Starting phenix.real_space_refine on Sun Jul 5 16:21:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jhb_61477/07_2026/9jhb_61477.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jhb_61477/07_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_61477/07_2026/9jhb_61477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jhb_61477/07_2026/9jhb_61477.map" model { file = "/net/cci-nas-00/data/ceres_data/9jhb_61477/07_2026/9jhb_61477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jhb_61477/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 6.17, per 1000 atoms: 0.22 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: 2.03 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: 2.91 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: 5.38 Time building geometry restraints manager: 2.82 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=" N1 C A 30 " pdb=" C6 C A 30 " ideal model delta sigma weight residual 1.367 1.353 0.014 6.00e-03 2.78e+04 5.53e+00 bond pdb=" N9 A A 22 " pdb=" C4 A A 22 " ideal model delta sigma weight residual 1.374 1.360 0.014 6.00e-03 2.78e+04 5.40e+00 bond pdb=" N9 A A 31 " pdb=" C4 A A 31 " ideal model delta sigma weight residual 1.374 1.361 0.013 6.00e-03 2.78e+04 4.68e+00 bond pdb=" N7 G A 29 " pdb=" C5 G A 29 " ideal model delta sigma weight residual 1.388 1.377 0.011 6.00e-03 2.78e+04 3.46e+00 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 ... (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=" C2 U A 39 " ideal model delta sigma weight residual 117.70 126.36 -8.66 1.20e+00 6.94e-01 5.21e+01 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 1.40e+00 5.10e-01 4.80e+01 angle pdb=" C1' C A 13 " pdb=" N1 C A 13 " pdb=" C2 C A 13 " ideal model delta sigma weight residual 118.80 123.79 -4.99 1.10e+00 8.26e-01 2.06e+01 angle pdb=" N1 C A 13 " pdb=" C2 C A 13 " pdb=" O2 C A 13 " ideal model delta sigma weight residual 118.90 121.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" C1' G A 29 " pdb=" N9 G A 29 " pdb=" C4 G A 29 " ideal model delta sigma weight residual 126.50 131.61 -5.11 1.30e+00 5.92e-01 1.55e+01 ... (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: 4.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 26.610 Find NCS groups from input model: 0.450 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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= 0.198 Angle : 0.487 9.695 39723 Z= 0.282 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/Z covalent geometry : bond 0.00372 / 0.20 (29222) covalent geometry : angle 0.48708 / 0.28 (39723) hydrogen bonds : bond 0.27449 / 26.81 ( 1272) hydrogen bonds : angle 8.55138 / 8.67 ( 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 : 1.114 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: 0.1913 time to fit residues: 270.6101 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 : 0.950 ------------------------------------------------------------------------------- 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... B 84 GLN B 102 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS C 112 ASN C 240 GLN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 ASN G 84 GLN I 58 ASN I 112 GLN J 102 GLN K 6 ASN K 22 ASN K 150 GLN K 240 GLN K 249 HIS ** L 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 240 GLN N 70 GLN O 131 GLN P 112 ASN P 131 GLN Q 216 ASN ** Q 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 78 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.078137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.054341 restraints weight = 124119.283| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 4.27 r_work: 0.2982 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 29222 Z= 0.218 Angle : 0.732 18.339 39723 Z= 0.385 Chirality : 0.048 0.280 4410 Planarity : 0.005 0.059 5013 Dihedral : 14.191 179.278 4653 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.73 % Allowed : 12.98 % Favored : 83.28 % 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: -0.09 (0.14), residues: 3418 helix: 0.88 (0.13), residues: 1399 sheet: -0.33 (0.23), residues: 540 loop : -0.79 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 72 TYR 0.023 0.002 TYR E 109 PHE 0.031 0.002 PHE R 93 TRP 0.020 0.002 TRP N 211 HIS 0.013 0.001 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.22 (29222) covalent geometry : angle 0.73161 / 0.39 (39723) hydrogen bonds : bond 0.06991 / 6.65 ( 1272) hydrogen bonds : angle 6.28402 / 6.45 ( 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 645 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 536 time to evaluate : 1.072 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: B 13 LEU cc_start: 0.9325 (mt) cc_final: 0.8979 (tp) REVERT: B 23 LYS cc_start: 0.8025 (tptt) cc_final: 0.7648 (tptp) REVERT: B 53 HIS cc_start: 0.9155 (p90) cc_final: 0.8631 (p90) REVERT: B 54 MET cc_start: 0.9500 (OUTLIER) cc_final: 0.9154 (tpp) REVERT: B 101 GLU cc_start: 0.9335 (mm-30) cc_final: 0.9000 (mp0) REVERT: B 110 TYR cc_start: 0.9069 (m-80) cc_final: 0.8098 (m-80) REVERT: C 30 MET cc_start: 0.9127 (mtp) cc_final: 0.8530 (mtm) REVERT: C 36 GLU cc_start: 0.8334 (mp0) cc_final: 0.7953 (mp0) REVERT: C 138 MET cc_start: 0.9415 (mtt) cc_final: 0.9199 (mpp) REVERT: C 175 MET cc_start: 0.8704 (mtm) cc_final: 0.8454 (mtm) REVERT: C 229 MET cc_start: 0.9009 (mtt) cc_final: 0.8778 (mtt) REVERT: D 137 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8429 (mm110) REVERT: D 186 TYR cc_start: 0.6566 (m-80) cc_final: 0.6258 (m-80) REVERT: E 54 MET cc_start: 0.8969 (mtm) cc_final: 0.8521 (ptp) REVERT: E 82 MET cc_start: 0.8929 (mtm) cc_final: 0.8706 (mtt) REVERT: F 4 ASP cc_start: 0.8886 (t0) cc_final: 0.8601 (t0) REVERT: F 57 LYS cc_start: 0.8671 (mttm) cc_final: 0.8263 (mmtm) REVERT: G 25 GLN cc_start: 0.8190 (tt0) cc_final: 0.7962 (tt0) REVERT: G 47 ASN cc_start: 0.9047 (m-40) cc_final: 0.8797 (m-40) REVERT: G 83 MET cc_start: 0.8505 (mmm) cc_final: 0.8228 (mmt) REVERT: G 105 PHE cc_start: 0.8376 (t80) cc_final: 0.8083 (t80) REVERT: H 17 LEU cc_start: 0.9006 (tp) cc_final: 0.8676 (tp) REVERT: H 39 ARG cc_start: 0.8480 (mpt180) cc_final: 0.8221 (mpt180) REVERT: H 51 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.8024 (m) REVERT: H 83 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8237 (mmt) REVERT: H 99 SER cc_start: 0.8033 (m) cc_final: 0.7783 (p) REVERT: H 102 GLN cc_start: 0.7995 (mt0) cc_final: 0.7750 (mt0) REVERT: I 12 TYR cc_start: 0.8682 (t80) cc_final: 0.8261 (t80) REVERT: I 66 LEU cc_start: 0.7749 (tp) cc_final: 0.7460 (tp) REVERT: I 79 TYR cc_start: 0.9230 (m-10) cc_final: 0.8898 (m-10) REVERT: I 83 MET cc_start: 0.9550 (mtt) cc_final: 0.9235 (tmm) REVERT: I 110 TYR cc_start: 0.8966 (m-80) cc_final: 0.8700 (m-80) REVERT: J 13 LEU cc_start: 0.8821 (mt) cc_final: 0.8619 (mt) REVERT: J 52 PHE cc_start: 0.9411 (m-10) cc_final: 0.9035 (m-10) REVERT: J 72 ARG cc_start: 0.6998 (mtm180) cc_final: 0.6770 (ptp-170) REVERT: J 79 TYR cc_start: 0.8095 (m-10) cc_final: 0.7597 (m-10) REVERT: J 82 MET cc_start: 0.9155 (ptp) cc_final: 0.8708 (ptp) REVERT: K 150 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7441 (mm-40) REVERT: K 179 HIS cc_start: 0.8159 (m90) cc_final: 0.7919 (m90) REVERT: M 138 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8415 (mtm) REVERT: M 221 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8468 (t0) REVERT: N 157 MET cc_start: 0.8091 (mtp) cc_final: 0.7133 (mmt) REVERT: N 285 GLU cc_start: 0.8254 (tt0) cc_final: 0.7743 (tm-30) REVERT: O 217 MET cc_start: 0.8708 (ptt) cc_final: 0.8432 (ptp) REVERT: O 221 ASP cc_start: 0.8532 (t70) cc_final: 0.8300 (t0) REVERT: P 175 MET cc_start: 0.7136 (ppp) cc_final: 0.6556 (ptt) REVERT: P 191 PHE cc_start: 0.9477 (OUTLIER) cc_final: 0.9175 (m-80) REVERT: Q 9 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7962 (tp30) REVERT: Q 75 LEU cc_start: 0.9586 (mt) cc_final: 0.9381 (mp) REVERT: Q 127 VAL cc_start: 0.9604 (OUTLIER) cc_final: 0.9305 (p) REVERT: Q 131 GLN cc_start: 0.8797 (pt0) cc_final: 0.8450 (pm20) REVERT: Q 186 TYR cc_start: 0.9315 (m-80) cc_final: 0.8941 (m-80) REVERT: Q 191 