Starting phenix.real_space_refine on Tue May 20 17:21:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tsw_41601/05_2025/8tsw_41601_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tsw_41601/05_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_41601/05_2025/8tsw_41601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tsw_41601/05_2025/8tsw_41601.map" model { file = "/net/cci-nas-00/data/ceres_data/8tsw_41601/05_2025/8tsw_41601_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tsw_41601/05_2025/8tsw_41601_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.68, per 1000 atoms: 0.57 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: 4.83 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 1.92 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: 5.98 Time building geometry restraints manager: 5.67 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: 0.02 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: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 42.770 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.080 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.210 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.022 0.001 TRP I 16 HIS 0.013 0.001 HIS C 65 PHE 0.027 0.001 PHE C 61 TYR 0.028 0.001 TYR J 78 ARG 0.017 0.000 ARG H 177 Details of bonding type rmsd hydrogen bonds : bond 0.10695 ( 1243) hydrogen bonds : angle 5.63135 ( 3645) covalent geometry : bond 0.00280 (20770) covalent geometry : angle 0.62034 (28170) *********************** 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 : 2.289 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: 0.3095 time to fit residues: 196.8043 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 : 2.246 ------------------------------------------------------------------------------- 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 206 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 191 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.143963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.103992 restraints weight = 39076.838| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.48 r_work: 0.3322 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20770 Z= 0.114 Angle : 0.507 6.358 28170 Z= 0.259 Chirality : 0.040 0.159 3224 Planarity : 0.004 0.057 3536 Dihedral : 3.742 36.409 2800 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.76 % Allowed : 25.99 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.17), residues: 2448 helix: 1.96 (0.13), residues: 1488 sheet: 0.89 (0.33), residues: 284 loop : -1.71 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 16 HIS 0.004 0.000 HIS C 65 PHE 0.016 0.001 PHE D 61 TYR 0.023 0.001 TYR E 20 ARG 0.004 0.000 ARG H 177 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 1243) hydrogen bonds : angle 4.28633 ( 3645) covalent geometry : bond 0.00254 (20770) covalent geometry : angle 0.50711 (28170) *********************** 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 478 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 417 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8022 (mmt) cc_final: 0.7793 (mmp) REVERT: A 145 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7007 (p0) REVERT: A 160 PHE cc_start: 0.6531 (OUTLIER) cc_final: 0.5664 (m-80) REVERT: A 212 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7520 (mm) REVERT: B 123 MET cc_start: 0.7603 (mmt) cc_final: 0.7347 (mmp) REVERT: B 145 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7067 (p0) REVERT: B 146 TYR cc_start: 0.8351 (m-80) cc_final: 0.8092 (m-80) REVERT: B 184 MET cc_start: 0.8603 (tpp) cc_final: 0.8318 (tpt) REVERT: C 31 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8353 (tm-30) REVERT: C 61 PHE cc_start: 0.8732 (m-80) cc_final: 0.8353 (m-80) REVERT: C 139 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8522 (mp) REVERT: C 217 ASN cc_start: 0.8720 (t0) cc_final: 0.8466 (t0) REVERT: D 139 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8456 (mp) REVERT: D 217 ASN cc_start: 0.8766 (t0) cc_final: 0.8520 (t0) REVERT: F 3 MET cc_start: 0.4521 (pmm) cc_final: 0.3795 (pmm) REVERT: F 135 ASP cc_start: 0.7948 (p0) cc_final: 0.7714 (p0) REVERT: F 352 CYS cc_start: 0.8315 (m) cc_final: 0.8095 (m) REVERT: F 366 ILE cc_start: 0.9124 (mm) cc_final: 0.8685 (tp) REVERT: H 94 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7728 (mp10) REVERT: I 86 MET cc_start: 0.8598 (tpp) cc_final: 0.8267 (tpp) REVERT: I 344 ASN cc_start: 0.9235 (m-40) cc_final: 0.8810 (m110) REVERT: J 135 ASP cc_start: 0.7892 (p0) cc_final: 0.7650 (p0) outliers start: 61 outliers final: 22 residues processed: 461 average time/residue: 0.3103 time to fit residues: 223.1428 Evaluate side-chains 431 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 402 time to evaluate : 2.363 ------------------------------------------------------------------------------- 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 109 VAL Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain F residue 21 LEU 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 94 GLN Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 325 