Starting phenix.real_space_refine on Sun Aug 24 13:37:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tsw_41601/08_2025/8tsw_41601_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tsw_41601/08_2025/8tsw_41601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tsw_41601/08_2025/8tsw_41601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tsw_41601/08_2025/8tsw_41601.map" model { file = "/net/cci-nas-00/data/ceres_data/8tsw_41601/08_2025/8tsw_41601_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tsw_41601/08_2025/8tsw_41601_neut.cif" } resolution = 3.1 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= -0.002 sd= 0.889 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: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 13184 2.51 5 N 3474 2.21 5 O 3570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20326 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1687 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 4, 'TRANS': 209} Chain breaks: 1 Chain: "B" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1687 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 4, 'TRANS': 209} Chain breaks: 1 Chain: "C" Number of atoms: 2033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2033 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} Chain: "D" Number of atoms: 2033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2033 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} Chain: "E" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1624 Classifications: {'peptide': 198} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 189} Chain breaks: 2 Chain: "F" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1672 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 8, 'TRANS': 195} Chain breaks: 2 Chain: "G" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1713 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 2 Chain: "H" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1434 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain breaks: 2 Chain: "I" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1624 Classifications: {'peptide': 198} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 189} Chain breaks: 2 Chain: "J" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1672 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 8, 'TRANS': 195} Chain breaks: 2 Chain: "K" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1713 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 2 Chain: "L" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1434 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain breaks: 2 Time building chain proxies: 4.04, per 1000 atoms: 0.20 Number of scatterers: 20326 At special positions: 0 Unit cell: (132.84, 132.84, 140.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 3570 8.00 N 3474 7.00 C 13184 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: 1.72 Conformation dependent library (CDL) restraints added in 856.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 14 sheets defined 63.2% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 43 through 52 Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 98 through 114 Processing helix chain 'A' and resid 127 through 142 removed outlier: 3.782A pdb=" N PHE A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 173 removed outlier: 3.531A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 190 Processing helix chain 'A' and resid 207 through 219 removed outlier: 3.902A pdb=" N GLY A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 52 Processing helix chain 'B' and resid 74 through 78 Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 98 through 114 Processing helix chain 'B' and resid 127 through 142 removed outlier: 3.951A pdb=" N PHE B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 172 removed outlier: 3.527A pdb=" N ARG B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 207 through 219 removed outlier: 3.844A pdb=" N GLY B 211 " --> pdb=" O ASP B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 36 Processing helix chain 'C' and resid 41 through 69 removed outlier: 3.694A pdb=" N TRP C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Proline residue: C 50 - end of helix removed outlier: 6.233A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ALA C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 97 Proline residue: C 84 - end of helix removed outlier: 4.275A pdb=" N LEU C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET C 96 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU C 97 " --> pdb=" O THR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.528A pdb=" N PHE C 106 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 143 removed outlier: 3.873A pdb=" N THR C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 117 " --> pdb=" O PRO C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 176 Processing helix chain 'C' and resid 179 through 197 removed outlier: 3.563A pdb=" N ARG C 183 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU C 191 " --> pdb=" O ARG C 187 " (cutoff:3.500A) Proline residue: C 192 - end of helix removed outlier: 3.595A pdb=" N PHE C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 210 through 215 Processing helix chain 'C' and resid 217 through 231 removed outlier: 3.524A pdb=" N HIS C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 263 Processing helix chain 'D' and resid 17 through 36 Processing helix chain 'D' and resid 36 through 41 removed outlier: 4.309A pdb=" N TRP D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 69 removed outlier: 3.712A pdb=" N TRP D 45 " --> pdb=" O LEU D 41 " (cutoff:3.500A) Proline residue: D 50 - end of helix removed outlier: 6.206A pdb=" N LEU D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ALA D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 97 Proline residue: D 84 - end of helix removed outlier: 4.272A pdb=" N LEU D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET D 96 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 removed outlier: 3.554A pdb=" N PHE D 106 " --> pdb=" O ARG D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 143 removed outlier: 3.895A pdb=" N THR D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D 117 " --> pdb=" O PRO D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 176 Processing helix chain 'D' and resid 179 through 197 removed outlier: 3.573A pdb=" N ARG D 183 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) Proline residue: D 192 - end of helix removed outlier: 3.594A pdb=" N PHE D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 210 through 215 Processing helix chain 'D' and resid 217 through 231 removed outlier: 3.508A pdb=" N HIS D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 263 Processing helix chain 'E' and resid 10 through 19 Processing helix chain 'E' and resid 19 through 33 Processing helix chain 'E' and resid 72 through 84 removed outlier: 3.883A pdb=" N HIS E 84 " --> pdb=" O GLN E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 97 Processing helix chain 'E' and resid 97 through 102 