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: R 52 PHE cc_start: 0.7585 (m-80) cc_final: 0.7066 (m-80) REVERT: R 58 ASN cc_start: 0.8899 (m-40) cc_final: 0.8632 (p0) outliers start: 109 outliers final: 52 residues processed: 605 average time/residue: 0.1933 time to fit residues: 183.3858 Evaluate side-chains 500 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 439 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 ARG 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 C residue 16 VAL Chi-restraints excluded: chain C residue 17 GLU 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 D residue 11 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 83 MET 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 181 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 42 VAL 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 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 138 MET Chi-restraints excluded: chain M residue 221 ASP Chi-restraints excluded: chain N residue 105 VAL Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain O residue 55 VAL Chi-restraints excluded: chain O residue 157 MET Chi-restraints excluded: chain O residue 288 GLU Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 123 MET 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 98 LYS Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 174 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 213 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 289 optimal weight: 10.0000 chunk 332 optimal weight: 0.0980 chunk 145 optimal weight: 30.0000 chunk 100 optimal weight: 7.9990 chunk 335 optimal weight: 30.0000 chunk 334 optimal weight: 7.9990 chunk 320 optimal weight: 5.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 HIS C 216 ASN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN ** F 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 240 GLN K 249 HIS M 150 GLN M 240 GLN ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 240 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.080920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.057240 restraints weight = 121655.574| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 4.20 r_work: 0.2952 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 29222 Z= 0.264 Angle : 0.731 17.488 39723 Z= 0.378 Chirality : 0.047 0.235 4410 Planarity : 0.005 0.086 5013 Dihedral : 14.119 179.162 4642 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.91 % Allowed : 13.22 % Favored : 82.87 % 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: -0.16 (0.14), residues: 3418 helix: 0.68 (0.13), residues: 1424 sheet: -0.15 (0.23), residues: 540 loop : -0.79 (0.17), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 113 TYR 0.026 0.002 TYR R 109 PHE 0.043 0.002 PHE J 93 TRP 0.039 0.003 TRP C 211 HIS 0.010 0.001 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.26 (29222) covalent geometry : angle 0.73054 / 0.38 (39723) hydrogen bonds : bond 0.05539 / 5.33 ( 1272) hydrogen bonds : angle 5.95284 / 6.15 ( 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 579 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 465 time to evaluate : 1.163 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: B 54 MET cc_start: 0.9532 (OUTLIER) cc_final: 0.9093 (tpp) REVERT: B 101 GLU cc_start: 0.9340 (mm-30) cc_final: 0.8996 (mp0) REVERT: B 106 MET cc_start: 0.9440 (mmm) cc_final: 0.8862 (mmm) REVERT: B 110 TYR cc_start: 0.9320 (m-80) cc_final: 0.8121 (m-80) REVERT: C 30 MET cc_start: 0.9127 (mtp) cc_final: 0.8550 (mtm) REVERT: C 36 GLU cc_start: 0.8468 (mp0) cc_final: 0.8250 (mp0) REVERT: C 109 MET cc_start: 0.9073 (mtp) cc_final: 0.8864 (mtp) REVERT: C 114 TYR cc_start: 0.8667 (t80) cc_final: 0.8465 (t80) REVERT: C 175 MET cc_start: 0.8721 (mtm) cc_final: 0.8447 (mtm) REVERT: C 207 LEU cc_start: 0.9518 (tp) cc_final: 0.9070 (tp) REVERT: C 211 TRP cc_start: 0.8453 (m-10) cc_final: 0.8114 (m-90) REVERT: D 137 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8498 (mm110) REVERT: D 186 TYR cc_start: 0.6581 (m-80) cc_final: 0.6206 (m-10) REVERT: D 229 MET cc_start: 0.5978 (mmm) cc_final: 0.5091 (mmt) REVERT: E 106 MET cc_start: 0.9447 (mmm) cc_final: 0.9055 (mmm) REVERT: F 97 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8507 (mtp) REVERT: F 102 GLN cc_start: 0.8577 (mt0) cc_final: 0.8018 (mm-40) REVERT: G 90 ILE cc_start: 0.8533 (mm) cc_final: 0.8245 (mt) REVERT: G 109 TYR cc_start: 0.8350 (t80) cc_final: 0.8016 (t80) REVERT: H 17 LEU cc_start: 0.9027 (tp) cc_final: 0.8815 (tp) REVERT: H 40 TYR cc_start: 0.6447 (m-80) cc_final: 0.6085 (m-80) REVERT: H 80 GLU cc_start: 0.9446 (pt0) cc_final: 0.8845 (tm-30) REVERT: H 99 SER cc_start: 0.8081 (m) cc_final: 0.7781 (p) REVERT: H 102 GLN cc_start: 0.8371 (mt0) cc_final: 0.8162 (mt0) REVERT: I 12 TYR cc_start: 0.8757 (t80) cc_final: 0.8198 (t80) REVERT: I 16 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8599 (mmt180) REVERT: I 66 LEU cc_start: 0.7640 (tp) cc_final: 0.7288 (tp) REVERT: I 79 TYR cc_start: 0.9215 (m-10) cc_final: 0.8811 (m-10) REVERT: I 83 MET cc_start: 0.9553 (mtt) cc_final: 0.9151 (tmm) REVERT: I 113 ARG cc_start: 0.9421 (ptt90) cc_final: 0.9027 (ttp-110) REVERT: J 10 ARG cc_start: 0.8819 (tmm-80) cc_final: 0.8087 (tpp80) REVERT: J 79 TYR cc_start: 0.8099 (m-10) cc_final: 0.7777 (m-10) REVERT: J 82 MET cc_start: 0.9192 (ptp) cc_final: 0.8885 (ptp) REVERT: J 102 GLN cc_start: 0.9011 (mt0) cc_final: 0.8680 (mm-40) REVERT: K 98 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8888 (pttm) REVERT: K 123 MET cc_start: 0.7306 (mpp) cc_final: 0.7084 (mpp) REVERT: K 150 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7908 (mm-40) REVERT: K 179 HIS cc_start: 0.8197 (OUTLIER) cc_final: 0.7904 (m90) REVERT: M 183 TYR cc_start: 0.9202 (t80) cc_final: 0.9001 (t80) REVERT: M 221 ASP cc_start: 0.8937 (OUTLIER) cc_final: 0.8514 (t0) REVERT: N 115 ASP cc_start: 0.8122 (p0) cc_final: 0.7897 (p0) REVERT: N 157 MET cc_start: 0.8133 (mtp) cc_final: 0.7203 (mmt) REVERT: O 207 LEU cc_start: 0.9362 (tp) cc_final: 0.8704 (tp) REVERT: O 221 ASP cc_start: 0.8528 (t70) cc_final: 0.8239 (t0) REVERT: O 289 MET cc_start: 0.8293 (mtt) cc_final: 0.8055 (mtt) REVERT: P 98 LYS cc_start: 0.9395 (mttt) cc_final: 0.9131 (mtmt) REVERT: P 138 MET cc_start: 0.9404 (mtm) cc_final: 0.8326 (mtm) REVERT: P 175 MET cc_start: 0.7075 (ppp) cc_final: 0.6651 (ppp) REVERT: P 191 PHE cc_start: 0.9472 (OUTLIER) cc_final: 0.9138 (m-80) REVERT: Q 9 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8098 (tp30) REVERT: Q 30 MET cc_start: 0.9312 (tpp) cc_final: 0.8889 (tpp) REVERT: Q 75 LEU cc_start: 0.9583 (mt) cc_final: 0.9300 (mp) REVERT: Q 114 TYR cc_start: 0.8587 (t80) cc_final: 0.8382 (t80) REVERT: Q 127 VAL cc_start: 0.9611 (OUTLIER) cc_final: 0.9323 (p) REVERT: Q 131 GLN cc_start: 0.8793 (pt0) cc_final: 0.8523 (pm20) REVERT: R 52 PHE cc_start: 0.7596 (m-80) cc_final: 0.7059 (m-80) REVERT: R 58 ASN cc_start: 0.8914 (m-40) cc_final: 0.8602 (p0) outliers start: 114 outliers final: 68 residues processed: 533 average time/residue: 0.1906 time to fit residues: 159.9081 Evaluate side-chains 491 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 414 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 THR 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 116 ILE Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 SER 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 D residue 289 MET Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain I residue 16 ARG Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 100 ASP Chi-restraints excluded: chain I residue 109 TYR 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 98 LYS 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 42 VAL 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 138 MET 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 69 ILE Chi-restraints excluded: chain M residue 221 ASP Chi-restraints excluded: chain N residue 105 VAL Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain O residue 157 MET Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 243 LEU Chi-restraints excluded: chain O residue 