cc_start: 0.9344 (mmm) cc_final: 0.9083 (mmp) REVERT: J 102 GLN cc_start: 0.9010 (mt0) cc_final: 0.8657 (mm-40) REVERT: K 150 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7797 (mm110) REVERT: K 179 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.7845 (m90) REVERT: M 109 MET cc_start: 0.9086 (tpp) cc_final: 0.8831 (tpp) REVERT: N 30 MET cc_start: 0.8663 (mmm) cc_final: 0.8378 (mmm) REVERT: N 157 MET cc_start: 0.8155 (mtp) cc_final: 0.7310 (mmt) REVERT: O 57 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9394 (tt) REVERT: Q 75 LEU cc_start: 0.9616 (mt) cc_final: 0.9385 (mp) REVERT: Q 127 VAL cc_start: 0.9625 (OUTLIER) cc_final: 0.9414 (p) REVERT: R 106 MET cc_start: 0.7885 (mmp) cc_final: 0.7670 (mmp) outliers start: 104 outliers final: 66 residues processed: 482 average time/residue: 0.1945 time to fit residues: 150.0469 Evaluate side-chains 461 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 385 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 ASN Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 100 ASP Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 105 PHE Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 131 GLN Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 179 HIS Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 191 PHE Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 105 VAL Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 157 MET Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain Q residue 138 MET Chi-restraints excluded: chain Q residue 154 ILE Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 191 PHE Chi-restraints excluded: chain Q residue 216 ASN Chi-restraints excluded: chain R residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 82 optimal weight: 9.9990 chunk 292 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 311 optimal weight: 0.6980 chunk 297 optimal weight: 0.0870 chunk 266 optimal weight: 10.0000 overall best weight: 3.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 ASN ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 84 GLN K 22 ASN K 137 GLN L 70 GLN L 220 HIS ** M 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 150 GLN ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 216 ASN ** Q 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.079622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.056115 restraints weight = 121745.078| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 4.13 r_work: 0.2931 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 29222 Z= 0.207 Angle : 0.640 12.804 39723 Z= 0.326 Chirality : 0.045 0.286 4410 Planarity : 0.004 0.042 5013 Dihedral : 13.917 178.058 4634 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.29 % Allowed : 14.53 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.15), residues: 3418 helix: 1.16 (0.14), residues: 1432 sheet: 0.05 (0.23), residues: 540 loop : -0.72 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 67 TYR 0.016 0.002 TYR F 110 PHE 0.021 0.002 PHE R 93 TRP 0.017 0.002 TRP O 211 HIS 0.011 0.001 HIS D 179 Details of bonding type rmsd covalent geometry : bond 0.00448 (29222) covalent geometry : angle 0.63983 (39723) hydrogen bonds : bond 0.03967 ( 1272) hydrogen bonds : angle 5.22086 ( 3738) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 409 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 LEU cc_start: 0.9413 (mt) cc_final: 0.8894 (tp) REVERT: B 101 GLU cc_start: 0.9300 (mm-30) cc_final: 0.8931 (mp0) REVERT: B 106 MET cc_start: 0.9520 (mmm) cc_final: 0.8639 (mmm) REVERT: B 110 TYR cc_start: 0.9532 (m-80) cc_final: 0.8440 (m-80) REVERT: C 36 GLU cc_start: 0.8763 (mp0) cc_final: 0.8398 (mp0) REVERT: C 131 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8484 (tt0) REVERT: D 89 LYS cc_start: 0.9144 (mttt) cc_final: 0.8918 (tmtt) REVERT: D 90 PRO cc_start: 0.6977 (Cg_endo) cc_final: 0.6622 (Cg_exo) REVERT: D 186 TYR cc_start: 0.6511 (m-80) cc_final: 0.6083 (m-80) REVERT: D 229 MET cc_start: 0.6036 (mmm) cc_final: 0.4918 (mmt) REVERT: D 289 MET cc_start: 0.9202 (mtp) cc_final: 0.8815 (ptm) REVERT: E 54 MET cc_start: 0.8875 (mtm) cc_final: 0.8336 (ptp) REVERT: F 39 ARG cc_start: 0.8135 (mtt-85) cc_final: 0.7639 (tpt90) REVERT: F 97 MET cc_start: 0.8817 (mtp) cc_final: 0.8563 (mtp) REVERT: F 102 GLN cc_start: 0.8803 (mt0) cc_final: 0.8305 (mt0) REVERT: G 47 ASN cc_start: 0.9221 (m-40) cc_final: 0.8866 (m-40) REVERT: G 83 MET cc_start: 0.8862 (tpp) cc_final: 0.8387 (mpp) REVERT: G 102 GLN cc_start: 0.8767 (mt0) cc_final: 0.8331 (mt0) REVERT: H 10 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7900 (mmm-85) REVERT: H 80 