VAL 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 162 optimal weight: 0.9980 chunk 239 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 224 optimal weight: 0.7980 chunk 208 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 196 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.143028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.101151 restraints weight = 39207.202| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.60 r_work: 0.3287 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1043 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= 0.140 Angle : 0.520 6.034 28170 Z= 0.264 Chirality : 0.041 0.185 3224 Planarity : 0.004 0.053 3536 Dihedral : 3.583 16.795 2794 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.30 % Allowed : 25.68 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.17), residues: 2448 helix: 2.10 (0.13), residues: 1488 sheet: 0.79 (0.33), residues: 284 loop : -1.69 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 16 HIS 0.005 0.000 HIS C 65 PHE 0.015 0.001 PHE D 85 TYR 0.020 0.001 TYR E 20 ARG 0.006 0.000 ARG A 17 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 1243) hydrogen bonds : angle 4.11814 ( 3645) covalent geometry : bond 0.00323 (20770) covalent geometry : angle 0.52033 (28170) *********************** 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 477 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 404 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8125 (mmt) cc_final: 0.7895 (mmp) REVERT: A 145 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7038 (p0) REVERT: A 160 PHE cc_start: 0.6649 (OUTLIER) cc_final: 0.5753 (m-80) REVERT: B 123 MET cc_start: 0.7758 (mmt) cc_final: 0.7535 (mmp) REVERT: B 145 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.6974 (p0) REVERT: C 61 PHE cc_start: 0.8690 (m-80) cc_final: 0.8323 (m-80) REVERT: C 139 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8492 (mp) REVERT: C 217 ASN cc_start: 0.8835 (t0) cc_final: 0.8519 (t0) REVERT: D 139 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8450 (mp) REVERT: D 217 ASN cc_start: 0.8820 (t0) cc_final: 0.8484 (t0) REVERT: E 179 GLN cc_start: 0.6496 (mm-40) cc_final: 0.6101 (mm-40) REVERT: E 356 TYR cc_start: 0.7757 (t80) cc_final: 0.7463 (t80) REVERT: F 135 ASP cc_start: 0.7992 (p0) cc_final: 0.7722 (p0) REVERT: F 352 CYS cc_start: 0.8344 (m) cc_final: 0.8017 (m) REVERT: F 366 ILE cc_start: 0.9170 (mm) cc_final: 0.8747 (tp) REVERT: H 94 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7672 (mp10) REVERT: I 344 ASN cc_start: 0.9257 (m-40) cc_final: 0.8824 (m110) REVERT: J 135 ASP cc_start: 0.8059 (p0) cc_final: 0.7754 (p0) outliers start: 73 outliers final: 35 residues processed: 450 average time/residue: 0.2954 time to fit residues: 205.4806 Evaluate side-chains 430 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 389 time to evaluate : 2.087 ------------------------------------------------------------------------------- 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 140 MET Chi-restraints excluded: chain B residue 145 ASP 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 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 78 LEU 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 331 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 165 GLU 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 94 GLN 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 49 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 331 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 321 LEU Chi-restraints excluded: chain K residue 326 VAL Chi-restraints excluded: chain L residue 24 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 56 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 11 optimal weight: 0.0000 chunk 108 optimal weight: 0.7980 chunk 151 optimal weight: 9.9990 chunk 240 optimal weight: 9.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.143459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.101663 restraints weight = 39662.477| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.61 r_work: 0.3290 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1181 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= 0.128 Angle : 0.511 6.306 28170 Z= 0.260 Chirality : 0.040 0.183 3224 Planarity : 0.004 0.052 3536 Dihedral : 3.577 16.639 2794 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.25 % Allowed : 26.40 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.17), residues: 2448 helix: 2.14 (0.13), residues: 1488 sheet: 0.90 (0.34), residues: 270 loop : -1.66 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 16 HIS 0.005 0.001 HIS C 65 PHE 0.020 0.001 PHE D 61 TYR 0.021 0.001 TYR B 146 ARG 0.004 0.000 ARG A 17 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 1243) hydrogen bonds : angle 4.03221 ( 3645) covalent geometry : bond 0.00293 (20770) covalent geometry : angle 0.51119 (28170) *********************** 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 483 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 411 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7994 (mmt) cc_final: 