288 GLU Chi-restraints excluded: chain P residue 41 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 191 PHE Chi-restraints excluded: chain P residue 231 SER Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 98 LYS Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain Q residue 154 ILE Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 174 THR Chi-restraints excluded: chain Q residue 191 PHE Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 214 LEU Chi-restraints excluded: chain Q residue 216 ASN Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 99 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 92 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 243 optimal weight: 0.7980 chunk 266 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 256 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 325 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 ASN I 58 ASN ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 HIS L 70 GLN ** M 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.080435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.056782 restraints weight = 120622.516| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 4.19 r_work: 0.2931 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 29222 Z= 0.261 Angle : 0.706 13.159 39723 Z= 0.365 Chirality : 0.047 0.347 4410 Planarity : 0.005 0.066 5013 Dihedral : 14.092 179.827 4640 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.08 % Allowed : 13.43 % Favored : 82.49 % 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: -0.18 (0.14), residues: 3418 helix: 0.69 (0.13), residues: 1432 sheet: -0.13 (0.23), residues: 540 loop : -0.85 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 72 TYR 0.038 0.002 TYR R 109 PHE 0.019 0.002 PHE H 93 TRP 0.031 0.002 TRP O 211 HIS 0.015 0.001 HIS G 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.26 (29222) covalent geometry : angle 0.70560 / 0.36 (39723) hydrogen bonds : bond 0.04959 / 4.76 ( 1272) hydrogen bonds : angle 5.76003 / 5.94 ( 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 560 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 441 time to evaluate : 1.357 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: B 54 MET cc_start: 0.9541 (OUTLIER) cc_final: 0.9170 (tpp) REVERT: B 101 GLU cc_start: 0.9330 (mm-30) cc_final: 0.8993 (mp0) REVERT: B 106 MET cc_start: 0.9421 (mmm) cc_final: 0.8587 (mmm) REVERT: B 110 TYR cc_start: 0.9340 (m-80) cc_final: 0.8210 (m-80) REVERT: C 30 MET cc_start: 0.9133 (mtp) cc_final: 0.8530 (mtm) REVERT: C 175 MET cc_start: 0.8708 (mtm) cc_final: 0.8415 (mtm) REVERT: C 207 LEU cc_start: 0.9566 (tp) cc_final: 0.9035 (tp) REVERT: C 211 TRP cc_start: 0.8549 (m-10) cc_final: 0.8233 (m-90) REVERT: D 137 GLN cc_start: 0.9102 (mm-40) cc_final: 0.8564 (mm-40) REVERT: D 186 TYR cc_start: 0.6636 (m-80) cc_final: 0.6311 (m-10) REVERT: D 229 MET cc_start: 0.6113 (mmm) cc_final: 0.5518 (mmm) REVERT: E 54 MET cc_start: 0.9017 (mtm) cc_final: 0.8785 (mtm) REVERT: E 102 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8590 (mm-40) REVERT: E 106 MET cc_start: 0.9406 (mmm) cc_final: 0.9072 (mmm) REVERT: F 66 LEU cc_start: 0.9271 (tp) cc_final: 0.9032 (mt) REVERT: F 68 LYS cc_start: 0.8840 (mmmt) cc_final: 0.8600 (mmtm) REVERT: G 97 MET cc_start: 0.8715 (mmm) cc_final: 0.8428 (mmm) REVERT: H 26 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7587 (mm-30) REVERT: H 40 TYR cc_start: 0.6371 (m-80) cc_final: 0.5996 (m-80) REVERT: H 80 GLU cc_start: 0.9338 (pt0) cc_final: 0.8818 (tm-30) REVERT: H 102 GLN cc_start: 0.8336 (mt0) cc_final: 0.8088 (mt0) REVERT: H 107 ILE cc_start: 0.9095 (mm) cc_final: 0.8816 (mm) REVERT: I 9 ASP cc_start: 0.8036 (t70) cc_final: 0.7590 (m-30) REVERT: I 12 TYR cc_start: 0.8748 (t80) cc_final: 0.8221 (t80) REVERT: I 66 LEU cc_start: 0.7577 (tp) cc_final: 0.7260 (tp) REVERT: I 79 TYR cc_start: 0.9244 (m-10) cc_final: 0.8858 (m-10) REVERT: I 83 MET cc_start: 0.9573 (mtt) cc_final: 0.9204 (tmm) REVERT: I 100 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7276 (t0) REVERT: I 110 TYR cc_start: 0.8734 (m-80) cc_final: 0.8459 (m-80) REVERT: I 113 ARG cc_start: 0.9483 (ptt90) cc_final: 0.9276 (ptt90) REVERT: J 10 ARG cc_start: 0.8796 (tmm-80) cc_final: 0.8454 (ttp80) REVERT: J 97 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6132 (tpp) REVERT: J 102 GLN cc_start: 0.9065 (mt0) cc_final: 0.8634 (mm-40) REVERT: K 30 MET cc_start: 0.9237 (mtp) cc_final: 0.8953 (mtp) REVERT: K 123 MET cc_start: 0.7242 (mpp) cc_final: 0.6947 (mpp) REVERT: K 150 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8126 (mm-40) REVERT: K 179 HIS cc_start: 0.8195 (OUTLIER) cc_final: 0.7883 (m90) REVERT: M 138 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8568 (mtm) REVERT: M 221 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8543 (t0) REVERT: N 150 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8238 (mm-40) REVERT: N 156 ARG cc_start: 0.8703 (ptm160) cc_final: 0.8358 (ptp-110) REVERT: N 157 MET cc_start: 0.8149 (mtp) cc_final: 0.7192 (mmt) REVERT: N 186 TYR cc_start: 0.9384 (m-80) cc_final: 0.9112 (m-80) REVERT: O 26 ASP cc_start: 0.9523 (OUTLIER) cc_final: 0.9266 (t0) REVERT: O 30 MET cc_start: 0.8594 (mmm) cc_final: 0.8349 (mmm) REVERT: O 57 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9429 (tt) REVERT: O 221 ASP cc_start: 0.8575 (t70) cc_final: 0.8239 (t0) REVERT: Q 9 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8073 (tp30) REVERT: Q 30 MET cc_start: 0.9383 (tpp) cc_final: 0.9180 (tpp) REVERT: Q 75 LEU cc_start: 0.9602 (mt) cc_final: 0.9374 (mp) REVERT: Q 127 VAL cc_start: 0.9609 (OUTLIER) cc_final: 0.9337 (p) REVERT: Q 131 GLN cc_start: 0.8779 (pt0) cc_final: 0.8571 (pm20) REVERT: R 52 PHE cc_start: 0.7454 (m-80) cc_final: 0.7182 (m-10) REVERT: R 58 ASN cc_start: 0.8897 (m-40) cc_final: 0.8583 (p0) outliers start: 119 outliers final: 84 residues processed: 512 average time/residue: 0.1949 time to fit residues: 159.9173 Evaluate side-chains 488 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 393 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 35 THR 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 C residue 16 VAL Chi-restraints excluded: chain C residue 17 GLU 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 258 SER 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 E residue 23 LYS Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 102 GLN Chi-restraints excluded: chain F residue 8 THR 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 53 HIS Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 16 ARG Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 100 ASP Chi-restraints excluded: chain J residue 55 LEU 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 97 MET 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 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 K residue 277 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 42 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 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 138 MET Chi-restraints excluded: chain M residue 221 ASP Chi-restraints excluded: chain N residue 105 VAL Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain O residue 26 ASP Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain O residue 157 MET Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 206 ASP Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain O residue 288 GLU Chi-restraints excluded: chain P residue 41 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 191 PHE 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 127 VAL Chi-restraints excluded: chain Q residue 154 ILE Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 174 THR Chi-restraints excluded: chain Q residue 191 PHE Chi-restraints excluded: chain Q residue 214 LEU Chi-restraints excluded: chain Q residue 216 ASN Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 99 SER 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: 2.9990 chunk 116 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 254 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 311 optimal