Processing helix chain 'E' and resid 118 through 129 Processing helix chain 'E' and resid 149 through 179 removed outlier: 4.080A pdb=" N MET E 175 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN E 179 " --> pdb=" O MET E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 362 removed outlier: 3.541A pdb=" N VAL E 362 " --> pdb=" O VAL E 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 10 removed outlier: 3.823A pdb=" N LEU F 9 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR F 10 " --> pdb=" O VAL F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 19 Processing helix chain 'F' and resid 19 through 32 Processing helix chain 'F' and resid 73 through 84 removed outlier: 3.893A pdb=" N HIS F 84 " --> pdb=" O GLN F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 97 removed outlier: 3.656A pdb=" N LEU F 89 " --> pdb=" O SER F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 103 removed outlier: 3.639A pdb=" N GLY F 103 " --> pdb=" O ARG F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 129 Processing helix chain 'F' and resid 149 through 176 removed outlier: 3.913A pdb=" N ALA F 176 " --> pdb=" O SER F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 371 removed outlier: 3.646A pdb=" N ASN F 344 " --> pdb=" O ARG F 340 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP F 371 " --> pdb=" O ARG F 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 19 Processing helix chain 'G' and resid 19 through 32 Processing helix chain 'G' and resid 72 through 84 removed outlier: 4.022A pdb=" N HIS G 84 " --> pdb=" O GLN G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 97 Processing helix chain 'G' and resid 97 through 103 Processing helix chain 'G' and resid 118 through 129 Processing helix chain 'G' and resid 149 through 180 removed outlier: 3.992A pdb=" N GLN G 179 " --> pdb=" O MET G 175 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY G 180 " --> pdb=" O ALA G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 368 Processing helix chain 'H' and resid 20 through 33 Processing helix chain 'H' and resid 72 through 84 removed outlier: 4.132A pdb=" N HIS H 84 " --> pdb=" O GLN H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 97 removed outlier: 3.826A pdb=" N LEU H 89 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 103 removed outlier: 3.560A pdb=" N GLY H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 112 removed outlier: 3.806A pdb=" N ARG H 112 " --> pdb=" O PRO H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 129 Processing helix chain 'H' and resid 149 through 178 removed outlier: 3.949A pdb=" N MET H 175 " --> pdb=" O LEU H 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 351 Processing helix chain 'I' and resid 10 through 19 Processing helix chain 'I' and resid 19 through 32 Processing helix chain 'I' and resid 72 through 84 removed outlier: 3.828A pdb=" N HIS I 84 " --> pdb=" O GLN I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 97 Processing helix chain 'I' and resid 97 through 102 Processing helix chain 'I' and resid 118 through 129 Processing helix chain 'I' and resid 149 through 178 removed outlier: 3.500A pdb=" N GLN I 154 " --> pdb=" O PRO I 150 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET I 175 " --> pdb=" O LEU I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 340 through 362 removed outlier: 3.610A pdb=" N VAL I 362 " --> pdb=" O VAL I 358 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 10 Processing helix chain 'J' and resid 11 through 19 Processing helix chain 'J' and resid 19 through 32 Processing helix chain 'J' and resid 73 through 84 removed outlier: 3.849A pdb=" N HIS J 84 " --> pdb=" O GLN J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 97 removed outlier: 3.636A pdb=" N LEU J 89 " --> pdb=" O SER J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 103 removed outlier: 3.631A pdb=" N GLY J 103 " --> pdb=" O ARG J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 129 Processing helix chain 'J' and resid 149 through 176 removed outlier: 3.917A pdb=" N ALA J 176 " --> pdb=" O SER J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 371 removed outlier: 3.627A pdb=" N ASN J 344 " --> pdb=" O ARG J 340 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP J 371 " --> pdb=" O ARG J 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 19 Processing helix chain 'K' and resid 19 through 32 Processing helix chain 'K' and resid 72 through 84 removed outlier: 4.045A pdb=" N HIS K 84 " --> pdb=" O GLN K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 97 Processing helix chain 'K' and resid 97 through 103 Processing helix chain 'K' and resid 118 through 129 Processing helix chain 'K' and resid 149 through 180 Processing helix chain 'K' and resid 340 through 368 Processing helix chain 'K' and resid 369 through 371 No H-bonds generated for 'chain 'K' and resid 369 through 371' Processing helix chain 'L' and resid 20 through 31 Processing helix chain 'L' and resid 72 through 84 removed outlier: 4.140A pdb=" N HIS L 84 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 97 removed outlier: 3.810A pdb=" N LEU L 89 " --> pdb=" O SER L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 103 removed outlier: 3.550A pdb=" N GLY L 103 " --> pdb=" O ARG L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 129 Processing helix chain 'L' and resid 149 through 178 removed outlier: 3.780A pdb=" N MET L 175 " --> pdb=" O LEU L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 340 through 351 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 27 removed outlier: 7.171A pdb=" N VAL A 20 " --> pdb=" O TRP A 10 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N TRP A 10 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARG A 22 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR A 8 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LEU A 24 " --> pdb=" O ASN A 6 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 26 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU A 7 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU A 59 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 38 removed outlier: 3.656A pdb=" N GLY A 35 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 195 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 149 removed outlier: 5.759A pdb=" N TYR A 147 " --> pdb=" O ILE A 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 21 through 27 removed outlier: 6.004A pdb=" N LEU B 7 " --> pdb=" O ASN B 23 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASN B 25 " --> pdb=" O ARG B 5 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ARG B 5 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ARG B 27 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLU B 3 " --> pdb=" O ARG B 27 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU B 4 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL B 63 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ASN B 6 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLU B 61 " --> pdb=" O ASN B 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 