0.7782 (mmp) REVERT: A 145 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.6928 (p0) REVERT: A 160 PHE cc_start: 0.6748 (OUTLIER) cc_final: 0.5804 (m-80) REVERT: A 201 GLN cc_start: 0.7344 (mm-40) cc_final: 0.6697 (pm20) REVERT: B 123 MET cc_start: 0.7757 (mmt) cc_final: 0.7549 (mmp) REVERT: B 144 PHE cc_start: 0.6842 (m-80) cc_final: 0.6608 (m-10) REVERT: B 145 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7118 (p0) REVERT: B 184 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8632 (tpt) REVERT: B 201 GLN cc_start: 0.8530 (mp10) cc_final: 0.8251 (mm-40) REVERT: C 61 PHE cc_start: 0.8717 (m-80) cc_final: 0.8318 (m-80) REVERT: C 139 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8489 (mp) REVERT: C 217 ASN cc_start: 0.8808 (t0) cc_final: 0.8554 (t0) REVERT: D 139 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8470 (mp) REVERT: D 217 ASN cc_start: 0.8865 (t0) cc_final: 0.8443 (t0) REVERT: E 20 TYR cc_start: 0.8298 (m-80) cc_final: 0.7978 (m-80) REVERT: E 179 GLN cc_start: 0.6539 (mm-40) cc_final: 0.6096 (mm-40) REVERT: E 356 TYR cc_start: 0.7775 (t80) cc_final: 0.7383 (t80) REVERT: F 3 MET cc_start: 0.4082 (pmm) cc_final: 0.3245 (pmm) REVERT: F 135 ASP cc_start: 0.8061 (p0) cc_final: 0.7806 (p0) REVERT: F 352 CYS cc_start: 0.8344 (m) cc_final: 0.8028 (m) REVERT: F 366 ILE cc_start: 0.9191 (mm) cc_final: 0.8769 (tp) REVERT: H 94 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7761 (mp10) REVERT: I 344 ASN cc_start: 0.9268 (m-40) cc_final: 0.8844 (m110) REVERT: J 135 ASP cc_start: 0.8089 (p0) cc_final: 0.7769 (p0) outliers start: 72 outliers final: 41 residues processed: 456 average time/residue: 0.2914 time to fit residues: 207.2856 Evaluate side-chains 442 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 394 time to evaluate : 2.252 ------------------------------------------------------------------------------- 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 B residue 184 MET 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 139 LEU 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 139 LEU 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 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 363 VAL Chi-restraints excluded: chain G residue 23 MET 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 94 GLN Chi-restraints excluded: chain H residue 110 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 49 THR Chi-restraints excluded: chain I residue 90 GLN 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 46 VAL 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 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 30 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 183 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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** E 169 ASN F 15 GLN G 173 HIS I 169 ASN J 15 GLN K 173 HIS ** L 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 94 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.141585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.099340 restraints weight = 39871.891| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.60 r_work: 0.3215 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20770 Z= 0.230 Angle : 0.593 7.060 28170 Z= 0.302 Chirality : 0.043 0.252 3224 Planarity : 0.004 0.055 3536 Dihedral : 3.828 19.307 2794 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.29 % Allowed : 25.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.17), residues: 2448 helix: 2.04 (0.13), residues: 1488 sheet: 0.47 (0.32), residues: 308 loop : -1.68 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 16 HIS 0.006 0.001 HIS C 65 PHE 0.030 0.001 PHE B 21 TYR 0.026 0.002 TYR F 338 ARG 0.004 0.000 ARG J 37 Details of bonding type rmsd hydrogen bonds : bond 0.04339 ( 1243) hydrogen bonds : angle 4.12585 ( 3645) covalent geometry : bond 0.00543 (20770) covalent geometry : angle 0.59295 (28170) *********************** 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 495 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 400 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8795 (mtpp) cc_final: 0.8555 (mtpp) REVERT: A 126 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.5727 (t80) REVERT: A 145 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.6793 (p0) REVERT: A 160 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.5913 (m-80) REVERT: B 102 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8023 (ptp) REVERT: B 144 PHE cc_start: 0.6824 (m-80) cc_final: 0.6622 (m-10) REVERT: B 145 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.6841 (p0) REVERT: B 184 MET cc_start: 0.9082 (tpt) cc_final: 0.8607 (tpt) REVERT: B 201 GLN cc_start: 0.8526 (mp10) cc_final: 0.8232 (mm-40) REVERT: C 61 PHE cc_start: 0.8661 (m-80) cc_final: 0.8267 (m-80) REVERT: C 139 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8533 (mp) REVERT: C 217 ASN cc_start: 0.8879 (t0) cc_final: 0.8647 (t0) REVERT: D 39 ARG cc_start: 0.6810 (OUTLIER) cc_final: 0.6062 (tpt-90) REVERT: D 110 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8166 (mp10) REVERT: D 217 ASN cc_start: 0.8910 (t0) cc_final: 