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8734 (pt0) REVERT: H 102 GLN cc_start: 0.8340 (mt0) cc_final: 0.8103 (mt0) REVERT: I 9 ASP cc_start: 0.7733 (t70) cc_final: 0.7312 (m-30) REVERT: I 10 ARG cc_start: 0.8587 (ttp-170) cc_final: 0.8269 (mtm110) REVERT: I 12 TYR cc_start: 0.8353 (t80) cc_final: 0.7649 (t80) REVERT: I 80 GLU cc_start: 0.9308 (pp20) cc_final: 0.8960 (pp20) REVERT: I 81 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.8990 (pt) REVERT: I 100 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7475 (t70) REVERT: I 110 TYR cc_start: 0.8824 (m-80) cc_final: 0.8524 (m-80) REVERT: J 17 LEU cc_start: 0.9425 (pp) cc_final: 0.9225 (pp) REVERT: J 21 LEU cc_start: 0.9325 (mt) cc_final: 0.9018 (pp) REVERT: J 79 TYR cc_start: 0.8023 (m-10) cc_final: 0.7672 (m-10) REVERT: J 82 MET cc_start: 0.9118 (ptp) cc_final: 0.8875 (ptp) REVERT: J 101 GLU cc_start: 0.9388 (mt-10) cc_final: 0.8943 (mt-10) REVERT: J 102 GLN cc_start: 0.9030 (mt0) cc_final: 0.8734 (mt0) REVERT: K 150 GLN cc_start: 0.8450 (mm-40) cc_final: 0.7803 (mm110) REVERT: K 179 HIS cc_start: 0.8141 (OUTLIER) cc_final: 0.7814 (m90) REVERT: K 217 MET cc_start: 0.8667 (ptm) cc_final: 0.8281 (ttp) REVERT: K 219 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8029 (mt-10) REVERT: L 217 MET cc_start: 0.8924 (ptp) cc_final: 0.8428 (ptp) REVERT: M 36 GLU cc_start: 0.8513 (mp0) cc_final: 0.8281 (mp0) REVERT: M 109 MET cc_start: 0.9121 (tpp) cc_final: 0.8878 (tpp) REVERT: M 289 MET cc_start: 0.9254 (mmm) cc_final: 0.9047 (mmm) REVERT: N 30 MET cc_start: 0.8663 (mmm) cc_final: 0.8336 (tpt) REVERT: N 109 MET cc_start: 0.9122 (mmm) cc_final: 0.8892 (mmm) REVERT: N 157 MET cc_start: 0.8235 (mtp) cc_final: 0.7397 (mmt) REVERT: P 238 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8584 (tptp) REVERT: Q 75 LEU cc_start: 0.9629 (mt) cc_final: 0.9398 (mp) REVERT: R 65 LYS cc_start: 0.8657 (mtmt) cc_final: 0.8386 (pttt) outliers start: 96 outliers final: 65 residues processed: 474 average time/residue: 0.1918 time to fit residues: 145.9487 Evaluate side-chains 448 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 378 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 89 ASN Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 100 ASP Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 105 PHE Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 131 GLN Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 179 HIS Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 191 PHE Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 279 GLN Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 131 GLN Chi-restraints excluded: chain P residue 238 LYS Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 138 MET Chi-restraints excluded: chain Q residue 154 ILE Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 191 PHE Chi-restraints excluded: chain R residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 82 optimal weight: 3.9990 chunk 313 optimal weight: 9.9990 chunk 311 optimal weight: 0.9980 chunk 164 optimal weight: 7.9990 chunk 340 optimal weight: 4.9990 chunk 209 optimal weight: 9.9990 chunk 183 optimal weight: 0.8980 chunk 211 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 ASN C 18 ASN ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 HIS ** G 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 220 HIS ** M 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 HIS ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.080857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.057274 restraints weight = 119586.132| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 4.19 r_work: 0.2941 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29222 Z= 0.180 Angle : 0.633 12.854 39723 Z= 0.321 Chirality : 0.045 0.343 4410 Planarity : 0.004 0.043 5013 Dihedral : 13.878 178.580 4631 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.05 % Allowed : 15.66 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.15), residues: 3418 helix: 1.21 (0.14), residues: 1432 sheet: 0.18 (0.24), residues: 522 loop : -0.70 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 113 TYR 0.013 0.002 TYR I 12 PHE 0.022 0.002 PHE R 93 TRP 0.052 0.002 TRP O 211 HIS 0.014 0.001 HIS D 179 Details of bonding type rmsd covalent geometry : bond 0.00390 (29222) covalent geometry : angle 0.63320 (39723) hydrogen bonds : bond 0.03801 ( 1272) hydrogen bonds : angle 5.16217 ( 3738) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 411 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 LEU cc_start: 0.9416 (mt) cc_final: 0.8897 (tp) REVERT: B 54 MET cc_start: 0.9176 (ttt) cc_final: 0.8733 (tpp) REVERT: B 101 