34 through 38 removed outlier: 3.518A pdb=" N GLY B 35 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL B 195 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 149 removed outlier: 5.993A pdb=" N TYR B 147 " --> pdb=" O ILE B 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 130 through 135 removed outlier: 6.416A pdb=" N VAL E 43 " --> pdb=" O VAL E 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 130 through 134 removed outlier: 6.497A pdb=" N VAL F 43 " --> pdb=" O VAL F 327 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 130 through 135 removed outlier: 7.074A pdb=" N THR G 45 " --> pdb=" O VAL G 326 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL G 326 " --> pdb=" O THR G 45 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG G 47 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU G 324 " --> pdb=" O ARG G 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 130 through 135 removed outlier: 7.203A pdb=" N THR H 45 " --> pdb=" O VAL H 326 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL H 326 " --> pdb=" O THR H 45 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG H 47 " --> pdb=" O LEU H 324 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LEU H 324 " --> pdb=" O ARG H 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 130 through 135 removed outlier: 6.427A pdb=" N VAL I 43 " --> pdb=" O VAL I 327 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 130 through 134 removed outlier: 6.465A pdb=" N VAL J 43 " --> pdb=" O VAL J 327 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 130 through 135 removed outlier: 6.712A pdb=" N THR K 45 " --> pdb=" O VAL K 326 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N VAL K 326 " --> pdb=" O THR K 45 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG K 47 " --> pdb=" O LEU K 324 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU K 324 " --> pdb=" O ARG K 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 130 through 135 removed outlier: 7.223A pdb=" N THR L 45 " --> pdb=" O VAL L 326 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL L 326 " --> pdb=" O THR L 45 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ARG L 47 " --> pdb=" O LEU L 324 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU L 324 " --> pdb=" O ARG L 47 " (cutoff:3.500A) 1243 hydrogen bonds defined for protein. 3645 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6392 1.34 - 1.46: 3797 1.46 - 1.58: 10417 1.58 - 1.70: 0 1.70 - 1.82: 164 Bond restraints: 20770 Sorted by residual: bond pdb=" N VAL E 28 " pdb=" CA VAL E 28 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.11e+00 bond pdb=" N VAL E 25 " pdb=" CA VAL E 25 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.87e+00 bond pdb=" N LEU E 24 " pdb=" CA LEU E 24 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.19e-02 7.06e+03 5.72e+00 bond pdb=" N THR E 27 " pdb=" CA THR E 27 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.26e+00 bond pdb=" N MET E 23 " pdb=" CA MET E 23 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.21e+00 ... (remaining 20765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 27682 2.03 - 4.06: 376 4.06 - 6.08: 88 6.08 - 8.11: 20 8.11 - 10.14: 4 Bond angle restraints: 28170 Sorted by residual: angle pdb=" C ASP L 93 " pdb=" N GLN L 94 " pdb=" CA GLN L 94 " ideal model delta sigma weight residual 122.38 115.94 6.44 1.81e+00 3.05e-01 1.27e+01 angle pdb=" C THR F 10 " pdb=" N ALA F 11 " pdb=" CA ALA F 11 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 angle pdb=" CB MET B 184 " pdb=" CG MET B 184 " pdb=" SD MET B 184 " ideal model delta sigma weight residual 112.70 122.84 -10.14 3.00e+00 1.11e-01 1.14e+01 angle pdb=" CA GLN L 94 " pdb=" CB GLN L 94 " pdb=" CG GLN L 94 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 angle pdb=" C ARG B 22 " pdb=" N ASN B 23 " pdb=" CA ASN B 23 " ideal model delta sigma weight residual 122.46 127.09 -4.63 1.41e+00 5.03e-01 1.08e+01 ... (remaining 28165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 10456 17.93 - 35.87: 1457 35.87 - 53.80: 373 53.80 - 71.73: 82 71.73 - 89.66: 26 Dihedral angle restraints: 12394 sinusoidal: 5044 harmonic: 7350 Sorted by residual: dihedral pdb=" CA MET J 134 " pdb=" C MET J 134 " pdb=" N ASP J 135 " pdb=" CA ASP J 135 " ideal model delta harmonic sigma weight residual 180.00 162.44 17.56 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CG ARG G 144 " pdb=" CD ARG G 144 " pdb=" NE ARG G 144 " pdb=" CZ ARG G 144 " ideal model delta sinusoidal sigma weight residual -180.00 -135.57 -44.43 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CA ASN A 23 " pdb=" C ASN A 23 " pdb=" N LEU A 24 " pdb=" CA LEU A 24 " ideal model delta harmonic sigma weight residual 180.00 164.10 15.90 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 12391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2448 0.044 - 0.088: 548 0.088 - 0.132: 196 0.132 - 0.176: 28 0.176 - 0.219: 4 Chirality restraints: 3224 Sorted by residual: chirality pdb=" CB ILE B 115 " pdb=" CA ILE B 115 " pdb=" CG1 ILE B 115 " pdb=" CG2 ILE B 115 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE D 240 " pdb=" CA ILE D 240 " pdb=" CG1 ILE D 240 " pdb=" CG2 ILE D 240 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ASN A 6 " pdb=" N ASN A 6 " pdb=" C ASN A 6 " pdb=" CB ASN A 6 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.29e-01 ... (remaining 3221 not shown) Planarity restraints: 3536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 74 " -0.045 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO C 75 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 75 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 75 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 11 " -0.010 2.00e-02 2.50e+03 2.00e-02 4.02e+00 pdb=" C ALA F 11 " 0.035 2.00e-02 2.50e+03 pdb=" O ALA F 11 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS F 12 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR D 74 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO D 75 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " 0.028 5.00e-02 4.00e+02 ... (remaining 3533 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1967 2.75 - 3.29: 19517 3.29 - 3.82: 34518 3.82 - 4.36: 37720 4.36 - 4.90: 67189 Nonbonded interactions: 160911 Sorted by model distance: nonbonded pdb=" O MET I 23 " pdb=" OG1 THR I 27 " model vdw 2.210 3.040 nonbonded pdb=" OG SER D 101 " pdb=" OD1 ASN D 102 " model vdw 2.224 3.040 nonbonded pdb=" OG SER C 101 " pdb=" OD1 ASN C 102 " model vdw 2.226 3.040 nonbonded pdb=" O GLN H 90 " pdb=" NE2 GLN H 94 " model vdw 2.255 3.120 nonbonded pdb=" O MET H 23 " pdb=" OG1 THR H 27 " model vdw 2.273 3.040 ... (remaining 160906 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 19 through 50 or resid 72 through 176 or resid 321 through \ 351)) selection = (chain 'F' and resid 19 through 351) selection = (chain 'G' and (resid 19 through 50 or resid 72 through 176 or resid 321 through \ 351)) selection = (chain 'H' and (resid 19 through 50 or resid 72 through 176 or resid 321 through \ 