weight: 0.9990 chunk 297 optimal weight: 1.9990 chunk 266 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 78 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 HIS ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 220 HIS K 249 HIS O 112 ASN ** 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 = 0.3827 r_free = 0.3827 target = 0.081529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.057710 restraints weight = 118530.380| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 4.20 r_work: 0.2951 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29222 Z= 0.185 Angle : 0.660 14.312 39723 Z= 0.339 Chirality : 0.046 0.319 4410 Planarity : 0.005 0.058 5013 Dihedral : 14.105 179.898 4638 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.46 % Allowed : 14.56 % Favored : 81.98 % 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 (0.15), residues: 3418 helix: 0.81 (0.14), residues: 1432 sheet: -0.10 (0.23), residues: 540 loop : -0.83 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 113 TYR 0.023 0.002 TYR J 40 PHE 0.024 0.002 PHE E 93 TRP 0.025 0.002 TRP O 211 HIS 0.020 0.001 HIS G 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (29222) covalent geometry : angle 0.66043 / 0.34 (39723) hydrogen bonds : bond 0.04549 / 4.38 ( 1272) hydrogen bonds : angle 5.56898 / 5.80 ( 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 529 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 428 time to evaluate : 1.194 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: B 13 LEU cc_start: 0.9402 (mt) cc_final: 0.9066 (tp) REVERT: B 54 MET cc_start: 0.9525 (OUTLIER) cc_final: 0.9148 (tpp) REVERT: B 101 GLU cc_start: 0.9338 (mm-30) cc_final: 0.8995 (mp0) REVERT: B 106 MET cc_start: 0.9446 (mmm) cc_final: 0.8541 (mmm) REVERT: B 110 TYR cc_start: 0.9420 (m-80) cc_final: 0.8272 (m-80) REVERT: C 30 MET cc_start: 0.9148 (mtp) cc_final: 0.8521 (mtm) REVERT: C 36 GLU cc_start: 0.8639 (mp0) cc_final: 0.8297 (mp0) REVERT: C 123 MET cc_start: 0.8323 (mtm) cc_final: 0.7924 (mtm) REVERT: C 175 MET cc_start: 0.8650 (mtm) cc_final: 0.8324 (mtm) REVERT: D 186 TYR cc_start: 0.6622 (m-80) cc_final: 0.6328 (m-10) REVERT: D 229 MET cc_start: 0.6004 (mmm) cc_final: 0.5411 (mmm) REVERT: E 93 PHE cc_start: 0.8288 (m-80) cc_final: 0.8030 (m-80) REVERT: E 106 MET cc_start: 0.9336 (mmm) cc_final: 0.9061 (mmm) REVERT: F 66 LEU cc_start: 0.9279 (tp) cc_final: 0.9076 (mt) REVERT: F 68 LYS cc_start: 0.8920 (mmmt) cc_final: 0.8682 (mmtm) REVERT: F 102 GLN cc_start: 0.8716 (mt0) cc_final: 0.8094 (mm-40) REVERT: G 97 MET cc_start: 0.8637 (mmm) cc_final: 0.8024 (mmm) REVERT: G 101 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8909 (mm-30) REVERT: G 102 GLN cc_start: 0.8310 (mt0) cc_final: 0.8033 (mp10) REVERT: H 10 ARG cc_start: 0.8194 (ttp80) cc_final: 0.7950 (ttp-170) REVERT: H 21 LEU cc_start: 0.8895 (tt) cc_final: 0.8667 (mt) REVERT: H 40 TYR cc_start: 0.6422 (m-80) cc_final: 0.6089 (m-80) REVERT: H 80 GLU cc_start: 0.9356 (pt0) cc_final: 0.8867 (tm-30) REVERT: H 102 GLN cc_start: 0.8209 (mt0) cc_final: 0.8001 (mt0) REVERT: H 107 ILE cc_start: 0.9086 (mm) cc_final: 0.8869 (mm) REVERT: I 9 ASP cc_start: 0.7963 (t70) cc_final: 0.7469 (m-30) REVERT: I 12 TYR cc_start: 0.8797 (t80) cc_final: 0.7956 (t80) REVERT: I 66 LEU cc_start: 0.7604 (tp) cc_final: 0.7303 (tp) REVERT: I 79 TYR cc_start: 0.9235 (m-10) cc_final: 0.8791 (m-10) REVERT: I 81 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.8969 (pt) REVERT: I 83 MET cc_start: 0.9583 (mtt) cc_final: 0.9213 (tmm) REVERT: I 100 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7488 (t0) REVERT: I 110 TYR cc_start: 0.8839 (m-80) cc_final: 0.8578 (m-80) REVERT: J 47 ASN cc_start: 0.7803 (m-40) cc_final: 0.7462 (p0) REVERT: K 30 MET cc_start: 0.9247 (mtp) cc_final: 0.8922 (mtp) REVERT: K 123 MET cc_start: 0.7293 (mpp) cc_final: 0.6995 (mpp) REVERT: K 150 GLN cc_start: 0.8336 (mm-40) cc_final: 0.7646 (mm110) REVERT: K 179 HIS cc_start: 0.8117 (OUTLIER) cc_final: 0.7781 (m90) REVERT: M 221 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8576 (t0) REVERT: N 150 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8269 (mm-40) REVERT: N 156 ARG cc_start: 0.8659 (ptm160) cc_final: 0.8269 (ptp-110) REVERT: N 157 MET cc_start: 0.8091 (mtp) cc_final: 0.7202 (mmt) REVERT: N 186 TYR cc_start: 0.9343 (m-80) cc_final: 0.9109 (m-80) REVERT: O 30 MET cc_start: 0.8579 (mmm) cc_final: 0.8329 (mmm) REVERT: O 221 ASP cc_start: 0.8477 (t70) cc_final: 0.8143 (t0) REVERT: Q 30 MET cc_start: 0.9380 (tpp) cc_final: 0.9171 (tpp) REVERT: Q 75 LEU cc_start: 0.9607 (mt) cc_final: 0.9376 (mp) REVERT: Q 127 VAL cc_start: 0.9607 (OUTLIER) cc_final: 0.9351 (p) REVERT: R 3 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8774 (mp) REVERT: R 58 ASN cc_start: 0.8933 (m-40) cc_final: 0.8715 (m-40) REVERT: R 65 LYS cc_start: 0.8352 (mtmm) cc_final: 0.8037 (pttm) outliers start: 101 outliers final: 63 residues processed: 495 average time/residue: 0.1894 time to fit residues: 150.8114 Evaluate side-chains 462 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 392 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASP 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 C residue 16 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 SER 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 E residue 23 LYS 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 53 HIS Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 40 TYR 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 J residue 40 TYR Chi-restraints excluded: chain J residue 55 LEU 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 16 VAL Chi-restraints excluded: chain K residue 43 THR 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 K residue 277 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 37 THR 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 138 MET 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 M residue 221 ASP Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain P residue 41 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 191 PHE Chi-restraints excluded: chain P residue 238 LYS 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 3 LEU Chi-restraints excluded: chain R residue 78 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 82 optimal weight: 10.0000 chunk 313 optimal weight: 8.9990 chunk 311 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 340 optimal weight: 20.0000 chunk 209 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 25 optimal weight: 0.0870 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 112 GLN C 131 GLN ** D 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN J 50 GLN ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 HIS ** L 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 70 GLN ** P 131 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.082152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.058461 restraints weight = 117268.647| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 4.21 r_work: 0.2972 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 29222 Z= 0.155 Angle : 0.657 12.629 39723 Z= 0.338 Chirality : 0.046 0.403 4410 Planarity : 0.004 0.059 5013 Dihedral : 14.042 179.306 4635 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.01 % Allowed : 16.14 % Favored : 80.85 % 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: -0.02 (0.15), residues: 3418 helix: 0.84 (0.14), residues: 1432 sheet: -0.03 (0.23), residues: 540 loop : -0.81 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 16 TYR 0.031 0.002 TYR I 12 PHE 0.025 0.002 PHE J 93 TRP 0.048 0.002 TRP O 211 HIS 0.017 0.001 HIS G 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (29222) covalent geometry : angle 0.65715 / 0.34 (39723) hydrogen bonds : bond 0.04364 / 4.20 ( 1272) hydrogen bonds : angle 5.49234 / 5.72 ( 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 518 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 430 time to evaluate : 1.178 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: B 13 LEU cc_start: 0.9391 (mt) cc_final: 0.9068 (tp) REVERT: B 54 MET cc_start: 