0.8501 (t0) REVERT: E 20 TYR cc_start: 0.8427 (m-80) cc_final: 0.8101 (m-80) REVERT: E 356 TYR cc_start: 0.7830 (t80) cc_final: 0.7426 (t80) REVERT: F 135 ASP cc_start: 0.7918 (p0) cc_final: 0.7695 (p0) REVERT: F 366 ILE cc_start: 0.9169 (mm) cc_final: 0.8823 (tp) REVERT: I 16 TRP cc_start: 0.7794 (t-100) cc_final: 0.7549 (t-100) REVERT: I 23 MET cc_start: 0.8861 (tpp) cc_final: 0.8418 (mmm) REVERT: J 135 ASP cc_start: 0.8049 (p0) cc_final: 0.7827 (p0) outliers start: 95 outliers final: 57 residues processed: 460 average time/residue: 0.2842 time to fit residues: 203.7265 Evaluate side-chains 456 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 391 time to evaluate : 2.101 ------------------------------------------------------------------------------- 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 102 MET 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 215 TYR Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 59 THR 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 102 ASN Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 224 GLU 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 60 LEU 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 224 GLU Chi-restraints excluded: chain E residue 10 THR 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 350 VAL Chi-restraints excluded: chain F residue 363 VAL 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 110 LEU 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 165 GLU Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 363 VAL 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 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 205 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 184 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 I 15 GLN J 15 GLN K 173 HIS L 94 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.143593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.101985 restraints weight = 39421.196| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.59 r_work: 0.3294 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20770 Z= 0.110 Angle : 0.519 7.322 28170 Z= 0.263 Chirality : 0.040 0.196 3224 Planarity : 0.003 0.052 3536 Dihedral : 3.626 17.042 2794 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.30 % Allowed : 26.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.17), residues: 2448 helix: 2.11 (0.13), residues: 1486 sheet: 0.55 (0.33), residues: 290 loop : -1.58 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 16 HIS 0.006 0.001 HIS C 65 PHE 0.020 0.001 PHE D 61 TYR 0.019 0.001 TYR B 146 ARG 0.005 0.000 ARG K 177 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 1243) hydrogen bonds : angle 3.99802 ( 3645) covalent geometry : bond 0.00245 (20770) covalent geometry : angle 0.51925 (28170) *********************** 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 484 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 411 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7102 (tpt) cc_final: 0.6893 (tpp) REVERT: A 89 LYS cc_start: 0.8791 (mtpp) cc_final: 0.8495 (mtpp) REVERT: A 126 TYR cc_start: 0.7267 (OUTLIER) cc_final: 0.5820 (t80) REVERT: A 145 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.6901 (p0) REVERT: A 160 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.5968 (m-80) REVERT: B 102 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8134 (ptp) REVERT: B 144 PHE cc_start: 0.6935 (m-80) cc_final: 0.6712 (m-10) REVERT: B 145 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.6904 (p0) REVERT: B 160 PHE cc_start: 0.6501 (OUTLIER) cc_final: 0.5781 (m-80) REVERT: B 184 MET cc_start: 0.9116 (tpt) cc_final: 0.8639 (tpt) REVERT: B 201 GLN cc_start: 0.8544 (mp10) cc_final: 0.8273 (mm-40) REVERT: C 61 PHE cc_start: 0.8676 (m-80) cc_final: 0.8274 (m-80) REVERT: C 139 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8507 (mp) REVERT: C 217 ASN cc_start: 0.8848 (t0) cc_final: 0.8563 (t0) REVERT: D 110 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8182 (mp10) REVERT: D 139 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8477 (mp) REVERT: D 217 ASN cc_start: 0.8883 (t0) cc_final: 0.8445 (t0) REVERT: E 20 TYR cc_start: 0.8507 (m-80) cc_final: 0.8137 (m-80) REVERT: E 179 GLN cc_start: 0.6328 (mm-40) cc_final: 0.5979 (mm-40) REVERT: E 344 ASN cc_start: 0.9243 (m-40) cc_final: 0.8921 (m110) REVERT: F 135 ASP cc_start: 0.8059 (p0) cc_final: 0.7805 (p0) REVERT: F 366 ILE cc_start: 0.9197 (mm) cc_final: 0.8765 (tp) REVERT: I 16 TRP cc_start: 0.7769 (t-100) cc_final: 0.7470 (t-100) REVERT: I 36 ASP cc_start: 0.8721 (p0) cc_final: 0.8443 (p0) REVERT: I 86 MET cc_start: 0.8645 (tpp) cc_final: 0.7390 (tpp) REVERT: I 90 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8010 (mp10) REVERT: I 344 ASN cc_start: 0.9250 (m-40) cc_final: 0.8827 (m110) REVERT: J 135 ASP cc_start: 0.8202 (p0) cc_final: 0.7932 (p0) REVERT: K 14 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8765 (mp) REVERT: K 177 ARG cc_start: 0.7854 (ttm110) cc_final: 0.7375 (ttp-110) outliers start: 73 outliers final: 41 residues processed: 457 average time/residue: 0.2987 time to fit residues: 211.9711 