351)) selection = (chain 'I' and (resid 19 through 50 or resid 72 through 176 or resid 321 through \ 351)) selection = (chain 'J' and resid 19 through 351) selection = (chain 'K' and (resid 19 through 50 or resid 72 through 176 or resid 321 through \ 351)) selection = (chain 'L' and (resid 19 through 50 or resid 72 through 176 or resid 321 through \ 351)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.780 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 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 : 0.003 0.044 20770 Z= 0.137 Angle : 0.620 10.140 28170 Z= 0.322 Chirality : 0.043 0.219 3224 Planarity : 0.004 0.068 3536 Dihedral : 17.905 89.663 7634 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.32 % Allowed : 28.39 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 aren not related in a simple way. whole: 0.87 (0.17), residues: 2448 helix: 1.60 (0.13), residues: 1456 sheet: 1.09 (0.34), residues: 280 loop : -1.85 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG H 177 TYR 0.028 0.001 TYR J 78 PHE 0.027 0.001 PHE C 61 TRP 0.022 0.001 TRP I 16 HIS 0.013 0.001 HIS C 65 Details of bonding type rmsd covalent geometry : bond 0.00280 (20770) covalent geometry : angle 0.62034 (28170) hydrogen bonds : bond 0.10695 ( 1243) hydrogen bonds : angle 5.63135 ( 3645) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 413 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 184 MET cc_start: 0.8658 (ttt) cc_final: 0.8336 (mmt) REVERT: B 184 MET cc_start: 0.8507 (tpp) cc_final: 0.8036 (tpt) REVERT: E 23 MET cc_start: 0.8819 (mmm) cc_final: 0.8543 (mmm) outliers start: 7 outliers final: 3 residues processed: 415 average time/residue: 0.1375 time to fit residues: 88.4016 Evaluate side-chains 409 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 406 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain E residue 24 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 ASN F 15 GLN G 173 HIS J 15 GLN K 173 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.141165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.098668 restraints weight = 39820.294| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.60 r_work: 0.3212 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 20770 Z= 0.250 Angle : 0.602 6.841 28170 Z= 0.310 Chirality : 0.044 0.238 3224 Planarity : 0.004 0.061 3536 Dihedral : 4.050 36.740 2800 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.48 % Allowed : 25.00 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 aren not related in a simple way. whole: 1.12 (0.17), residues: 2448 helix: 1.84 (0.13), residues: 1486 sheet: 0.43 (0.32), residues: 304 loop : -1.72 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 177 TYR 0.025 0.002 TYR J 338 PHE 0.017 0.002 PHE D 85 TRP 0.016 0.001 TRP I 16 HIS 0.004 0.001 HIS C 65 Details of bonding type rmsd covalent geometry : bond 0.00589 (20770) covalent geometry : angle 0.60238 (28170) hydrogen bonds : bond 0.04489 ( 1243) hydrogen bonds : angle 4.41033 ( 3645) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 411 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.6970 (p0) REVERT: A 160 PHE cc_start: 0.6559 (OUTLIER) cc_final: 0.5725 (m-80) REVERT: A 212 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7628 (mm) REVERT: B 79 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7339 (mm-40) REVERT: B 83 THR cc_start: 0.5664 (OUTLIER) cc_final: 0.5414 (p) REVERT: B 145 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.6848 (p0) REVERT: C 31 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8298 (tm-30) REVERT: C 139 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8514 (mp) REVERT: D 139 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8450 (mp) REVERT: D 153 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8286 (mp0) REVERT: D 217 ASN cc_start: 0.8831 (t0) cc_final: 0.8612 (t0) REVERT: F 135 ASP cc_start: 0.7914 (p0) cc_final: 0.7696 (p0) REVERT: F 352 CYS cc_start: 0.8281 (m) cc_final: 0.7984 (m) REVERT: I 16 TRP cc_start: 0.7923 (t-100) cc_final: 0.7541 (t-100) REVERT: I 174 ARG cc_start: 0.7419 (mtm180) cc_final: 0.7184 (mtp180) REVERT: J 135 ASP cc_start: 0.7922 (p0) cc_final: 0.7691 (p0) outliers start: 99 outliers final: 42 residues processed: 479 average time/residue: 0.1407 time to fit residues: 104.3754 Evaluate side-chains 447 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 397 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 325 VAL Chi-restraints excluded: chain G residue 353 CYS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 324 LEU Chi-restraints excluded: chain H residue 325 VAL Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 326 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 326 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 65 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN E 169 ASN F 15 GLN G 173 HIS I 169 ASN J 15 GLN K 173 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.142187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.101800 restraints weight = 39021.105| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.48 r_work: 0.3287 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20770 Z= 0.135 Angle : 0.529 6.072 28170 Z= 0.269 Chirality : 0.041 0.206 3224 Planarity : 0.004 0.055 3536 Dihedral : 3.717 17.483 2794 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.12 % Allowed : 26.31 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 aren not related in a simple way. whole: 1.29 (0.17), residues: 2448 helix: 2.01 (0.13), residues: 1482 sheet: 0.43 (0.32), residues: 304 loop : -1.68 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 17 TYR 0.020 0.001 TYR E 20 PHE 0.015 0.001 PHE D 85 TRP 0.010 0.001 TRP I 16 HIS 0.005 0.001 HIS C 65 Details of bonding type rmsd covalent geometry : bond 0.00309 (20770) covalent geometry : angle 0.52893 (28170) hydrogen bonds : bond 0.03826 ( 1243) hydrogen bonds : angle 4.17705 ( 3645) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 417 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7002 (p0) REVERT: A 160 PHE cc_start: 0.6686 (OUTLIER) cc_final: 0.5794 (m-80) REVERT: B 145 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7104 (p0) REVERT: B 184 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8559 (tpt) REVERT: C 31 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8480 (tp30) REVERT: C 139 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8567 (mp) REVERT: D 139 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8485 (mp) REVERT: D 217 ASN cc_start: 0.8826 (t0) cc_final: 0.8517 (t0) REVERT: E 36 ASP cc_start: 0.8634 (p0) cc_final: 0.8392 (p0) REVERT: E 86 MET cc_start: 0.8737 (tpp) cc_final: 0.8453 (tpp) REVERT: E 179 GLN cc_start: 0.6515 (mm-40) cc_final: 0.6132 (mm-40) REVERT: E 356 TYR cc_start: 0.7711 (t80) cc_final: 0.7382 (t80) REVERT: F 135 ASP cc_start: 0.8036 (p0) cc_final: 0.7792 (p0) REVERT: F 352 CYS cc_start: 0.8306 (m) cc_final: 0.8002 (m) REVERT: I 16 TRP cc_start: 0.7845 (t-100) cc_final: 0.7473 (t-100) REVERT: I 86 MET cc_start: 0.8683 (tpp) cc_final: 0.8284 (tpp) REVERT: I 344 ASN cc_start: 0.9223 (m-40) cc_final: 0.8744 (m110) REVERT: J 135 ASP cc_start: 0.8178 (p0) cc_final: 0.7895 (p0) REVERT: L 94 GLN cc_start: 0.7877 (pm20) cc_final: 0.7643 (mp10) outliers start: 69 outliers final: 36 residues processed: 460 average time/residue: 0.1423 time to fit residues: 102.1708 Evaluate side-chains 439 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 397 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 325 VAL Chi-restraints excluded: chain G residue 353 CYS Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 324 LEU Chi-restraints excluded: chain L residue 326 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 201 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 204 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 152 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 55 optimal weight: 0.1980 chunk 151 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 169 ASN F 15 GLN G 173 HIS J 15 GLN K 173 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.143565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.101430 restraints weight = 39712.424| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.64 r_work: 0.3265 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20770 Z= 0.113 Angle : 0.511 6.139 28170 Z= 0.260 Chirality : 0.040 0.185 3224 Planarity : 0.004 0.052 3536 Dihedral : 3.618 16.459 2794 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.44 % Allowed : 26.31 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 aren not related in a simple way. whole: 1.42 (0.17), residues: 2448 helix: 2.11 (0.13), residues: 1484 sheet: 0.86 (0.34), residues: 270 loop : -1.73 (0.21), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 17 TYR 0.023 0.001 TYR E 20 PHE 0.028 0.001 PHE B 21 TRP 0.010 0.001 TRP I 16 HIS 0.005 0.001 HIS C 65 Details of bonding type rmsd covalent geometry : bond 0.00253 (20770) covalent geometry : angle 0.51100 (28170) hydrogen bonds : bond 0.03540 ( 1243) hydrogen bonds : angle 4.05209 ( 3645) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 411 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.6873 (p0) REVERT: A 160 PHE cc_start: 0.6749 (OUTLIER) cc_final: 0.5855 (m-80) REVERT: A 201 GLN cc_start: 0.7409 (mm-40) cc_final: 0.6829 (pm20) REVERT: B 145 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7109 (p0) REVERT: B 184 MET cc_start: 0.9073 (tpt) cc_final: 0.8557 (tpt) REVERT: C 31 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8387 (tp30) REVERT: C 61 PHE cc_start: 0.8675 (m-80) cc_final: 0.8333 (m-80) REVERT: C 139 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8497 (mp) REVERT: D 110 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8145 (mp10) REVERT: D 139 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8494 (mp) REVERT: D 217 ASN cc_start: 0.8799 (t0) cc_final: 0.8378 (t0) REVERT: E 36 ASP cc_start: 0.8462 (p0) cc_final: 0.8142 (p0) REVERT: E 179 GLN cc_start: 0.6836 (mm-40) cc_final: 0.6371 (mm-40) REVERT: E 344 ASN cc_start: 0.9164 (m-40) cc_final: 0.8811 (m110) REVERT: E 356 TYR cc_start: 0.7862 (t80) cc_final: 0.7473 (t80) REVERT: I 16 TRP cc_start: 0.7918 (t-100) cc_final: 0.7645 (t-100) REVERT: I 344 ASN cc_start: 0.9205 (m-40) cc_final: 0.8765 (m110) REVERT: J 135 ASP cc_start: 0.8043 (p0) cc_final: 0.7792 (p0) REVERT: L 94 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7597 (mp10) outliers start: 76 outliers final: 39 residues processed: 457 average time/residue: 0.1359 time to fit residues: 97.1718 Evaluate side-chains 448 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 402 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 325 VAL Chi-restraints excluded: chain G residue 353 CYS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 137 ILE Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 326 VAL Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 324 LEU Chi-restraints excluded: chain L residue 326 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 171 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 chunk 238 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 172 optimal weight: 0.7980 chunk 152 optimal weight: 9.9990 chunk 216 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN G 173 HIS H 94 GLN J 15 GLN K 173 HIS L 48 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.142596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.100620 restraints weight = 39604.229| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.60 r_work: 0.3236 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20770 Z= 0.166 Angle : 0.546 6.513 28170 Z= 0.278 Chirality : 0.042 0.216 3224 Planarity : 0.004 0.053 3536 Dihedral : 3.698 17.829 2794 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.48 % Allowed : 26.81 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 aren not related in a simple way. whole: 1.38 (0.17), residues: 2448 helix: 2.11 (0.13), residues: 1484 sheet: 0.47 (0.33), residues: 290 loop : -1.67 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 177 TYR 0.023 0.001 TYR E 20 PHE 0.015 0.001 PHE C 85 TRP 0.010 0.001 TRP I 16 HIS 0.006 0.001 HIS C 65 Details of bonding type rmsd covalent geometry : bond 0.00389 (20770) covalent geometry : angle 0.54600 (28170) hydrogen bonds : bond 0.03918 ( 1243) hydrogen bonds : angle 4.06313 ( 3645) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 408 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 TYR cc_start: 0.7291 (OUTLIER) cc_final: 0.6015 (t80) REVERT: A 145 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.6730 (p0) REVERT: A 160 PHE cc_start: 0.6778 (OUTLIER) cc_final: 0.6035 (m-80) REVERT: B 102 MET cc_start: 0.8299 (ptp) cc_final: 0.8069 (ptp) REVERT: B 145 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.6876 (p0) REVERT: B 184 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8631 (tpt) REVERT: B 201 GLN cc_start: 0.8549 (mp10) cc_final: 0.8199 (mm-40) REVERT: C 31 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8467 (tp30) REVERT: C 139 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8510 (mp) REVERT: D 110 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8179 (mp10) REVERT: D 139 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8465 (mp) REVERT: D 217 ASN cc_start: 0.8848 (t0) cc_final: 0.8430 (t0) REVERT: E 20 TYR cc_start: 0.8390 (m-80) cc_final: 0.8122 (m-80) REVERT: E 36 ASP cc_start: 0.8496 (p0) cc_final: 0.8171 (p0) REVERT: E 179 GLN cc_start: 0.6703 (mm-40) cc_final: 0.6498 (mm-40) REVERT: E 356 TYR cc_start: 0.7828 (t80) cc_final: 0.7386 (t80) REVERT: F 352 CYS cc_start: 0.8161 (m) cc_final: 0.7875 (m) REVERT: G 371 ASP cc_start: 0.7911 (p0) cc_final: 0.7632 (t70) REVERT: I 344 ASN cc_start: 0.9212 (m-40) cc_final: 0.8711 (m110) REVERT: J 135 ASP cc_start: 0.8013 (p0) cc_final: 0.7802 (p0) REVERT: L 94 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7607 (mp10) outliers start: 77 outliers final: 52 residues processed: 454 average time/residue: 0.1290 time to fit residues: 91.8651 Evaluate side-chains 457 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 396 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 325 VAL Chi-restraints excluded: chain G residue 353 CYS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 324 LEU Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 326 VAL Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 324 LEU Chi-restraints excluded: chain L residue 326 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 1.9990 chunk 72 optimal weight: 0.0670 chunk 164 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 243 optimal weight: 0.0670 chunk 66 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 20.0000 overall best weight: 1.