0.9496 (OUTLIER) cc_final: 0.9101 (tpp) REVERT: B 101 GLU cc_start: 0.9318 (mm-30) cc_final: 0.8980 (mp0) REVERT: B 106 MET cc_start: 0.9465 (mmm) cc_final: 0.8505 (mmm) REVERT: B 110 TYR cc_start: 0.9465 (m-80) cc_final: 0.8332 (m-80) REVERT: C 30 MET cc_start: 0.9167 (mtp) cc_final: 0.8526 (mtm) REVERT: C 36 GLU cc_start: 0.8634 (mp0) cc_final: 0.8277 (mp0) REVERT: C 175 MET cc_start: 0.8610 (mtm) cc_final: 0.8296 (mtm) REVERT: D 186 TYR cc_start: 0.6555 (m-80) cc_final: 0.6277 (m-10) REVERT: D 229 MET cc_start: 0.5948 (mmm) cc_final: 0.5335 (mmm) REVERT: E 54 MET cc_start: 0.8958 (mtm) cc_final: 0.8427 (ptp) REVERT: E 106 MET cc_start: 0.9336 (mmm) cc_final: 0.9073 (mmm) REVERT: F 29 VAL cc_start: 0.9168 (m) cc_final: 0.8953 (p) REVERT: F 66 LEU cc_start: 0.9291 (tp) cc_final: 0.9074 (mt) REVERT: F 68 LYS cc_start: 0.8956 (mmmt) cc_final: 0.8738 (mmtm) REVERT: F 102 GLN cc_start: 0.8706 (mt0) cc_final: 0.8204 (mt0) REVERT: G 101 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8885 (mm-30) REVERT: G 102 GLN cc_start: 0.8302 (mt0) cc_final: 0.7924 (mm-40) REVERT: H 38 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: H 80 GLU cc_start: 0.9342 (pt0) cc_final: 0.8847 (tm-30) REVERT: H 102 GLN cc_start: 0.8210 (mt0) cc_final: 0.8005 (mt0) REVERT: I 9 ASP cc_start: 0.7857 (t70) cc_final: 0.7335 (m-30) REVERT: I 12 TYR cc_start: 0.8807 (t80) cc_final: 0.8477 (t80) REVERT: I 41 LEU cc_start: 0.9531 (tt) cc_final: 0.9301 (tp) REVERT: I 66 LEU cc_start: 0.7555 (tp) cc_final: 0.7266 (tp) REVERT: I 79 TYR cc_start: 0.9230 (m-10) cc_final: 0.8770 (m-10) REVERT: I 81 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8981 (pt) REVERT: I 83 MET cc_start: 0.9581 (mtt) cc_final: 0.9219 (tmm) REVERT: I 100 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7493 (t0) REVERT: I 110 TYR cc_start: 0.8832 (m-80) cc_final: 0.8487 (m-80) REVERT: J 47 ASN cc_start: 0.8112 (m-40) cc_final: 0.7492 (p0) REVERT: J 52 PHE cc_start: 0.9269 (m-10) cc_final: 0.9012 (m-10) REVERT: J 80 GLU cc_start: 0.9419 (mt-10) cc_final: 0.8921 (tm-30) REVERT: J 82 MET cc_start: 0.9162 (ptp) cc_final: 0.8957 (ptp) REVERT: J 93 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8229 (t80) REVERT: J 97 MET cc_start: 0.6389 (tpp) cc_final: 0.6181 (tpp) REVERT: J 102 GLN cc_start: 0.8782 (mt0) cc_final: 0.8362 (mm-40) REVERT: K 30 MET cc_start: 0.9251 (mtp) cc_final: 0.8883 (mtp) REVERT: K 123 MET cc_start: 0.7515 (mpp) cc_final: 0.7220 (mpp) REVERT: K 148 VAL cc_start: 0.9184 (OUTLIER) cc_final: 0.8839 (m) REVERT: K 150 GLN cc_start: 0.8363 (mm-40) cc_final: 0.7572 (mm110) REVERT: K 179 HIS cc_start: 0.8076 (OUTLIER) cc_final: 0.7719 (m90) REVERT: K 217 MET cc_start: 0.8642 (ptm) cc_final: 0.8273 (ttp) REVERT: L 217 MET cc_start: 0.8902 (ptp) cc_final: 0.8602 (ptp) REVERT: N 150 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8424 (mm-40) REVERT: N 156 ARG cc_start: 0.8665 (ptm160) cc_final: 0.8265 (ptp-110) REVERT: N 157 MET cc_start: 0.8096 (mtp) cc_final: 0.7193 (mmt) REVERT: N 186 TYR cc_start: 0.9354 (m-80) cc_final: 0.9101 (m-80) REVERT: O 30 MET cc_start: 0.8564 (mmm) cc_final: 0.8285 (mmm) REVERT: O 221 ASP cc_start: 0.8424 (t70) cc_final: 0.8072 (t0) REVERT: Q 75 LEU cc_start: 0.9600 (mt) cc_final: 0.9376 (mp) REVERT: Q 127 VAL cc_start: 0.9622 (OUTLIER) cc_final: 0.9411 (p) REVERT: R 3 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8748 (mp) outliers start: 88 outliers final: 61 residues processed: 486 average time/residue: 0.1886 time to fit residues: 148.4834 Evaluate side-chains 459 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 389 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 35 THR 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 116 ILE Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 214 LEU 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 23 LYS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 52 PHE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 8 THR 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 J residue 40 TYR Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 93 PHE 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 131 GLN 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 K residue 277 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain L residue 179 HIS 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 106 THR Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 41 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 191 PHE Chi-restraints excluded: chain P residue 238 LYS 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 3 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 58 optimal weight: 0.0040 chunk 307 optimal weight: 7.9990 chunk 284 optimal weight: 0.9980 chunk 210 optimal weight: 0.1980 chunk 5 optimal weight: 8.9990 chunk 300 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 HIS ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 HIS ** L 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 179 HIS P 131 GLN ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 240 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.082635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.058987 restraints weight = 117446.454| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 4.23 r_work: 0.2995 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29222 Z= 0.136 Angle : 0.664 13.611 39723 Z= 0.338 Chirality : 0.046 0.278 4410 Planarity : 0.004 0.063 5013 Dihedral : 14.033 179.803 4635 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.71 % Allowed : 16.92 % Favored : 80.37 % 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: -0.01 (0.15), residues: 3418 helix: 0.82 (0.14), residues: 1432 sheet: 0.05 (0.23), residues: 540 loop : -0.79 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 113 TYR 0.029 0.002 TYR M 183 PHE 0.037 0.002 PHE E 52 TRP 0.085 0.002 TRP O 211 HIS 0.011 0.001 HIS Q 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (29222) covalent geometry : angle 0.66389 / 0.34 (39723) hydrogen bonds : bond 0.04224 / 4.10 ( 1272) hydrogen bonds : angle 5.40571 / 5.68 ( 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 500 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 421 time to evaluate : 1.039 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: B 13 LEU cc_start: 0.9370 (mt) cc_final: 0.9049 (tp) REVERT: B 54 MET cc_start: 0.9473 (OUTLIER) cc_final: 0.9113 (tpp) REVERT: B 101 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8907 (mp0) REVERT: B 106 MET cc_start: 0.9481 (mmm) cc_final: 0.8436 (mmm) REVERT: B 110 TYR cc_start: 0.9474 (m-80) cc_final: 0.8423 (m-80) REVERT: C 36 GLU cc_start: 0.8618 (mp0) cc_final: 0.8252 (mp0) REVERT: C 123 MET cc_start: 0.8526 (mtm) cc_final: 0.8315 (mtm) REVERT: C 175 MET cc_start: 0.8626 (mtm) cc_final: 0.8345 (mtm) REVERT: D 186 TYR cc_start: 0.6499 (m-80) cc_final: 0.6218 (m-10) REVERT: D 229 MET cc_start: 0.5926 (mmm) cc_final: 0.5293 (mmm) REVERT: E 54 MET cc_start: 0.8842 (mtm) cc_final: 0.8380 (ptp) REVERT: E 93 PHE cc_start: 0.8289 (m-80) cc_final: 0.8076 (m-80) REVERT: E 106 MET cc_start: 0.9350 (mmm) cc_final: 0.9062 (mmm) REVERT: F 4 ASP cc_start: 0.8925 (t0) cc_final: 0.8501 (t0) REVERT: F 29 VAL cc_start: 0.9197 (m) cc_final: 0.8956 (p) REVERT: F 102 GLN cc_start: 0.8751 (mt0) cc_final: 0.8244 (mt0) REVERT: G 97 MET cc_start: 0.8741 (mmm) cc_final: 0.8241 (mmm) REVERT: G 101 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8850 (mm-30) REVERT: G 102 GLN cc_start: 0.8258 (mt0) cc_final: 0.7994 (mp10) REVERT: H 38 ASP cc_start: 0.8428 (t70) cc_final: 0.7867 (m-30) REVERT: H 80 GLU cc_start: 0.9343 (pt0) cc_final: 0.8871 (tm-30) REVERT: H 102 GLN cc_start: 0.8234 (mt0) cc_final: 0.8014 (mt0) REVERT: H 107 ILE cc_start: 0.9033 (mm) cc_final: 0.8768 (mm) REVERT: I 9 ASP cc_start: 0.7837 (t70) cc_final: 0.7305 (m-30) REVERT: I 12 TYR cc_start: 0.8830 (t80) cc_final: 0.8448 (t80) REVERT: I 41 LEU cc_start: 0.9533 (tt) cc_final: 0.9297 (tp) REVERT: I 66 LEU cc_start: 0.7510 (tp) cc_final: 0.7196 (tp) REVERT: I 79 TYR cc_start: 0.9220 (m-10) cc_final: 0.8751 (m-10) REVERT: I 81 