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8845 (mp0) REVERT: B 106 MET cc_start: 0.9431 (mmm) cc_final: 0.8598 (mmm) REVERT: B 110 TYR cc_start: 0.9542 (m-80) cc_final: 0.8389 (m-80) REVERT: C 36 GLU cc_start: 0.8826 (mp0) cc_final: 0.8405 (mp0) REVERT: C 131 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8519 (tt0) REVERT: D 89 LYS cc_start: 0.9168 (mttt) cc_final: 0.8961 (tmtt) REVERT: D 90 PRO cc_start: 0.6984 (Cg_endo) cc_final: 0.6696 (Cg_exo) REVERT: D 186 TYR cc_start: 0.6565 (m-80) cc_final: 0.6139 (m-80) REVERT: D 289 MET cc_start: 0.9222 (mtp) cc_final: 0.8819 (ptm) REVERT: E 54 MET cc_start: 0.8949 (mtm) cc_final: 0.8467 (ptp) REVERT: F 39 ARG cc_start: 0.8109 (mtt-85) cc_final: 0.7636 (tpt170) REVERT: F 92 ASP cc_start: 0.8858 (p0) cc_final: 0.8387 (p0) REVERT: G 47 ASN cc_start: 0.9219 (m-40) cc_final: 0.9000 (m110) REVERT: G 102 GLN cc_start: 0.8749 (mt0) cc_final: 0.8338 (mt0) REVERT: H 54 MET cc_start: 0.9142 (mtt) cc_final: 0.8887 (ptp) REVERT: H 80 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8687 (pt0) REVERT: I 10 ARG cc_start: 0.8557 (ttp-170) cc_final: 0.8307 (mtm110) REVERT: I 12 TYR cc_start: 0.8358 (t80) cc_final: 0.7748 (t80) REVERT: I 16 ARG cc_start: 0.9412 (mtp180) cc_final: 0.9187 (mtm-85) REVERT: I 83 MET cc_start: 0.9359 (ppp) cc_final: 0.9121 (mpp) REVERT: I 100 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7769 (t0) REVERT: I 107 ILE cc_start: 0.9474 (mt) cc_final: 0.9197 (tt) REVERT: I 110 TYR cc_start: 0.8849 (m-80) cc_final: 0.8544 (m-80) REVERT: I 113 ARG cc_start: 0.9502 (ptt90) cc_final: 0.9244 (ptt-90) REVERT: J 52 PHE cc_start: 0.9418 (m-80) cc_final: 0.9201 (m-80) REVERT: J 82 MET cc_start: 0.9166 (ptp) cc_final: 0.8880 (ptp) REVERT: J 93 PHE cc_start: 0.8878 (m-80) cc_final: 0.8628 (t80) REVERT: J 101 GLU cc_start: 0.9428 (mt-10) cc_final: 0.9206 (mt-10) REVERT: K 150 GLN cc_start: 0.8455 (mm-40) cc_final: 0.7792 (mm110) REVERT: K 179 HIS cc_start: 0.8123 (OUTLIER) cc_final: 0.7787 (m90) REVERT: K 183 TYR cc_start: 0.8419 (t80) cc_final: 0.8002 (t80) REVERT: K 217 MET cc_start: 0.8640 (ptm) cc_final: 0.8246 (ttp) REVERT: K 219 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8008 (mt-10) REVERT: L 217 MET cc_start: 0.8917 (ptp) cc_final: 0.8451 (ptp) REVERT: L 289 MET cc_start: 0.9199 (mmm) cc_final: 0.8930 (mmt) REVERT: M 36 GLU cc_start: 0.8544 (mp0) cc_final: 0.8335 (mp0) REVERT: M 109 MET cc_start: 0.9102 (tpp) cc_final: 0.8845 (tpp) REVERT: M 131 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8420 (pt0) REVERT: N 30 MET cc_start: 0.8651 (mmm) cc_final: 0.8356 (tpt) REVERT: N 157 MET cc_start: 0.8198 (mtp) cc_final: 0.7329 (mmt) REVERT: O 229 MET cc_start: 0.8105 (ttm) cc_final: 0.7287 (ttm) REVERT: P 30 MET cc_start: 0.8828 (mtt) cc_final: 0.8555 (mpp) REVERT: P 109 MET cc_start: 0.7654 (mtp) cc_final: 0.7065 (mtm) REVERT: Q 9 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: Q 75 LEU cc_start: 0.9618 (mt) cc_final: 0.9353 (mp) REVERT: Q 86 CYS cc_start: 0.8036 (m) cc_final: 0.7753 (p) REVERT: R 65 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8445 (pttm) outliers start: 89 outliers final: 64 residues processed: 474 average time/residue: 0.1869 time to fit residues: 143.6685 Evaluate side-chains 454 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 385 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 89 ASN Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 100 ASP Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 131 GLN Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 179 HIS Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain N residue 105 VAL Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 131 GLN Chi-restraints excluded: chain P residue 238 LYS Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 138 MET Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 191 PHE Chi-restraints excluded: chain Q residue 216 ASN Chi-restraints excluded: chain R residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 58 optimal weight: 9.9990 chunk 307 optimal weight: 0.9980 chunk 284 optimal weight: 8.9990 chunk 210 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 300 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 HIS I 61 ASN ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN L 70 GLN ** M 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 HIS ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.079863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.056256 restraints weight = 120059.346| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 4.17 r_work: 0.2904 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 