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN G 173 HIS H 94 GLN J 15 GLN K 173 HIS L 48 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.143478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.101753 restraints weight = 39469.396| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.59 r_work: 0.3280 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20770 Z= 0.133 Angle : 0.526 7.139 28170 Z= 0.267 Chirality : 0.041 0.189 3224 Planarity : 0.004 0.051 3536 Dihedral : 3.637 17.114 2794 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.62 % Allowed : 26.63 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 aren not related in a simple way. whole: 1.39 (0.17), residues: 2448 helix: 2.13 (0.13), residues: 1482 sheet: 0.31 (0.32), residues: 304 loop : -1.67 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 177 TYR 0.019 0.001 TYR B 146 PHE 0.021 0.001 PHE D 61 TRP 0.029 0.001 TRP I 16 HIS 0.006 0.001 HIS C 65 Details of bonding type rmsd covalent geometry : bond 0.00309 (20770) covalent geometry : angle 0.52570 (28170) hydrogen bonds : bond 0.03669 ( 1243) hydrogen bonds : angle 4.00304 ( 3645) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 411 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7132 (tpt) cc_final: 0.6922 (tpp) REVERT: A 145 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.6761 (p0) REVERT: A 160 PHE cc_start: 0.6831 (OUTLIER) cc_final: 0.5957 (m-80) REVERT: B 144 PHE cc_start: 0.6876 (m-80) cc_final: 0.6653 (m-10) REVERT: B 145 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.6894 (p0) REVERT: B 184 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8689 (tpt) REVERT: B 201 GLN cc_start: 0.8524 (mp10) cc_final: 0.8224 (mm-40) REVERT: C 31 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8563 (tp30) REVERT: C 61 PHE cc_start: 0.8676 (m-80) cc_final: 0.8324 (m-80) REVERT: C 139 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8532 (mp) REVERT: D 39 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6022 (tpt-90) REVERT: D 110 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8280 (mp10) REVERT: D 139 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8484 (mp) REVERT: D 217 ASN cc_start: 0.8875 (t0) cc_final: 0.8559 (t0) REVERT: E 20 TYR cc_start: 0.8543 (m-80) cc_final: 0.8214 (m-80) REVERT: E 36 ASP cc_start: 0.8717 (p0) cc_final: 0.8410 (p0) REVERT: E 179 GLN cc_start: 0.6655 (mm-40) cc_final: 0.6428 (mm-40) REVERT: E 344 ASN cc_start: 0.9251 (m-40) cc_final: 0.8902 (m110) REVERT: F 166 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8428 (ttp80) REVERT: G 371 ASP cc_start: 0.7955 (p0) cc_final: 0.7636 (t70) REVERT: H 322 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7799 (mtmm) REVERT: I 86 MET cc_start: 0.8681 (tpp) cc_final: 0.8335 (tpp) REVERT: I 344 ASN cc_start: 0.9287 (m-40) cc_final: 0.8854 (m110) REVERT: J 135 ASP cc_start: 0.8114 (p0) cc_final: 0.7843 (p0) REVERT: K 14 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8764 (mp) REVERT: L 94 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7717 (mp10) outliers start: 80 outliers final: 51 residues processed: 459 average time/residue: 0.1441 time to fit residues: 103.1799 Evaluate side-chains 464 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 401 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 325 VAL Chi-restraints excluded: chain G residue 353 CYS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 322 LYS Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 326 VAL Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 324 LEU Chi-restraints excluded: chain L residue 326 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 194 optimal weight: 2.9990 chunk 61 optimal weight: 0.0020 chunk 228 optimal weight: 10.0000 chunk 236 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 32 optimal weight: 0.0670 overall best weight: 2.2132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN G 173 HIS H 94 GLN J 15 GLN K 173 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.141958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.099894 restraints weight = 39752.015| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.60 r_work: 0.3222 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20770 Z= 0.203 Angle : 0.582 7.874 28170 Z= 0.296 Chirality : 0.043 0.228 3224 Planarity : 0.004 0.053 3536 Dihedral : 3.809 18.840 2794 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.02 % Allowed : 26.27 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 aren not related in a simple way. whole: 1.31 (0.17), residues: 2448 helix: 2.07 (0.13), residues: 1484 sheet: 0.23 (0.31), residues: 322 loop : -1.76 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 340 TYR 0.023 0.002 TYR J 338 PHE 0.016 0.001 PHE C 85 TRP 0.015 0.001 TRP I 16 HIS 0.007 0.001 HIS C 65 Details of bonding type rmsd covalent geometry : bond 0.00479 (20770) covalent geometry : angle 0.58172 (28170) hydrogen bonds : bond 0.04164 ( 1243) hydrogen bonds : angle 4.09637 ( 3645) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 403 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 TYR cc_start: 0.7382 (OUTLIER) cc_final: 0.5982 (t80) REVERT: A 145 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.6608 (p0) REVERT: A 160 PHE cc_start: 0.6695 (OUTLIER) cc_final: 0.5829 (m-80) REVERT: B 145 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.6886 (p0) REVERT: B 184 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8701 (tpt) REVERT: B 201 GLN cc_start: 0.8531 (mp10) cc_final: 0.8207 (mm-40) REVERT: C 31 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8411 (tp30) REVERT: C 61 PHE cc_start: 0.8632 (m-80) cc_final: 0.8298 (m-80) REVERT: C 139 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8542 (mp) REVERT: D 39 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.6099 (tpt-90) REVERT: D 110 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8248 (mp10) REVERT: D 139 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8470 (mp) REVERT: D 217 ASN cc_start: 0.8875 (t0) cc_final: 0.8496 (t0) REVERT: E 20 TYR cc_start: 0.8552 (m-80) cc_final: 0.8177 (m-80) REVERT: E 36 ASP cc_start: 0.8542 (p0) cc_final: 0.8224 (p0) REVERT: E 179 GLN cc_start: 0.6759 (mm-40) cc_final: 0.6535 (mm-40) REVERT: E 356 TYR cc_start: 0.7828 (t80) cc_final: 0.7400 (t80) REVERT: F 166 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8351 (ttp80) REVERT: F 352 CYS cc_start: 0.8208 (m) cc_final: 0.7938 (m) REVERT: G 14 