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8996 (pt) REVERT: I 83 MET cc_start: 0.9579 (mtt) cc_final: 0.9224 (tmm) REVERT: I 100 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7729 (t0) REVERT: I 107 ILE cc_start: 0.9242 (mm) cc_final: 0.8858 (tt) REVERT: I 110 TYR cc_start: 0.8813 (m-80) cc_final: 0.8562 (m-80) REVERT: J 47 ASN cc_start: 0.8239 (m-40) cc_final: 0.7695 (p0) REVERT: J 52 PHE cc_start: 0.9315 (m-10) cc_final: 0.9010 (m-10) REVERT: J 93 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8166 (t80) REVERT: J 97 MET cc_start: 0.6804 (tpp) cc_final: 0.6238 (tpp) REVERT: J 102 GLN cc_start: 0.8764 (mt0) cc_final: 0.8417 (mm-40) REVERT: K 30 MET cc_start: 0.9251 (mtp) cc_final: 0.8941 (mtp) REVERT: K 123 MET cc_start: 0.7494 (mpp) cc_final: 0.7198 (mpp) REVERT: K 148 VAL cc_start: 0.9200 (OUTLIER) cc_final: 0.8850 (m) REVERT: K 150 GLN cc_start: 0.8358 (mm-40) cc_final: 0.7523 (mm110) REVERT: K 217 MET cc_start: 0.8603 (ptm) cc_final: 0.8208 (ttp) REVERT: L 217 MET cc_start: 0.8854 (ptp) cc_final: 0.8327 (ptp) REVERT: M 131 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8295 (pt0) REVERT: N 150 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8450 (mm-40) REVERT: N 156 ARG cc_start: 0.8636 (ptm160) cc_final: 0.8229 (ptp-110) REVERT: N 157 MET cc_start: 0.8089 (mtp) cc_final: 0.7262 (mmt) REVERT: N 186 TYR cc_start: 0.9361 (m-80) cc_final: 0.9094 (m-80) REVERT: O 207 LEU cc_start: 0.9386 (tp) cc_final: 0.8798 (tp) REVERT: O 211 TRP cc_start: 0.8119 (m-90) cc_final: 0.7833 (m-90) REVERT: O 221 ASP cc_start: 0.8390 (t70) cc_final: 0.8133 (t0) REVERT: P 289 MET cc_start: 0.9054 (mtt) cc_final: 0.8686 (mtt) REVERT: Q 30 MET cc_start: 0.9340 (tpp) cc_final: 0.8834 (tpp) REVERT: R 3 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8757 (mp) REVERT: R 58 ASN cc_start: 0.8612 (m-40) cc_final: 0.8079 (p0) REVERT: R 65 LYS cc_start: 0.8299 (mtmm) cc_final: 0.7901 (mmtt) outliers start: 79 outliers final: 46 residues processed: 471 average time/residue: 0.1813 time to fit residues: 138.3233 Evaluate side-chains 438 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 385 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 116 ILE Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 52 PHE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 40 TYR 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 109 TYR Chi-restraints excluded: chain J residue 40 TYR Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 93 PHE Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 131 GLN 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 K residue 254 LEU Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 127 VAL 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 69 ILE Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain N residue 107 ASP 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 Q residue 16 VAL Chi-restraints excluded: chain Q residue 191 PHE Chi-restraints excluded: chain Q residue 216 ASN Chi-restraints excluded: chain R residue 3 LEU Chi-restraints excluded: chain R residue 78 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 182 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 123 optimal weight: 0.4980 chunk 165 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 323 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN ** K 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 HIS ** L 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 240 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.081275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.057732 restraints weight = 119980.898| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 4.22 r_work: 0.2967 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 29222 Z= 0.182 Angle : 0.679 13.621 39723 Z= 0.348 Chirality : 0.046 0.338 4410 Planarity : 0.004 0.060 5013 Dihedral : 13.942 179.136 4630 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.74 % Allowed : 16.89 % Favored : 80.37 % 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: 0.06 (0.15), residues: 3418 helix: 0.87 (0.14), residues: 1432 sheet: 0.11 (0.23), residues: 540 loop : -0.75 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 10 TYR 0.023 0.002 TYR M 183 PHE 0.025 0.002 PHE G 105 TRP 0.061 0.002 TRP O 211 HIS 0.011 0.001 HIS I 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (29222) covalent geometry : angle 0.67914 / 0.35 (39723) hydrogen bonds : bond 0.04203 / 4.06 ( 1272) hydrogen bonds : angle 5.39787 / 5.66 ( 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 480 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 400 time to evaluate : 1.147 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: B 13 LEU cc_start: 0.9379 (mt) cc_final: 0.9068 (tp) REVERT: B 54 MET cc_start: 0.9491 (OUTLIER) cc_final: 0.9148 (tpp) REVERT: B 101 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8881 (mp0) REVERT: B 106 MET cc_start: 0.9569 (mmm) cc_final: 0.8373 (mmm) REVERT: B 110 TYR cc_start: 0.9499 (m-80) cc_final: 0.8463 (m-80) REVERT: C 36 GLU cc_start: 0.8690 (mp0) cc_final: 0.8335 (mp0) REVERT: C 175 MET cc_start: 0.8593 (mtm) cc_final: 0.8338 (mtm) REVERT: D 186 TYR cc_start: 0.6526 (m-80) cc_final: 0.6162 (m-80) REVERT: D 229 MET cc_start: 0.5857 (mmm) cc_final: 0.4895 (mmt) REVERT: E 54 MET cc_start: 0.8888 (mtm) cc_final: 0.8282 (ptp) REVERT: E 106 MET cc_start: 0.9341 (mmm) cc_final: 0.9078 (mmm) REVERT: F 4 ASP cc_start: 0.8956 (t0) cc_final: 0.8533 (t0) REVERT: F 29 VAL cc_start: 0.9173 (m) cc_final: 0.8935 (p) REVERT: F 66 LEU cc_start: 0.9292 (mt) cc_final: 0.9038 (tp) REVERT: F 83 MET cc_start: 0.9435 (mmt) cc_final: 0.9205 (mmt) REVERT: G 75 SER cc_start: 0.9295 (t) cc_final: 0.8948 (p) REVERT: H 38 ASP cc_start: 0.8402 (t70) cc_final: 0.7805 (m-30) REVERT: H 54 MET cc_start: 0.9026 (mtt) cc_final: 0.8767 (ptp) REVERT: H 62 HIS cc_start: 0.8958 (m-70) cc_final: 0.8598 (t-90) REVERT: H 80 GLU cc_start: 0.9352 (pt0) cc_final: 0.8915 (tm-30) REVERT: H 102 GLN cc_start: 0.8374 (mt0) cc_final: 0.8020 (mt0) REVERT: I 9 ASP cc_start: 0.7907 (t70) cc_final: 0.7340 (m-30) REVERT: I 12 TYR cc_start: 0.8835 (t80) cc_final: 0.8394 (t80) REVERT: I 41 LEU cc_start: 0.9552 (tt) cc_final: 0.9333 (tp) REVERT: I 66 LEU cc_start: 0.7535 (tp) cc_final: 0.7209 (tp) REVERT: I 80 GLU cc_start: 0.8654 (pp20) cc_final: 0.8368 (pp20) REVERT: I 81 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8950 (pt) REVERT: I 100 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7731 (t0) REVERT: I 107 ILE cc_start: 0.9272 (mm) cc_final: 0.9063 (mm) REVERT: I 110 TYR cc_start: 0.8823 (m-80) cc_final: 0.8390 (m-80) REVERT: J 52 PHE cc_start: 0.9322 (m-10) cc_final: 0.9048 (m-10) REVERT: J 82 MET cc_start: 0.9129 (ptp) cc_final: 0.8867 (ptp) REVERT: J 93 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8358 (t80) REVERT: K 30 MET cc_start: 0.9254 (mtp) cc_final: 0.8883 (mtp) REVERT: K 123 MET cc_start: 0.7516 (mpp) cc_final: 0.7207 (mpp) REVERT: K 148 VAL cc_start: 0.9210 (OUTLIER) cc_final: 0.8857 (m) REVERT: K 150 GLN cc_start: 0.8400 (mm-40) cc_final: 0.7562 (mm110) REVERT: K 179 HIS cc_start: 0.8108 (OUTLIER) cc_final: 0.7776 (m90) REVERT: K 217 MET cc_start: 0.8599 (ptm) cc_final: 0.8250 (ttp) REVERT: L 37 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8715 (p) REVERT: L 217 MET cc_start: 0.8912 (ptp) cc_final: 0.8400 (ptp) REVERT: M 131 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8353 (pt0) REVERT: N 30 MET cc_start: 0.8615 (tpp) cc_final: 0.8349 (tpt) REVERT: N 150 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8476 (mm-40) REVERT: N 156 ARG cc_start: 0.8669 (ptm160) cc_final: 0.8282 (ptp-110) REVERT: N 157 MET cc_start: 0.8118 (mtp) cc_final: 0.7277 (mmt) REVERT: N 186 TYR cc_start: 0.9383 (m-80) cc_final: 0.9107 (m-80) REVERT: O 26 ASP cc_start: 0.9551 (OUTLIER) cc_final: 0.9293 (t0) REVERT: O 221 ASP cc_start: 0.8445 (t70) cc_final: 0.8179 (t0) REVERT: O 229 MET cc_start: 0.8233 (tpp) cc_final: 0.7948 (tpp) REVERT: P 238 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8693 (tptp) REVERT: P 289 MET cc_start: 0.9032 (mtt) cc_final: 