29222 Z= 0.255 Angle : 0.678 12.798 39723 Z= 0.346 Chirality : 0.046 0.324 4410 Planarity : 0.004 0.046 5013 Dihedral : 13.879 177.715 4628 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.22 % Allowed : 16.96 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 3418 helix: 1.12 (0.14), residues: 1432 sheet: 0.14 (0.24), residues: 522 loop : -0.75 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 72 TYR 0.015 0.002 TYR Q 114 PHE 0.020 0.002 PHE R 93 TRP 0.076 0.002 TRP O 211 HIS 0.011 0.001 HIS F 78 Details of bonding type rmsd covalent geometry : bond 0.00550 (29222) covalent geometry : angle 0.67838 (39723) hydrogen bonds : bond 0.03982 ( 1272) hydrogen bonds : angle 5.29021 ( 3738) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 388 time to evaluate : 1.131 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: B 13 LEU cc_start: 0.9444 (mt) cc_final: 0.8912 (tp) REVERT: B 50 GLN cc_start: 0.8813 (mt0) cc_final: 0.8050 (mp10) REVERT: B 54 MET cc_start: 0.9184 (ttt) cc_final: 0.8767 (tpp) REVERT: B 101 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8845 (mp0) REVERT: B 106 MET cc_start: 0.9473 (mmm) cc_final: 0.8580 (mmm) REVERT: B 110 TYR cc_start: 0.9536 (m-80) cc_final: 0.8407 (m-80) REVERT: C 36 GLU cc_start: 0.8914 (mp0) cc_final: 0.8564 (mp0) REVERT: C 131 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: C 207 LEU cc_start: 0.9420 (tp) cc_final: 0.9137 (tp) REVERT: D 89 LYS cc_start: 0.9248 (mttt) cc_final: 0.9018 (tmtt) REVERT: D 109 MET cc_start: 0.9149 (mmm) cc_final: 0.8809 (mmm) REVERT: D 157 MET cc_start: 0.5986 (tmm) cc_final: 0.5427 (tmm) REVERT: D 186 TYR cc_start: 0.6707 (m-80) cc_final: 0.6221 (m-80) REVERT: D 229 MET cc_start: 0.5288 (mmt) cc_final: 0.4810 (mmm) REVERT: F 29 VAL cc_start: 0.9174 (m) cc_final: 0.8947 (p) REVERT: F 39 ARG cc_start: 0.8150 (mtt-85) cc_final: 0.7691 (tpt170) REVERT: F 66 LEU cc_start: 0.9354 (mt) cc_final: 0.9120 (tp) REVERT: F 102 GLN cc_start: 0.8957 (mt0) cc_final: 0.8345 (mm-40) REVERT: G 47 ASN cc_start: 0.9271 (m-40) cc_final: 0.9063 (m110) REVERT: G 102 GLN cc_start: 0.8799 (mt0) cc_final: 0.8444 (mt0) REVERT: H 62 HIS cc_start: 0.8954 (m-70) cc_final: 0.8611 (t-90) REVERT: I 10 ARG cc_start: 0.8591 (ttp-170) cc_final: 0.8351 (mtm110) REVERT: I 12 TYR cc_start: 0.8398 (t80) cc_final: 0.7315 (t80) REVERT: I 16 ARG cc_start: 0.9432 (mtp180) cc_final: 0.9184 (mtm-85) REVERT: I 110 TYR cc_start: 0.8868 (m-80) cc_final: 0.8455 (m-80) REVERT: I 113 ARG cc_start: 0.9489 (ptt90) cc_final: 0.9233 (ptt-90) REVERT: J 82 MET cc_start: 0.9147 (ptp) cc_final: 0.8937 (ptp) REVERT: J 97 MET cc_start: 0.6818 (tpt) cc_final: 0.6278 (tpp) REVERT: J 101 GLU cc_start: 0.9421 (mt-10) cc_final: 0.9199 (mt-10) REVERT: J 102 GLN cc_start: 0.8910 (mt0) cc_final: 0.8373 (mm-40) REVERT: K 148 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.8949 (m) REVERT: K 150 GLN cc_start: 0.8519 (mm-40) cc_final: 0.7992 (mm110) REVERT: K 179 HIS cc_start: 0.8164 (OUTLIER) cc_final: 0.7791 (m90) REVERT: K 183 TYR cc_start: 0.8435 (t80) cc_final: 0.7972 (t80) REVERT: K 219 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8039 (mt-10) REVERT: L 217 MET cc_start: 0.8919 (ptp) cc_final: 0.8517 (ptp) REVERT: M 131 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8445 (pt0) REVERT: N 157 MET cc_start: 0.8289 (mtp) cc_final: 0.7375 (mmt) REVERT: O 123 MET cc_start: 0.8498 (mtp) cc_final: 0.8230 (mtp) REVERT: O 211 TRP cc_start: 0.8039 (m-90) cc_final: 0.7737 (m-90) REVERT: O 229 MET cc_start: 0.8193 (ttm) cc_final: 0.7320 (ttm) REVERT: P 30 MET cc_start: 0.8777 (mtt) cc_final: 0.8517 (mpp) REVERT: P 217 MET cc_start: 0.8898 (ptm) cc_final: 0.8600 (ptp) REVERT: P 238 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8613 (tptp) REVERT: Q 9 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: Q 75 LEU cc_start: 0.9644 (mt) cc_final: 0.9368 (mp) REVERT: Q 221 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8385 (t70) REVERT: R 65 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8483 (pttt) outliers start: 94 outliers final: 66 residues processed: 452 average time/residue: 0.1867 time to fit residues: 137.4208 Evaluate side-chains 433 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 360 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 89 ASN Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 105 PHE Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 179 HIS Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 179 HIS Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain N residue 105 VAL Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 243 LEU Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 