Evaluate side-chains 456 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 404 time to evaluate : 2.499 ------------------------------------------------------------------------------- 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 102 MET 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 160 PHE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 215 TYR 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 139 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 54 ILE 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 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 321 LEU 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 24 LEU Chi-restraints excluded: chain H residue 40 SER 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 162 GLU 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 46 VAL Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 326 VAL Chi-restraints excluded: chain L residue 110 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 230 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 2 optimal weight: 0.0870 chunk 190 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 204 optimal weight: 0.6980 overall best weight: 1.3562 ------------------------------------------------------------------------------- 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 94 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.142651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.100826 restraints weight = 39543.647| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.60 r_work: 0.3274 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1417 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= 0.143 Angle : 0.539 8.003 28170 Z= 0.273 Chirality : 0.041 0.204 3224 Planarity : 0.004 0.052 3536 Dihedral : 3.659 17.416 2794 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.57 % Allowed : 26.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.17), residues: 2448 helix: 2.16 (0.13), residues: 1478 sheet: 0.59 (0.32), residues: 302 loop : -1.79 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 16 HIS 0.006 0.001 HIS C 65 PHE 0.014 0.001 PHE C 85 TYR 0.025 0.001 TYR C 194 ARG 0.005 0.000 ARG L 177 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 1243) hydrogen bonds : angle 3.99536 ( 3645) covalent geometry : bond 0.00332 (20770) covalent geometry : angle 0.53875 (28170) *********************** 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 489 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 410 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7214 (tpt) cc_final: 0.7003 (tpp) REVERT: A 89 LYS cc_start: 0.8770 (mtpp) cc_final: 0.8445 (mtpp) REVERT: A 126 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.5900 (t80) REVERT: A 145 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.6721 (p0) REVERT: A 160 PHE cc_start: 0.6724 (OUTLIER) cc_final: 0.5825 (m-80) REVERT: B 102 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8156 (ptp) REVERT: B 144 PHE cc_start: 0.6968 (m-80) cc_final: 0.6734 (m-10) REVERT: B 145 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.6902 (p0) REVERT: B 160 PHE cc_start: 0.6517 (OUTLIER) cc_final: 0.5738 (m-80) REVERT: B 184 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8701 (tpt) REVERT: B 201 GLN cc_start: 0.8508 (mp10) cc_final: 0.8245 (mm-40) REVERT: C 61 PHE cc_start: 0.8653 (m-80) cc_final: 0.8253 (m-80) REVERT: C 139 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8515 (mp) REVERT: C 217 ASN cc_start: 0.8871 (t0) cc_final: 0.8619 (t0) REVERT: D 110 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8237 (mp10) REVERT: D 139 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8479 (mp) REVERT: D 217 ASN cc_start: 0.8909 (t0) cc_final: 0.8477 (t0) REVERT: E 20 TYR cc_start: 0.8566 (m-80) cc_final: 0.8093 (m-80) REVERT: E 179 GLN cc_start: 0.6273 (mm-40) cc_final: 0.5873 (mm-40) REVERT: E 356 TYR cc_start: 0.7821 (t80) cc_final: 0.7385 (t80) REVERT: F 135 ASP cc_start: 0.8080 (p0) cc_final: 0.7832 (p0) REVERT: F 166 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8448 (ttp80) REVERT: F 366 ILE cc_start: 0.9197 (mm) cc_final: 0.8765 (tp) REVERT: G 14 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8806 (mp) REVERT: I 16 TRP cc_start: 0.7825 (t-100) cc_final: 0.7537 (t-100) REVERT: I 36 ASP cc_start: 0.8737 (p0) cc_final: 0.8451 (p0) REVERT: I 344 ASN cc_start: 0.9287 (m-40) cc_final: 0.8830 (m110) REVERT: J 135 ASP cc_start: 0.8216 (p0) cc_final: 0.7915 (p0) REVERT: L 94 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7714 (mp10) outliers start: 79 outliers final: 54 residues processed: 457 average time/residue: 0.2878 time to fit residues: 204.7355 Evaluate side-chains 474 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 407 time to evaluate : 2.141 ------------------------------------------------------------------------------- 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 102 MET 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 160 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 63 LEU Chi-restraints excluded: chain C residue 78 LEU 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 