0.8678 (mtt) REVERT: R 3 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8730 (mp) outliers start: 80 outliers final: 56 residues processed: 449 average time/residue: 0.1832 time to fit residues: 134.1078 Evaluate side-chains 447 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 380 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 SER 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 96 THR Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain G residue 52 PHE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 40 TYR 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 J residue 7 ARG Chi-restraints excluded: chain J residue 40 TYR Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 93 PHE Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 131 GLN 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 K residue 277 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 138 MET 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 69 ILE Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain O residue 26 ASP Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain O residue 181 VAL 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 238 LYS 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 Q residue 216 ASN Chi-restraints excluded: chain R residue 3 LEU Chi-restraints excluded: chain R residue 78 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 270 optimal weight: 5.9990 chunk 322 optimal weight: 0.1980 chunk 231 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 226 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 312 optimal weight: 8.9990 chunk 191 optimal weight: 0.7980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 47 ASN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 ASN ** K 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 HIS ** L 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 172 ASN O 150 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.081324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.057775 restraints weight = 119575.671| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 4.23 r_work: 0.2970 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29222 Z= 0.165 Angle : 0.698 13.620 39723 Z= 0.357 Chirality : 0.047 0.300 4410 Planarity : 0.004 0.057 5013 Dihedral : 13.949 179.362 4630 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.91 % Allowed : 17.20 % Favored : 79.89 % 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: 0.07 (0.15), residues: 3418 helix: 0.84 (0.14), residues: 1432 sheet: 0.14 (0.23), residues: 540 loop : -0.73 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 72 TYR 0.020 0.002 TYR M 183 PHE 0.038 0.002 PHE E 93 TRP 0.021 0.002 TRP L 211 HIS 0.015 0.001 HIS J 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (29222) covalent geometry : angle 0.69753 / 0.36 (39723) hydrogen bonds : bond 0.04150 / 4.01 ( 1272) hydrogen bonds : angle 5.37975 / 5.63 ( 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 476 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 391 time to evaluate : 1.005 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: B 13 LEU cc_start: 0.9370 (mt) cc_final: 0.8988 (tp) REVERT: B 54 MET cc_start: 0.9500 (OUTLIER) cc_final: 0.9165 (tpp) REVERT: B 101 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8880 (mp0) REVERT: B 106 MET cc_start: 0.9587 (mmm) cc_final: 0.8438 (mmm) REVERT: B 110 TYR cc_start: 0.9486 (m-80) cc_final: 0.8431 (m-80) REVERT: C 36 GLU cc_start: 0.8706 (mp0) cc_final: 0.8330 (mp0) REVERT: C 175 MET cc_start: 0.8572 (mtm) cc_final: 0.8329 (mtm) REVERT: D 109 MET cc_start: 0.9056 (mmm) cc_final: 0.8615 (mmm) REVERT: D 123 MET cc_start: 0.7899 (mpp) cc_final: 0.7564 (pmm) REVERT: D 186 TYR cc_start: 0.6465 (m-80) cc_final: 0.6108 (m-80) REVERT: D 229 MET cc_start: 0.5876 (mmm) cc_final: 0.5633 (mmm) REVERT: E 54 MET cc_start: 0.8837 (mtm) cc_final: 0.8260 (ptp) REVERT: F 4 ASP cc_start: 0.8954 (t0) cc_final: 0.8530 (t0) REVERT: F 29 VAL cc_start: 0.9185 (m) cc_final: 0.8942 (p) REVERT: F 66 LEU cc_start: 0.9293 (mt) cc_final: 0.9060 (tp) REVERT: F 83 MET cc_start: 0.9421 (mmt) cc_final: 0.9199 (mmt) REVERT: G 75 SER cc_start: 0.9305 (t) cc_final: 0.8962 (p) REVERT: H 38 ASP cc_start: 0.8375 (t70) cc_final: 0.7768 (m-30) REVERT: H 54 MET cc_start: 0.9030 (mtt) cc_final: 0.8770 (ptp) REVERT: H 62 HIS cc_start: 0.8966 (m-70) cc_final: 0.8642 (t-90) REVERT: H 80 GLU cc_start: 0.9324 (pt0) cc_final: 0.8942 (tm-30) REVERT: H 102 GLN cc_start: 0.8315 (mt0) cc_final: 0.8012 (mt0) REVERT: H 107 ILE cc_start: 0.9160 (mm) cc_final: 0.8918 (mm) REVERT: I 9 ASP cc_start: 0.7875 (t70) cc_final: 0.7350 (m-30) REVERT: I 12 TYR cc_start: 0.8866 (t80) cc_final: 0.8431 (t80) REVERT: I 100 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7672 (t0) REVERT: I 107 ILE cc_start: 0.9256 (mm) cc_final: 0.9028 (mm) REVERT: I 110 TYR cc_start: 0.8826 (m-80) cc_final: 0.8501 (m-80) REVERT: J 52 PHE cc_start: 0.9277 (m-10) cc_final: 0.8961 (m-10) REVERT: J 80 GLU cc_start: 0.9385 (OUTLIER) cc_final: 0.8996 (pp20) REVERT: J 93 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8344 (t80) REVERT: J 97 MET cc_start: 0.6380 (tpp) cc_final: 0.5501 (tpp) REVERT: J 102 GLN cc_start: 0.8708 (mt0) cc_final: 0.8291 (mm-40) REVERT: K 30 MET cc_start: 0.9251 (mtp) cc_final: 0.8868 (mtp) REVERT: K 123 MET cc_start: 0.7430 (mpp) cc_final: 0.7124 (mpp) REVERT: K 148 VAL cc_start: 0.9205 (OUTLIER) cc_final: 0.8860 (m) REVERT: K 150 GLN cc_start: 0.8409 (mm-40) cc_final: 0.7576 (mm110) REVERT: K 179 HIS cc_start: 0.8134 (OUTLIER) cc_final: 0.7797 (m90) REVERT: K 217 MET cc_start: 0.8597 (ptm) cc_final: 0.8233 (ttp) REVERT: L 37 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8715 (p) REVERT: L 217 MET cc_start: 0.8890 (ptp) cc_final: 0.8406 (ptp) REVERT: M 131 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8317 (pt0) REVERT: N 30 MET cc_start: 0.8564 (tpp) cc_final: 0.8300 (tpt) REVERT: N 150 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8494 (mm-40) REVERT: N 156 ARG cc_start: 0.8691 (ptm160) cc_final: 0.8300 (ptp-110) REVERT: N 157 MET cc_start: 0.8082 (mtp) cc_final: 0.7239 (mmt) REVERT: N 186 TYR cc_start: 0.9372 (m-80) cc_final: 0.9104 (m-80) REVERT: O 123 MET cc_start: 0.8219 (mtp) cc_final: 0.7922 (mtp) REVERT: O 221 ASP cc_start: 0.8440 (t70) cc_final: 0.8178 (t0) REVERT: P 238 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8723 (tptp) REVERT: P 289 MET cc_start: 0.9026 (mtt) cc_final: 0.8664 (mtt) REVERT: R 3 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8758 (mp) REVERT: R 58 ASN cc_start: 0.8611 (m-40) cc_final: 0.8098 (p0) outliers start: 85 outliers final: 58 residues processed: 446 average time/residue: 0.1679 time to fit residues: 122.3976 Evaluate side-chains 446 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 378 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 C residue 16 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 SER 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 96 THR Chi-restraints excluded: chain F residue 98 SER 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 53 HIS Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 40 TYR 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 7 ARG Chi-restraints excluded: chain J residue 40 TYR Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 93 PHE Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 131 GLN 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 K residue 277 VAL 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 127 VAL 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 131 GLN Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 110 CYS 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 109 MET 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 P residue 238 LYS 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 R residue 3 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 147 optimal weight: 0.0770 chunk 61 optimal weight: 40.0000 chunk 271 optimal weight: 1.9990 chunk 234 optimal weight: 6.9990 chunk 162 optimal weight: 20.0000 chunk 183 