131 GLN Chi-restraints excluded: chain P residue 238 LYS Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 191 PHE Chi-restraints excluded: chain Q residue 221 ASP Chi-restraints excluded: chain R residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 182 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 154 optimal weight: 0.0980 chunk 97 optimal weight: 0.0030 chunk 323 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 GLN ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 HIS ** G 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 84 GLN L 70 GLN L 220 HIS M 70 GLN M 150 GLN N 70 GLN ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.080688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.057650 restraints weight = 120409.439| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 4.14 r_work: 0.2983 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29222 Z= 0.128 Angle : 0.658 13.990 39723 Z= 0.330 Chirality : 0.045 0.339 4410 Planarity : 0.004 0.045 5013 Dihedral : 13.883 179.939 4627 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.78 % Allowed : 18.26 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.15), residues: 3418 helix: 1.20 (0.14), residues: 1432 sheet: 0.22 (0.24), residues: 522 loop : -0.67 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 39 TYR 0.016 0.001 TYR I 79 PHE 0.028 0.001 PHE J 52 TRP 0.062 0.002 TRP O 211 HIS 0.007 0.001 HIS Q 179 Details of bonding type rmsd covalent geometry : bond 0.00276 (29222) covalent geometry : angle 0.65841 (39723) hydrogen bonds : bond 0.03736 ( 1272) hydrogen bonds : angle 5.07003 ( 3738) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 423 time to evaluate : 1.135 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: B 13 LEU cc_start: 0.9394 (mt) cc_final: 0.8899 (tp) REVERT: B 54 MET cc_start: 0.9204 (ttt) cc_final: 0.8909 (tmm) REVERT: B 101 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8895 (mp0) REVERT: B 106 MET cc_start: 0.9390 (mmm) cc_final: 0.8659 (mmm) REVERT: B 110 TYR cc_start: 0.9562 (m-80) cc_final: 0.8373 (m-80) REVERT: C 36 GLU cc_start: 0.8829 (mp0) cc_final: 0.8418 (mp0) REVERT: C 114 TYR cc_start: 0.8829 (t80) cc_final: 0.8412 (t80) REVERT: C 211 TRP cc_start: 0.8465 (m-10) cc_final: 0.8218 (m-10) REVERT: D 89 LYS cc_start: 0.9232 (mttt) cc_final: 0.9010 (tmtt) REVERT: D 109 MET cc_start: 0.9149 (mmm) cc_final: 0.8894 (mmm) REVERT: D 157 MET cc_start: 0.6451 (tmm) cc_final: 0.5998 (tmm) REVERT: D 186 TYR cc_start: 0.6584 (m-80) cc_final: 0.6179 (m-80) REVERT: D 229 MET cc_start: 0.5240 (mmt) cc_final: 0.4777 (mmm) REVERT: D 289 MET cc_start: 0.9034 (mtp) cc_final: 0.8072 (mpp) REVERT: E 54 MET cc_start: 0.9126 (mtm) cc_final: 0.8366 (ptp) REVERT: F 13 LEU cc_start: 0.9526 (mp) cc_final: 0.9215 (mp) REVERT: F 29 VAL cc_start: 0.9176 (m) cc_final: 0.8936 (p) REVERT: F 39 ARG cc_start: 0.8117 (mtt-85) cc_final: 0.7635 (ttm110) REVERT: F 66 LEU cc_start: 0.9291 (mt) cc_final: 0.9046 (tp) REVERT: F 83 MET cc_start: 0.9351 (mmt) cc_final: 0.9076 (mmt) REVERT: F 92 ASP cc_start: 0.8891 (p0) cc_final: 0.8513 (p0) REVERT: G 40 TYR cc_start: 0.6664 (m-10) cc_final: 0.6390 (m-10) REVERT: G 75 SER cc_start: 0.9361 (OUTLIER) cc_final: 0.9085 (p) REVERT: G 102 GLN cc_start: 0.8702 (mt0) cc_final: 0.8431 (mt0) REVERT: H 80 GLU cc_start: 0.9098 (tp30) cc_final: 0.8790 (pt0) REVERT: I 9 ASP cc_start: 0.7728 (t70) cc_final: 0.7120 (m-30) REVERT: I 10 ARG cc_start: 0.8556 (ttp-170) cc_final: 0.8313 (mtm110) REVERT: I 12 TYR cc_start: 0.8328 (t80) cc_final: 0.6040 (t80) REVERT: I 16 ARG cc_start: 0.9379 (mtp180) cc_final: 0.9046 (mtm110) REVERT: I 100 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7810 (t0) REVERT: I 110 TYR cc_start: 0.8903 (m-80) cc_final: 0.8375 (m-80) REVERT: I 113 ARG cc_start: 0.9523 (ptt90) cc_final: 0.9164 (ptt-90) REVERT: J 82 MET cc_start: 0.9136 (ptp) cc_final: 0.8857 (ptp) REVERT: J 92 ASP cc_start: 0.9273 (p0) cc_final: 0.8532 (m-30) REVERT: J 101 GLU cc_start: 0.9364 (mt-10) cc_final: 0.9119 (mt-10) REVERT: J 112 GLN cc_start: 0.9579 (tp40) cc_final: 0.9315 (tp40) REVERT: J 114 LYS cc_start: 0.8934 (ttmm) cc_final: 0.8672 (ttmm) REVERT: K 148 VAL cc_start: 0.9205 (OUTLIER) cc_final: 0.8947 (m) REVERT: K 150 GLN cc_start: 0.8459 (mm-40) cc_final: 0.7923 (mm110) REVERT: K 217 MET cc_start: 0.8650 (ptm) cc_final: 0.8249 (ttp) REVERT: L 37 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8773 (p) REVERT: L 177 ARG cc_start: 0.8767 (mpt-90) cc_final: 0.8439 (ttm-80) REVERT: L 289 MET cc_start: 0.9224 (mmm) cc_final: 0.8945 (mmt) REVERT: M 109 MET cc_start: 0.9009 (tpp) cc_final: 