60 LEU 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 E residue 10 THR 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 321 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 368 ASP 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 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 162 GLU 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 37 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 121 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 194 optimal weight: 0.4980 chunk 87 optimal weight: 5.9990 chunk 174 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 L 94 GLN 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 = 0.143965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.102317 restraints weight = 39747.613| |-----------------------------------------------------------------------------| 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: 0.3156 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1427 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= 0.121 Angle : 0.535 7.778 28170 Z= 0.271 Chirality : 0.041 0.202 3224 Planarity : 0.003 0.050 3536 Dihedral : 3.624 16.774 2794 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.21 % Allowed : 26.85 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.17), residues: 2448 helix: 2.13 (0.13), residues: 1484 sheet: 0.63 (0.32), residues: 302 loop : -1.76 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 16 HIS 0.007 0.001 HIS D 65 PHE 0.022 0.001 PHE D 61 TYR 0.022 0.001 TYR C 194 ARG 0.009 0.000 ARG L 177 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 1243) hydrogen bonds : angle 3.96056 ( 3645) covalent geometry : bond 0.00275 (20770) covalent geometry : angle 0.53457 (28170) *********************** 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 480 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 409 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7097 (tpt) cc_final: 0.6874 (tpp) REVERT: A 89 LYS cc_start: 0.8744 (mtpp) cc_final: 0.8470 (mtpp) REVERT: A 145 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.6764 (p0) REVERT: A 160 PHE cc_start: 0.6650 (OUTLIER) cc_final: 0.5823 (m-80) REVERT: B 83 THR cc_start: 0.5459 (OUTLIER) cc_final: 0.5131 (p) REVERT: B 102 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8110 (ptp) REVERT: B 123 MET cc_start: 0.7957 (mmt) cc_final: 0.7753 (mmp) REVERT: B 144 PHE cc_start: 0.6935 (m-80) cc_final: 0.6688 (m-10) REVERT: B 145 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.6931 (p0) REVERT: B 160 PHE cc_start: 0.6454 (OUTLIER) cc_final: 0.5686 (m-80) REVERT: B 184 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8665 (tpt) REVERT: B 201 GLN cc_start: 0.8511 (mp10) cc_final: 0.8266 (mm-40) REVERT: C 61 PHE cc_start: 0.8651 (m-80) cc_final: 0.8256 (m-80) REVERT: C 139 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8517 (mp) REVERT: C 217 ASN cc_start: 0.8853 (t0) cc_final: 0.8594 (t0) REVERT: D 110 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8233 (mp10) REVERT: D 139 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8494 (mp) REVERT: D 217 ASN cc_start: 0.8889 (t0) cc_final: 0.8459 (t0) REVERT: E 20 TYR cc_start: 0.8605 (m-80) cc_final: 0.7990 (m-80) REVERT: E 179 GLN cc_start: 0.6294 (mm-40) cc_final: 0.5868 (mm-40) REVERT: E 344 ASN cc_start: 0.9259 (m-40) cc_final: 0.8921 (m110) REVERT: E 356 TYR cc_start: 0.7806 (t80) cc_final: 0.7357 (t80) REVERT: F 135 ASP cc_start: 0.8061 (p0) cc_final: 0.7815 (p0) REVERT: F 366 ILE cc_start: 0.9183 (mm) cc_final: 0.8759 (tp) REVERT: G 14 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8778 (mp) REVERT: I 16 TRP cc_start: 0.7795 (t-100) cc_final: 0.7595 (t-100) REVERT: I 36 ASP cc_start: 0.8715 (p0) cc_final: 0.8431 (p0) REVERT: I 86 MET cc_start: 0.8642 (tpp) cc_final: 0.7497 (tpp) REVERT: I 90 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8052 (mp10) REVERT: I 344 ASN cc_start: 0.9271 (m-40) cc_final: 0.8834 (m110) REVERT: J 135 ASP cc_start: 0.8178 (p0) cc_final: 0.7900 (p0) REVERT: K 14 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8750 (mp) REVERT: K 177 ARG cc_start: 0.7787 (ttm110) cc_final: 0.7289 (ttp-110) outliers start: 71 outliers final: 50 residues processed: 454 average time/residue: 0.2919 time to fit residues: 206.2980 Evaluate side-chains 468 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 405 time to evaluate : 2.430 ------------------------------------------------------------------------------- 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 63 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 102 MET 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 160 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 60 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 78 LEU 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 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 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 321 LEU 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 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 I residue 331 VAL 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 