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 318 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 HIS L 70 GLN ** L 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.081347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.057814 restraints weight = 118862.791| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 4.22 r_work: 0.2965 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29222 Z= 0.169 Angle : 0.704 14.562 39723 Z= 0.360 Chirality : 0.047 0.337 4410 Planarity : 0.004 0.054 5013 Dihedral : 13.940 179.545 4628 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.67 % Allowed : 17.61 % Favored : 79.72 % 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 (0.15), residues: 3418 helix: 0.85 (0.14), residues: 1432 sheet: 0.18 (0.23), residues: 540 loop : -0.72 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 16 TYR 0.023 0.002 TYR Q 68 PHE 0.035 0.002 PHE E 52 TRP 0.020 0.001 TRP L 211 HIS 0.013 0.001 HIS I 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (29222) covalent geometry : angle 0.70431 / 0.36 (39723) hydrogen bonds : bond 0.04164 / 4.01 ( 1272) hydrogen bonds : angle 5.37711 / 5.64 ( 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 474 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 396 time to evaluate : 0.955 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: B 13 LEU cc_start: 0.9366 (mt) cc_final: 0.8887 (tp) REVERT: B 27 ASP cc_start: 0.8444 (t0) cc_final: 0.7714 (t0) REVERT: B 54 MET cc_start: 0.9499 (OUTLIER) cc_final: 0.9170 (tpp) REVERT: B 101 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8900 (mp0) REVERT: B 106 MET cc_start: 0.9586 (mmm) cc_final: 0.8436 (mmm) REVERT: B 110 TYR cc_start: 0.9490 (m-80) cc_final: 0.8422 (m-80) REVERT: C 36 GLU cc_start: 0.8720 (mp0) cc_final: 0.8309 (mp0) REVERT: C 123 MET cc_start: 0.8620 (mtp) cc_final: 0.8100 (mtp) REVERT: C 175 MET cc_start: 0.8541 (mtm) cc_final: 0.8305 (mtm) REVERT: D 109 MET cc_start: 0.9063 (mmm) cc_final: 0.8700 (mmm) REVERT: D 123 MET cc_start: 0.7872 (mpp) cc_final: 0.7537 (pmm) REVERT: D 186 TYR cc_start: 0.6486 (m-80) cc_final: 0.6139 (m-80) REVERT: D 229 MET cc_start: 0.5897 (mmm) cc_final: 0.5640 (mmm) REVERT: E 54 MET cc_start: 0.8892 (mtm) cc_final: 0.8400 (ptp) REVERT: F 29 VAL cc_start: 0.9204 (m) cc_final: 0.8954 (p) REVERT: F 66 LEU cc_start: 0.9277 (mt) cc_final: 0.9048 (tp) REVERT: F 83 MET cc_start: 0.9405 (mmt) cc_final: 0.9159 (mmt) REVERT: G 75 SER cc_start: 0.9289 (t) cc_final: 0.8955 (p) REVERT: H 38 ASP cc_start: 0.8442 (t70) cc_final: 0.7845 (m-30) REVERT: H 54 MET cc_start: 0.9033 (mtt) cc_final: 0.8767 (ptp) REVERT: H 80 GLU cc_start: 0.9395 (pt0) cc_final: 0.8992 (tm-30) REVERT: H 97 MET cc_start: 0.6165 (mtp) cc_final: 0.5323 (ttp) REVERT: H 102 GLN cc_start: 0.8212 (mt0) cc_final: 0.7903 (mt0) REVERT: H 107 ILE cc_start: 0.9155 (mm) cc_final: 0.8932 (mm) REVERT: I 9 ASP cc_start: 0.7831 (t70) cc_final: 0.7334 (m-30) REVERT: I 12 TYR cc_start: 0.8871 (t80) cc_final: 0.8411 (t80) REVERT: I 83 MET cc_start: 0.9578 (mtt) cc_final: 0.9255 (tmm) REVERT: I 100 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7943 (t70) REVERT: I 107 ILE cc_start: 0.9284 (mm) cc_final: 0.9059 (mm) REVERT: I 110 TYR cc_start: 0.8755 (m-80) cc_final: 0.8457 (m-80) REVERT: J 52 PHE cc_start: 0.9305 (m-10) cc_final: 0.8967 (m-10) REVERT: J 80 GLU cc_start: 0.9359 (OUTLIER) cc_final: 0.8957 (pp20) REVERT: J 93 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8362 (t80) REVERT: J 97 MET cc_start: 0.6105 (tpp) cc_final: 0.4557 (tpp) REVERT: J 102 GLN cc_start: 0.8687 (mt0) cc_final: 0.8269 (mm-40) REVERT: K 30 MET cc_start: 0.9227 (mtp) cc_final: 0.8829 (mtp) REVERT: K 123 MET cc_start: 0.7437 (mpp) cc_final: 0.7114 (mpp) REVERT: K 148 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8846 (m) REVERT: K 150 GLN cc_start: 0.8441 (mm-40) cc_final: 0.7587 (mm110) REVERT: K 179 HIS cc_start: 0.8153 (OUTLIER) cc_final: 0.7818 (m90) REVERT: K 183 TYR cc_start: 0.8395 (t80) cc_final: 0.8022 (t80) REVERT: K 217 MET cc_start: 0.8582 (ptm) cc_final: 0.8219 (ttp) REVERT: L 37 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8721 (p) REVERT: L 217 MET cc_start: 0.8930 (ptp) cc_final: 0.8473 (ptp) REVERT: M 36 GLU cc_start: 0.8484 (mp0) cc_final: 0.8212 (mp0) REVERT: M 131 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8301 (pt0) REVERT: N 30 MET cc_start: 0.8561 (tpp) cc_final: 0.8297 (tpt) REVERT: N 150 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8485 (mm-40) REVERT: N 156 ARG cc_start: 0.8643 (ptm160) cc_final: 0.8252 (ptp-110) REVERT: N 157 MET cc_start: 0.8041 (mtp) cc_final: 0.7168 (mmt) REVERT: N 186 TYR cc_start: 0.9385 (m-80) cc_final: 0.9118 (m-80) REVERT: O 26 ASP cc_start: 0.9509 (OUTLIER) cc_final: 0.9260 (t0) REVERT: O 221 ASP cc_start: 0.8449 (t70) cc_final: 0.8194 (t0) REVERT: O 229 MET cc_start: 0.8211 (tpp) cc_final: 0.7706 (mmt) REVERT: P 238 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8727 (tptp) REVERT: P 289 MET cc_start: 0.9043 (mtt) cc_final: 0.8682 (mtt) REVERT: Q 9 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: R 3 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8768 (mp) REVERT: R 58 ASN cc_start: 0.8586 (m-40) cc_final: 0.8091 (p0) outliers start: 78 outliers final: 59 residues processed: 446 average time/residue: 0.1850 time to fit residues: 134.2682 Evaluate side-chains 451 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 380 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 C residue 16 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 SER 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 96 THR Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 18 PHE 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 109 TYR Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 40 TYR Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 93 PHE Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 131 GLN 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 K residue 277 VAL 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 127 VAL 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 33 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 115 ASP Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain O residue 26 ASP Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 110 CYS 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 109 MET 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 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 R residue 3 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 206 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 270 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 319 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 72 optimal weight: 30.0000 chunk 13 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 HIS ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 ASN ** K 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 HIS L 70 GLN ** L 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.081239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.057723 restraints weight = 119753.657| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 4.25 r_work: 0.2964 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 29222 Z= 0.168 Angle : 0.717 14.340 39723 Z= 0.365 Chirality : 0.047 0.322 4410 Planarity : 0.004 0.055 5013 Dihedral : 13.939 179.425 4627 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.60 % Allowed : 17.61 % Favored : 79.79 % 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: 0.11 (0.15), residues: 3418 helix: 0.86 (0.14), residues: 1432 sheet: 0.20 (0.23), residues: 540 loop : -0.70 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 16 TYR 0.020 0.002 TYR I 12 PHE 0.028 0.002 PHE E 52 TRP 0.019 0.002 TRP L 211 HIS 0.013 0.001 HIS I 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (29222) covalent geometry : angle 0.71662 / 0.36 (39723) hydrogen bonds : bond 0.04128 / 3.99 ( 1272) hydrogen bonds : angle 5.36631 / 5.63 ( 3738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9002.03 seconds wall clock time: 154 minutes 56.14 seconds (9296.14 seconds total)