0.8784 (tpp) REVERT: M 131 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8259 (pt0) REVERT: N 30 MET cc_start: 0.8669 (tpp) cc_final: 0.8354 (tpt) REVERT: N 157 MET cc_start: 0.8120 (mtp) cc_final: 0.7273 (mmt) REVERT: O 229 MET cc_start: 0.8024 (ttm) cc_final: 0.7325 (ttm) REVERT: P 30 MET cc_start: 0.8816 (mtt) cc_final: 0.8562 (mpp) REVERT: P 127 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8264 (m) REVERT: Q 9 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: Q 187 VAL cc_start: 0.9554 (t) cc_final: 0.9334 (m) REVERT: Q 221 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8351 (t70) REVERT: R 58 ASN cc_start: 0.9019 (m-40) cc_final: 0.8565 (p0) REVERT: R 65 LYS cc_start: 0.8828 (mtmt) cc_final: 0.8577 (pttt) REVERT: R 80 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8913 (mm-30) outliers start: 52 outliers final: 34 residues processed: 459 average time/residue: 0.1913 time to fit residues: 141.2303 Evaluate side-chains 433 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 391 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 89 ASN Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 100 ASP Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 179 HIS Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 131 GLN Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 216 ASN Chi-restraints excluded: chain Q residue 221 ASP Chi-restraints excluded: chain R residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 270 optimal weight: 7.9990 chunk 322 optimal weight: 7.9990 chunk 231 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 226 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 137 optimal weight: 6.9990 chunk 216 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 312 optimal weight: 9.9990 chunk 191 optimal weight: 0.4980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 78 HIS J 61 ASN L 220 HIS M 70 GLN ** M 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 70 GLN ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.080154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.057127 restraints weight = 119991.089| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 4.13 r_work: 0.2964 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29222 Z= 0.157 Angle : 0.696 16.560 39723 Z= 0.347 Chirality : 0.046 0.343 4410 Planarity : 0.004 0.051 5013 Dihedral : 13.845 179.884 4623 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.88 % Allowed : 18.84 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.15), residues: 3418 helix: 1.21 (0.14), residues: 1432 sheet: 0.30 (0.24), residues: 522 loop : -0.71 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 39 TYR 0.025 0.002 TYR M 183 PHE 0.030 0.002 PHE J 52 TRP 0.105 0.003 TRP O 211 HIS 0.006 0.001 HIS Q 179 Details of bonding type rmsd covalent geometry : bond 0.00346 (29222) covalent geometry : angle 0.69603 (39723) hydrogen bonds : bond 0.03847 ( 1272) hydrogen bonds : angle 5.09849 ( 3738) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 398 time to evaluate : 1.130 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: B 13 LEU cc_start: 0.9407 (mt) cc_final: 0.9004 (tp) REVERT: B 54 MET cc_start: 0.9233 (ttt) cc_final: 0.8732 (tmm) REVERT: B 101 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8888 (mp0) REVERT: B 106 MET cc_start: 0.9400 (mmm) cc_final: 0.8636 (mmm) REVERT: B 110 TYR cc_start: 0.9541 (m-80) cc_final: 0.8450 (m-80) REVERT: C 36 GLU cc_start: 0.8841 (mp0) cc_final: 0.8514 (mp0) REVERT: D 89 LYS cc_start: 0.9222 (mttt) cc_final: 0.8991 (tmtt) REVERT: D 109 MET cc_start: 0.9212 (mmm) cc_final: 0.8889 (mmm) REVERT: D 157 MET cc_start: 0.6521 (tmm) cc_final: 0.6086 (tmm) REVERT: D 186 TYR cc_start: 0.6632 (m-80) cc_final: 0.6205 (m-80) REVERT: D 229 MET cc_start: 0.5522 (mmt) cc_final: 0.5054 (mmm) REVERT: E 54 MET cc_start: 0.9064 (mtm) cc_final: 0.8469 (ptp) REVERT: F 29 VAL cc_start: 0.9132 (m) cc_final: 0.8844 (p) REVERT: F 39 ARG cc_start: 0.8316 (mtt-85) cc_final: 0.7813 (ttp-170) REVERT: F 66 LEU cc_start: 0.9278 (mt) cc_final: 0.8998 (tp) REVERT: F 83 MET cc_start: 0.9363 (mmt) cc_final: 0.9098 (mmt) REVERT: F 92 ASP cc_start: 0.8861 (p0) cc_final: 0.8492 (p0) REVERT: G 22 GLU cc_start: 0.8607 (tt0) cc_final: 0.8363 (tt0) REVERT: G 25 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7527 (pt0) REVERT: G 102 GLN cc_start: 0.8759 (mt0) cc_final: 0.8454 (mt0) REVERT: H 62 HIS cc_start: 0.8918 (m-70) cc_final: 0.8631 (t-90) REVERT: I 10 ARG cc_start: 0.8525 (ttp-170) cc_final: 0.8297 (mtm110) REVERT: I 12 TYR cc_start: 0.8336 (t80) cc_final: 0.7304 (t80) REVERT: I 16 ARG cc_start: 0.9392 (mtp180) cc_final: 