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8835 (mp) REVERT: G 371 ASP cc_start: 0.7888 (p0) cc_final: 0.7674 (t70) REVERT: H 94 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7547 (mp10) REVERT: J 135 ASP cc_start: 0.8142 (p0) cc_final: 0.7892 (p0) REVERT: J 166 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8301 (ttp80) REVERT: K 14 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8781 (mp) REVERT: L 94 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7588 (mp10) outliers start: 89 outliers final: 60 residues processed: 461 average time/residue: 0.1495 time to fit residues: 106.4123 Evaluate side-chains 471 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 396 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 325 VAL Chi-restraints excluded: chain G residue 353 CYS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 324 LEU Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 166 ARG Chi-restraints excluded: chain J residue 175 MET Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 326 VAL Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 324 LEU Chi-restraints excluded: chain L residue 326 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 69 optimal weight: 0.9990 chunk 217 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 241 optimal weight: 8.9990 chunk 197 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN G 173 HIS H 94 GLN J 15 GLN K 173 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.143833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.102139 restraints weight = 39790.291| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.60 r_work: 0.3289 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20770 Z= 0.116 Angle : 0.539 8.252 28170 Z= 0.273 Chirality : 0.041 0.211 3224 Planarity : 0.003 0.049 3536 Dihedral : 3.669 16.845 2794 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.57 % Allowed : 26.94 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 aren not related in a simple way. whole: 1.38 (0.17), residues: 2448 helix: 2.12 (0.13), residues: 1486 sheet: 0.31 (0.31), residues: 322 loop : -1.72 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 93 TYR 0.018 0.001 TYR G 343 PHE 0.021 0.001 PHE D 61 TRP 0.020 0.001 TRP I 16 HIS 0.007 0.001 HIS C 65 Details of bonding type rmsd covalent geometry : bond 0.00259 (20770) covalent geometry : angle 0.53913 (28170) hydrogen bonds : bond 0.03593 ( 1243) hydrogen bonds : angle 3.99422 ( 3645) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 408 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7014 (tpt) cc_final: 0.6792 (tpp) REVERT: A 126 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.5983 (t80) REVERT: A 145 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.6598 (p0) REVERT: A 160 PHE cc_start: 0.6740 (OUTLIER) cc_final: 0.5836 (m-80) REVERT: B 145 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7196 (p0) REVERT: B 160 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.5884 (m-80) REVERT: B 184 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8721 (tpt) REVERT: B 201 GLN cc_start: 0.8548 (mp10) cc_final: 0.8240 (mm-40) REVERT: C 31 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8486 (tp30) REVERT: C 61 PHE cc_start: 0.8648 (m-80) cc_final: 0.8306 (m-80) REVERT: C 139 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8522 (mp) REVERT: D 65 HIS cc_start: 0.7588 (t-170) cc_final: 0.7364 (t-170) REVERT: D 110 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8351 (mp10) REVERT: D 139 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8484 (mp) REVERT: E 20 TYR cc_start: 0.8498 (m-80) cc_final: 0.8102 (m-80) REVERT: E 36 ASP cc_start: 0.8740 (p0) cc_final: 0.8440 (p0) REVERT: E 179 GLN cc_start: 0.6599 (mm-40) cc_final: 0.6362 (mm-40) REVERT: E 344 ASN cc_start: 0.9262 (m-40) cc_final: 0.8937 (m110) REVERT: F 166 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8435 (ttp80) REVERT: G 14 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8810 (mp) REVERT: I 36 ASP cc_start: 0.8742 (p0) cc_final: 0.8464 (p0) REVERT: I 86 MET cc_start: 0.8643 (tpp) cc_final: 0.7523 (tpp) REVERT: I 90 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8079 (mp10) REVERT: I 344 ASN cc_start: 0.9272 (m-40) cc_final: 0.8845 (m110) REVERT: J 135 ASP cc_start: 0.8147 (p0) cc_final: 0.7847 (p0) REVERT: K 14 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8760 (mp) REVERT: L 94 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7720 (mp10) outliers start: 79 outliers final: 48 residues processed: 459 average time/residue: 0.1440 time to fit residues: 103.8371 Evaluate side-chains 464 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 402 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 325 VAL Chi-restraints excluded: chain G residue 353 CYS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 324 LEU Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 326 VAL Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 324 LEU Chi-restraints excluded: chain L residue 326 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 162 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 243 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 199 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 242 optimal weight: 0.3980 chunk 233 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 HIS F 15 GLN G 173 HIS J 15 GLN K 173 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.143906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.101973 restraints weight = 39484.588| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.60 r_work: 0.3289 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20770 Z= 0.120 Angle : 0.548 10.752 28170 Z= 0.275 Chirality : 0.041 0.202 3224 Planarity : 0.003 0.051 3536 Dihedral : 3.640 16.577 2794 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.03 % Allowed : 27.17 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 aren not related in a simple way. whole: 1.43 (0.17), residues: 2448 helix: 2.16 (0.13), residues: 1486 sheet: 0.57 (0.32), residues: 302 loop : -1.79 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 93 TYR 0.018 0.001 TYR B 146 PHE 0.014 0.001 PHE C 85 TRP 0.019 0.001 TRP I 16 HIS 0.007 0.001 HIS C 65 Details of bonding type rmsd covalent geometry : bond 0.00272 (20770) covalent geometry : angle 0.54815 (28170) hydrogen bonds : bond 0.03566 ( 1243) hydrogen bonds : angle 3.96088 ( 3645) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 409 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7018 (tpt) cc_final: 0.6797 (tpp) REVERT: A 126 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.5984 (t80) REVERT: A 145 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.6635 (p0) REVERT: A 160 PHE cc_start: 0.6768 (OUTLIER) cc_final: 0.5819 (m-80) REVERT: B 145 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7198 (p0) REVERT: B 184 MET cc_start: 0.9111 (tpt) cc_final: 0.8682 (tpt) REVERT: B 201 GLN cc_start: 0.8559 (mp10) cc_final: 0.8259 (mm-40) REVERT: C 31 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8499 (tp30) REVERT: C 100 