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 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 22 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 chunk 177 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 6 optimal weight: 0.0060 chunk 41 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 219 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.144113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.102487 restraints weight = 39701.114| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.59 r_work: 0.3262 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1440 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 : 0.548 7.898 28170 Z= 0.277 Chirality : 0.041 0.200 3224 Planarity : 0.004 0.050 3536 Dihedral : 3.645 17.068 2794 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.30 % Allowed : 26.81 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.17), residues: 2448 helix: 2.09 (0.13), residues: 1500 sheet: 0.61 (0.32), residues: 302 loop : -1.76 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 16 HIS 0.007 0.001 HIS C 65 PHE 0.014 0.001 PHE D 85 TYR 0.022 0.001 TYR C 194 ARG 0.008 0.000 ARG L 177 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 1243) hydrogen bonds : angle 3.97016 ( 3645) covalent geometry : bond 0.00308 (20770) covalent geometry : angle 0.54841 (28170) *********************** 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 477 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 404 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7091 (tpt) cc_final: 0.6872 (tpp) REVERT: A 89 LYS cc_start: 0.8569 (mtpp) cc_final: 0.8315 (mtpp) REVERT: A 126 TYR cc_start: 0.7277 (OUTLIER) cc_final: 0.5846 (t80) REVERT: A 145 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6620 (p0) REVERT: A 160 PHE cc_start: 0.6639 (OUTLIER) cc_final: 0.5752 (m-80) REVERT: B 102 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8041 (ptp) REVERT: B 123 MET cc_start: 0.7943 (mmt) cc_final: 0.7706 (mmp) REVERT: B 145 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.6905 (p0) REVERT: B 160 PHE cc_start: 0.6409 (OUTLIER) cc_final: 0.5657 (m-80) REVERT: B 184 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8709 (tpt) REVERT: B 201 GLN cc_start: 0.8496 (mp10) cc_final: 0.8234 (mm-40) REVERT: C 61 PHE cc_start: 0.8628 (m-80) cc_final: 0.8216 (m-80) REVERT: C 100 ASP cc_start: 0.8278 (p0) cc_final: 0.8030 (p0) REVERT: C 139 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8497 (mp) REVERT: C 217 ASN cc_start: 0.8820 (t0) cc_final: 0.8551 (t0) REVERT: D 100 ASP cc_start: 0.8364 (p0) cc_final: 0.8128 (p0) REVERT: D 110 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8156 (mp10) REVERT: D 139 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8473 (mp) REVERT: D 217 ASN cc_start: 0.8846 (t0) cc_final: 0.8450 (t0) REVERT: E 20 TYR cc_start: 0.8629 (m-80) cc_final: 0.8119 (m-80) REVERT: E 179 GLN cc_start: 0.6448 (mm-40) cc_final: 0.6037 (mm-40) REVERT: E 344 ASN cc_start: 0.9204 (m-40) cc_final: 0.8834 (m110) REVERT: F 134 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8351 (ttp) REVERT: F 135 ASP cc_start: 0.7949 (p0) cc_final: 0.7738 (p0) REVERT: F 366 ILE cc_start: 0.9162 (mm) cc_final: 0.8745 (tp) REVERT: G 14 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8793 (mp) REVERT: I 36 ASP cc_start: 0.8514 (p0) cc_final: 0.8218 (p0) REVERT: I 86 MET cc_start: 0.8466 (tpp) cc_final: 0.8119 (tpp) REVERT: I 344 ASN cc_start: 0.9210 (m-40) cc_final: 0.8739 (m110) REVERT: J 135 ASP cc_start: 0.8003 (p0) cc_final: 0.7744 (p0) REVERT: K 14 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8743 (mp) REVERT: K 177 ARG cc_start: 0.7711 (ttm110) cc_final: 0.7243 (ttp-110) outliers start: 73 outliers final: 53 residues processed: 450 average time/residue: 0.2885 time to fit residues: 202.1102 Evaluate side-chains 470 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 404 time to evaluate : 2.095 ------------------------------------------------------------------------------- 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 102 MET 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 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 78 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 237 LEU 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 331 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 321 LEU 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 175 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 30.0000 chunk 90 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.143464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.101691 restraints weight = 39584.988| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.59 r_work: 0.3281 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1494 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= 0.144 Angle : 0.575 16.609 28170 Z= 0.289 Chirality : 0.042 0.206 3224 Planarity : 0.004 0.051 3536 Dihedral : 3.681 17.414 2794 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.16 % Allowed : 26.99 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.17), residues: 2448 