0.9132 (mtm-85) REVERT: I 107 ILE cc_start: 0.9471 (mt) cc_final: 0.9175 (tp) REVERT: I 110 TYR cc_start: 0.8915 (m-80) cc_final: 0.8488 (m-80) REVERT: J 82 MET cc_start: 0.9142 (ptp) cc_final: 0.8904 (ptp) REVERT: J 92 ASP cc_start: 0.9287 (p0) cc_final: 0.8614 (m-30) REVERT: J 102 GLN cc_start: 0.8887 (mt0) cc_final: 0.8437 (mm-40) REVERT: J 112 GLN cc_start: 0.9564 (tp40) cc_final: 0.9294 (tp40) REVERT: J 114 LYS cc_start: 0.8896 (ttmm) cc_final: 0.8619 (ttmm) REVERT: K 217 MET cc_start: 0.8630 (ptm) cc_final: 0.8221 (ttp) REVERT: L 37 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8790 (p) REVERT: L 289 MET cc_start: 0.9243 (mmm) cc_final: 0.8971 (mmt) REVERT: M 109 MET cc_start: 0.9070 (tpp) cc_final: 0.8820 (tpp) REVERT: M 131 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8302 (pt0) REVERT: M 175 MET cc_start: 0.8582 (mpp) cc_final: 0.8299 (mmt) REVERT: N 30 MET cc_start: 0.8650 (tpp) cc_final: 0.8287 (tpt) REVERT: N 157 MET cc_start: 0.8178 (mtp) cc_final: 0.7307 (mmt) REVERT: O 157 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6915 (pmm) REVERT: O 229 MET cc_start: 0.8166 (ttm) cc_final: 0.7449 (ttm) REVERT: P 30 MET cc_start: 0.8817 (mtt) cc_final: 0.8548 (mpp) REVERT: Q 9 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: Q 187 VAL cc_start: 0.9569 (t) cc_final: 0.9357 (m) REVERT: R 58 ASN cc_start: 0.9030 (m-40) cc_final: 0.8633 (p0) REVERT: R 65 LYS cc_start: 0.8823 (mtmt) cc_final: 0.8571 (pttt) outliers start: 55 outliers final: 41 residues processed: 430 average time/residue: 0.1869 time to fit residues: 129.3022 Evaluate side-chains 425 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 379 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain G residue 52 PHE Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 89 ASN Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 179 HIS Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 157 MET Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 131 GLN Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 191 PHE Chi-restraints excluded: chain Q residue 214 LEU Chi-restraints excluded: chain R residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 147 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 271 optimal weight: 0.8980 chunk 234 optimal weight: 6.9990 chunk 162 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 318 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.081001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.057892 restraints weight = 118884.086| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 4.16 r_work: 0.2975 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29222 Z= 0.148 Angle : 0.706 15.084 39723 Z= 0.353 Chirality : 0.046 0.341 4410 Planarity : 0.004 0.048 5013 Dihedral : 13.868 179.742 4623 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.99 % Allowed : 19.08 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3418 helix: 1.27 (0.14), residues: 1396 sheet: 0.31 (0.24), residues: 522 loop : -0.66 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 226 TYR 0.031 0.002 TYR O 186 PHE 0.037 0.002 PHE J 52 TRP 0.017 0.002 TRP O 211 HIS 0.026 0.001 HIS I 78 Details of bonding type rmsd covalent geometry : bond 0.00328 (29222) covalent geometry : angle 0.70624 (39723) hydrogen bonds : bond 0.03809 ( 1272) hydrogen bonds : angle 5.10422 ( 3738) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 395 time to evaluate : 1.113 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: B 13 LEU cc_start: 0.9397 (mt) cc_final: 0.8965 (tp) REVERT: B 39 ARG cc_start: 0.8549 (ttp-110) cc_final: 0.7939 (mtt-85) REVERT: B 40 TYR cc_start: 0.9225 (m-80) cc_final: 0.8666 (m-80) REVERT: B 54 MET cc_start: 0.9232 (ttt) cc_final: 0.8697 (tmm) REVERT: B 101 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8882 (mp0) REVERT: B 106 MET cc_start: 0.9351 (mmm) cc_final: 0.8548 (mmm) REVERT: B 110 TYR cc_start: 0.9545 (m-80) cc_final: 0.8422 (m-80) REVERT: C 36 GLU cc_start: 0.8843 (mp0) cc_final: 0.8546 (mp0) REVERT: D 109 MET cc_start: 0.9222 (mmm) cc_final: 0.8919 (mmm) REVERT: D 157 MET cc_start: 0.6549 (tmm) cc_final: 0.6140 (tmm) REVERT: D 186 TYR cc_start: 0.6623 (m-80) cc_final: 0.6197 (m-80) REVERT: D 229 MET cc_start: 0.5575 (mmt) cc_final: 0.5074 (mmm) REVERT: D 289 MET cc_start: 0.9128 (mtp) cc_final: 0.8883 (ptm) REVERT: E 54 MET cc_start: 0.9034 (mtm) cc_final: 0.8417 (ptp) REVERT: E 82 MET cc_start: 0.9367 (tpt) cc_final: 0.8723 (mmm) REVERT: F 29 VAL cc_start: 0.9147 (m) cc_final: 0.8896 (p) REVERT: F 39 ARG cc_start: 0.8313 (mtt-85) cc_final: 0.7809 (ttm110) REVERT: F 66 LEU cc_start: 0.9277 (mt) cc_final: 