ASP cc_start: 0.8375 (p0) cc_final: 0.8148 (p0) REVERT: C 139 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8509 (mp) REVERT: D 39 ARG cc_start: 0.6818 (OUTLIER) cc_final: 0.6022 (tpt-90) REVERT: D 65 HIS cc_start: 0.7617 (t-170) cc_final: 0.7403 (t-170) REVERT: D 100 ASP cc_start: 0.8407 (p0) cc_final: 0.8194 (p0) REVERT: D 110 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8378 (mp10) REVERT: D 139 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8482 (mp) REVERT: D 217 ASN cc_start: 0.8811 (t0) cc_final: 0.8555 (t0) REVERT: E 20 TYR cc_start: 0.8454 (m-80) cc_final: 0.8027 (m-80) REVERT: E 36 ASP cc_start: 0.8715 (p0) cc_final: 0.8403 (p0) REVERT: E 178 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: E 179 GLN cc_start: 0.6574 (mm-40) cc_final: 0.5734 (mp10) REVERT: E 344 ASN cc_start: 0.9261 (m-40) cc_final: 0.8936 (m110) REVERT: E 356 TYR cc_start: 0.7788 (t80) cc_final: 0.7392 (t80) REVERT: G 14 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8797 (mp) REVERT: G 171 LEU cc_start: 0.9007 (tt) cc_final: 0.8770 (mt) REVERT: I 36 ASP cc_start: 0.8715 (p0) cc_final: 0.8445 (p0) REVERT: I 86 MET cc_start: 0.8641 (tpp) cc_final: 0.8322 (tpp) REVERT: I 344 ASN cc_start: 0.9277 (m-40) cc_final: 0.8845 (m110) REVERT: J 135 ASP cc_start: 0.8124 (p0) cc_final: 0.7796 (p0) REVERT: L 94 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7722 (mp10) outliers start: 67 outliers final: 51 residues processed: 452 average time/residue: 0.1441 time to fit residues: 102.4771 Evaluate side-chains 465 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 403 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 325 VAL Chi-restraints excluded: chain G residue 353 CYS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 324 LEU Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 326 VAL Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain L residue 324 LEU Chi-restraints excluded: chain L residue 326 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 172 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 143 optimal weight: 0.8980 chunk 214 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 72 optimal weight: 0.0040 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN G 173 HIS J 15 GLN K 173 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.142906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.100623 restraints weight = 39771.898| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.61 r_work: 0.3237 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20770 Z= 0.174 Angle : 0.581 9.952 28170 Z= 0.293 Chirality : 0.042 0.233 3224 Planarity : 0.004 0.053 3536 Dihedral : 3.748 18.380 2794 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.12 % Allowed : 26.81 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 aren not related in a simple way. whole: 1.34 (0.17), residues: 2448 helix: 2.08 (0.13), residues: 1486 sheet: 0.24 (0.31), residues: 322 loop : -1.72 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 37 TYR 0.019 0.002 TYR K 343 PHE 0.025 0.001 PHE C 61 TRP 0.020 0.001 TRP I 16 HIS 0.008 0.001 HIS C 65 Details of bonding type rmsd covalent geometry : bond 0.00412 (20770) covalent geometry : angle 0.58063 (28170) hydrogen bonds : bond 0.03962 ( 1243) hydrogen bonds : angle 4.03008 ( 3645) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 402 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7189 (tpt) cc_final: 0.6973 (tpp) REVERT: A 126 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.5941 (t80) REVERT: A 145 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6564 (p0) REVERT: A 160 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.5780 (m-80) REVERT: B 145 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7030 (p0) REVERT: B 184 MET cc_start: 0.9114 (tpt) cc_final: 0.8720 (tpt) REVERT: B 201 GLN cc_start: 0.8551 (mp10) cc_final: 0.8227 (mm-40) REVERT: C 31 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8361 (tp30) REVERT: C 100 ASP cc_start: 0.8382 (p0) cc_final: 0.8149 (p0) REVERT: C 139 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8564 (mp) REVERT: D 39 ARG cc_start: 0.6801 (OUTLIER) cc_final: 0.6080 (tpt-90) REVERT: D 100 ASP cc_start: 0.8337 (p0) cc_final: 0.8100 (p0) REVERT: D 110 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8302 (mp10) REVERT: D 139 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8496 (mp) REVERT: D 217 ASN cc_start: 0.8810 (t0) cc_final: 0.8508 (t0) REVERT: E 20 TYR cc_start: 0.8536 (m-80) cc_final: 0.8056 (m-80) REVERT: E 36 ASP cc_start: 0.8528 (p0) cc_final: 0.8200 (p0) REVERT: E 179 GLN cc_start: 0.6786 (mm-40) cc_final: 0.5899 (mp10) REVERT: H 322 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7823 (mtmm) REVERT: I 36 ASP cc_start: 0.8558 (p0) cc_final: 0.8255 (p0) REVERT: I 86 MET cc_start: 0.8558 (tpp) cc_final: 0.8211 (tpp) REVERT: I 344 ASN cc_start: 0.9217 (m-40) cc_final: 0.8718 (m110) REVERT: J 135 ASP cc_start: 0.8004 (p0) cc_final: 0.7754 (p0) REVERT: L 94 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7555 (mp10) outliers start: 69 outliers final: 53 residues processed: 449 average time/residue: 0.1465 time to fit residues: 103.2416 Evaluate side-chains 462 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 399 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 325 VAL Chi-restraints excluded: chain G residue 353 CYS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 322 LYS Chi-restraints excluded: chain H residue 324 LEU Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 326 VAL Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain L residue 324 LEU Chi-restraints excluded: chain L residue 326 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 90 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 241 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 176 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN G 173 HIS I 15 GLN J 15 GLN K 173 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.143821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.103573 restraints weight = 39044.101| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.47 r_work: 0.3299 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20770 Z= 0.130 Angle : 0.553 8.094 28170 Z= 0.279 Chirality : 0.041 0.203 3224 Planarity : 0.004 0.053 3536 Dihedral : 3.672 16.847 2794 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.85 % Allowed : 27.17 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 aren not related in a simple way. whole: 1.37 (0.17), residues: 2448 helix: 2.06 (0.13), residues: 1492 sheet: 0.54 (0.32), residues: 302 loop : -1.71 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 17 TYR 0.022 0.001 TYR G 78 PHE 0.015 0.001 PHE C 85 TRP 0.020 0.001 TRP I 16 HIS 0.014 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00301 (20770) covalent geometry : angle 0.55320 (28170) hydrogen bonds : bond 0.03661 ( 1243) hydrogen bonds : angle 3.98230 ( 3645) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5948.49 seconds wall clock time: 102 minutes 25.43 seconds (6145.43 seconds total)