helix: 2.04 (0.13), residues: 1500 sheet: 0.59 (0.32), residues: 302 loop : -1.75 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP I 16 HIS 0.013 0.001 HIS D 65 PHE 0.023 0.001 PHE D 61 TYR 0.021 0.001 TYR C 194 ARG 0.008 0.000 ARG L 177 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 1243) hydrogen bonds : angle 4.01562 ( 3645) covalent geometry : bond 0.00335 (20770) covalent geometry : angle 0.57450 (28170) ********************** 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 475 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 405 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7127 (tpt) cc_final: 0.6894 (tpp) REVERT: A 126 TYR cc_start: 0.7335 (OUTLIER) cc_final: 0.5950 (t80) REVERT: A 145 ASP cc_start: 0.7152 (OUTLIER) cc_final: 0.6442 (p0) REVERT: A 160 PHE cc_start: 0.6632 (OUTLIER) cc_final: 0.5713 (m-80) REVERT: A 163 LYS cc_start: 0.7748 (pttm) cc_final: 0.7506 (pttm) REVERT: B 102 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8120 (ptp) REVERT: B 123 MET cc_start: 0.7971 (mmt) cc_final: 0.7722 (mmp) REVERT: B 145 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.6962 (p0) REVERT: B 160 PHE cc_start: 0.6575 (OUTLIER) cc_final: 0.5789 (m-80) REVERT: B 184 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8742 (tpt) REVERT: C 61 PHE cc_start: 0.8668 (m-80) cc_final: 0.8253 (m-80) REVERT: C 100 ASP cc_start: 0.8383 (p0) cc_final: 0.8159 (p0) REVERT: C 139 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8520 (mp) REVERT: C 217 ASN cc_start: 0.8867 (t0) cc_final: 0.8616 (t0) REVERT: D 100 ASP cc_start: 0.8473 (p0) cc_final: 0.8262 (p0) REVERT: D 110 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8229 (mp10) REVERT: D 139 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8493 (mp) REVERT: D 217 ASN cc_start: 0.8899 (t0) cc_final: 0.8517 (t0) REVERT: E 20 TYR cc_start: 0.8668 (m-80) cc_final: 0.8237 (m-80) REVERT: E 179 GLN cc_start: 0.6332 (mm-40) cc_final: 0.5932 (mm-40) REVERT: E 356 TYR cc_start: 0.7816 (t80) cc_final: 0.7403 (t80) REVERT: F 134 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8553 (ttp) REVERT: F 135 ASP cc_start: 0.8089 (p0) cc_final: 0.7822 (p0) REVERT: F 166 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8438 (ttp80) REVERT: F 366 ILE cc_start: 0.9180 (mm) cc_final: 0.8768 (tp) REVERT: G 14 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8782 (mp) REVERT: I 36 ASP cc_start: 0.8736 (p0) cc_final: 0.8457 (p0) REVERT: I 86 MET cc_start: 0.8680 (tpp) cc_final: 0.8329 (tpp) REVERT: I 344 ASN cc_start: 0.9281 (m-40) cc_final: 0.8833 (m110) REVERT: J 135 ASP cc_start: 0.8140 (p0) cc_final: 0.7806 (p0) REVERT: K 177 ARG cc_start: 0.7883 (ttm110) cc_final: 0.7411 (ttp-110) outliers start: 70 outliers final: 54 residues processed: 450 average time/residue: 0.3049 time to fit residues: 213.1685 Evaluate side-chains 470 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 403 time to evaluate : 2.422 ------------------------------------------------------------------------------- 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 102 MET 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 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 78 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 45 TRP 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 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 331 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 166 ARG 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 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 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 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 110 LEU 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 64 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 59 optimal weight: 0.0040 chunk 116 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 210 optimal weight: 6.9990 chunk 184 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- 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 = 0.142701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.102197 restraints weight = 39258.438| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.48 r_work: 0.3285 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1550 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= 0.158 Angle : 0.580 14.998 28170 Z= 0.292 Chirality : 0.042 0.215 3224 Planarity : 0.004 0.051 3536 Dihedral : 3.718 17.906 2794 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.25 % Allowed : 26.90 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.17), residues: 2448 helix: 2.04 (0.13), residues: 1496 sheet: 0.56 (0.32), residues: 302 loop : -1.75 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP I 16 HIS 0.013 0.001 HIS D 65 PHE 0.015 0.001 PHE D 85 TYR 0.021 0.001 TYR C 194 ARG 0.008 0.000 ARG L 177 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 1243) hydrogen bonds : angle 4.02903 ( 3645) covalent geometry : bond 0.00371 (20770) covalent geometry : angle 0.58041 (28170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12446.51 seconds wall clock time: 215 minutes 16.80 seconds (12916.80 seconds total)