0.8974 (tp) REVERT: F 83 MET cc_start: 0.9353 (mmt) cc_final: 0.9082 (mmt) REVERT: F 92 ASP cc_start: 0.8863 (p0) cc_final: 0.8523 (p0) REVERT: G 22 GLU cc_start: 0.8563 (tt0) cc_final: 0.8346 (tt0) REVERT: G 25 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7624 (pt0) REVERT: G 54 MET cc_start: 0.8505 (ttm) cc_final: 0.8210 (mtt) REVERT: G 102 GLN cc_start: 0.8757 (mt0) cc_final: 0.8430 (mt0) REVERT: H 23 LYS cc_start: 0.8403 (ptmt) cc_final: 0.8161 (ttpt) REVERT: H 62 HIS cc_start: 0.8925 (m-70) cc_final: 0.8652 (t-90) REVERT: I 12 TYR cc_start: 0.8300 (t80) cc_final: 0.7573 (t80) REVERT: I 13 LEU cc_start: 0.9330 (mt) cc_final: 0.8791 (tp) REVERT: I 16 ARG cc_start: 0.9402 (mtp180) cc_final: 0.9093 (mtm180) REVERT: I 80 GLU cc_start: 0.9200 (tp30) cc_final: 0.8312 (mt-10) REVERT: I 83 MET cc_start: 0.9618 (OUTLIER) cc_final: 0.9091 (mpp) REVERT: I 100 ASP cc_start: 0.8145 (p0) cc_final: 0.7848 (t70) REVERT: I 107 ILE cc_start: 0.9459 (mt) cc_final: 0.9216 (tp) REVERT: I 110 TYR cc_start: 0.8896 (m-80) cc_final: 0.8181 (m-80) REVERT: J 93 PHE cc_start: 0.8557 (t80) cc_final: 0.8101 (t80) REVERT: J 102 GLN cc_start: 0.8885 (mt0) cc_final: 0.8490 (mm-40) REVERT: J 112 GLN cc_start: 0.9548 (tp40) cc_final: 0.9289 (tp40) REVERT: J 114 LYS cc_start: 0.8918 (ttmm) cc_final: 0.8640 (ttmm) REVERT: K 157 MET cc_start: 0.8407 (mtp) cc_final: 0.8025 (mmm) REVERT: K 217 MET cc_start: 0.8612 (ptm) cc_final: 0.8219 (ttp) REVERT: L 37 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8798 (p) REVERT: L 289 MET cc_start: 0.9235 (mmm) cc_final: 0.8945 (mmt) REVERT: M 109 MET cc_start: 0.9051 (tpp) cc_final: 0.8802 (tpp) REVERT: M 131 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8295 (pt0) REVERT: M 175 MET cc_start: 0.8580 (mpp) cc_final: 0.8290 (mmt) REVERT: N 157 MET cc_start: 0.8128 (mtp) cc_final: 0.7259 (mmt) REVERT: O 157 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6963 (pmm) REVERT: O 229 MET cc_start: 0.8205 (ttm) cc_final: 0.7491 (ttm) REVERT: Q 9 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: Q 187 VAL cc_start: 0.9556 (t) cc_final: 0.9345 (m) REVERT: Q 221 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.8381 (t70) REVERT: R 58 ASN cc_start: 0.9034 (m-40) cc_final: 0.8658 (p0) REVERT: R 65 LYS cc_start: 0.8862 (mtmt) cc_final: 0.8611 (pttt) outliers start: 58 outliers final: 42 residues processed: 429 average time/residue: 0.1929 time to fit residues: 133.9385 Evaluate side-chains 431 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 382 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 89 ASN Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 98 LYS Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 157 MET Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain P residue 112 ASN Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 131 GLN Chi-restraints excluded: chain P residue 238 LYS Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 138 MET Chi-restraints excluded: chain Q residue 191 PHE Chi-restraints excluded: chain Q residue 214 LEU Chi-restraints excluded: chain Q residue 221 ASP Chi-restraints excluded: chain R residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 206 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 153 optimal weight: 20.0000 chunk 70 optimal weight: 8.9990 chunk 270 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 319 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 ASN ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 150 GLN L 220 HIS ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.080243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.057140 restraints weight = 119880.597| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 4.13 r_work: 0.2947 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29222 Z= 0.188 Angle : 0.720 14.811 39723 Z= 0.363 Chirality : 0.046 0.349 4410 Planarity : 0.004 0.056 5013 Dihedral : 13.884 179.096 4623 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.95 % Allowed : 19.29 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.15), residues: 3418 helix: 1.24 (0.14), residues: 1396 sheet: 0.33 (0.24), residues: 522 loop : -0.65 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 39 TYR 0.031 0.002 TYR R 109 PHE 0.035 0.002 PHE J 52 TRP 0.023 0.002 TRP O 211 HIS 0.015 0.001 HIS I 78 Details of bonding type rmsd covalent geometry : bond 0.00413 (29222) covalent geometry : angle 0.71954 (39723) hydrogen bonds : bond 0.03934 ( 1272) hydrogen bonds : angle 5.21468 ( 3738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10122.09 seconds wall clock time: 173 minutes 36.51 seconds (10416.51 seconds total)