Starting phenix.real_space_refine on Wed Aug 7 15:50:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsw_41601/08_2024/8tsw_41601_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsw_41601/08_2024/8tsw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsw_41601/08_2024/8tsw_41601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsw_41601/08_2024/8tsw_41601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsw_41601/08_2024/8tsw_41601_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsw_41601/08_2024/8tsw_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 Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "E GLU 41": "OE1" <-> "OE2" Residue "I GLU 74": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 11.53, 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 - 3.50 Amino acid : False - 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: 7.88 Conformation dependent library (CDL) restraints added in 3.6 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: 5.92 Time building geometry restraints manager: 8.58 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: 98.68 - 105.75: 417 105.75 - 112.83: 11031 112.83 - 119.90: 7062 119.90 - 126.97: 9417 126.97 - 134.05: 243 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: 0.00 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: 4.690 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: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 52.910 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.480 ------------------------------------------------------------------------------- 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= 0.180 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 *********************** 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 fitting. rotamer outliers: 7 poor density : 413 time to evaluate : 2.380 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: 0.3092 time to fit residues: 196.8580 Evaluate side-chains 409 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 406 time to evaluate : 2.276 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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= 0.164 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 *********************** 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 fitting. rotamer outliers: 61 poor density : 417 time to evaluate : 2.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8032 (mmt) cc_final: 0.7832 (mmp) REVERT: A 145 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.6941 (p0) REVERT: A 160 PHE cc_start: 0.6550 (OUTLIER) cc_final: 0.5752 (m-80) REVERT: A 212 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7479 (mm) REVERT: B 123 MET cc_start: 0.7609 (mmt) cc_final: 0.7386 (mmp) REVERT: B 145 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7004 (p0) REVERT: B 146 TYR cc_start: 0.8296 (m-80) cc_final: 0.8048 (m-80) REVERT: B 184 MET cc_start: 0.8556 (tpp) cc_final: 0.8284 (tpt) REVERT: C 31 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8216 (tm-30) REVERT: C 61 PHE cc_start: 0.8698 (m-80) cc_final: 0.8324 (m-80) REVERT: C 139 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8542 (mp) REVERT: C 217 ASN cc_start: 0.8725 (t0) cc_final: 0.8476 (t0) REVERT: D 139 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8497 (mp) REVERT: D 217 ASN cc_start: 0.8783 (t0) cc_final: 0.8549 (t0) REVERT: F 3 MET cc_start: 0.4302 (pmm) cc_final: 0.3625 (pmm) REVERT: F 366 ILE cc_start: 0.9111 (mm) cc_final: 0.8670 (tp) REVERT: H 94 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7583 (mp10) REVERT: I 86 MET cc_start: 0.8581 (tpp) cc_final: 0.8241 (tpp) REVERT: I 344 ASN cc_start: 0.9174 (m-40) cc_final: 0.8740 (m110) outliers start: 61 outliers final: 22 residues processed: 461 average time/residue: 0.2899 time to fit residues: 207.8519 Evaluate side-chains 431 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 402 time to evaluate : 2.382 ------------------------------------------------------------------------------- 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 123 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1019 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= 0.185 Angle : 0.513 6.147 28170 Z= 0.260 Chirality : 0.040 0.186 3224 Planarity : 0.004 0.053 3536 Dihedral : 3.550 16.468 2794 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.16 % Allowed : 25.72 % Favored : 71.11 % 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: 0.82 (0.33), residues: 284 loop : -1.70 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 16 HIS 0.005 0.001 HIS C 65 PHE 0.014 0.001 PHE D 85 TYR 0.020 0.001 TYR E 20 ARG 0.006 0.000 ARG A 17 *********************** 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 474 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 404 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.6958 (p0) REVERT: A 160 PHE cc_start: 0.6588 (OUTLIER) cc_final: 0.5771 (m-80) REVERT: B 145 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.6899 (p0) REVERT: C 31 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8328 (tp30) REVERT: C 61 PHE cc_start: 0.8649 (m-80) cc_final: 0.8286 (m-80) REVERT: C 139 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8540 (mp) REVERT: C 217 ASN cc_start: 0.8810 (t0) cc_final: 0.8499 (t0) REVERT: D 139 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8539 (mp) REVERT: D 217 ASN cc_start: 0.8809 (t0) cc_final: 0.8490 (t0) REVERT: E 179 GLN cc_start: 0.6706 (mm-40) cc_final: 0.6285 (mm-40) REVERT: E 356 TYR cc_start: 0.7775 (t80) cc_final: 0.7519 (t80) REVERT: F 366 ILE cc_start: 0.9141 (mm) cc_final: 0.8715 (tp) REVERT: G 134 MET cc_start: 0.8520 (tpp) cc_final: 0.8266 (tpt) REVERT: H 94 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7516 (mp10) REVERT: I 344 ASN cc_start: 0.9198 (m-40) cc_final: 0.8762 (m110) outliers start: 70 outliers final: 30 residues processed: 448 average time/residue: 0.3006 time to fit residues: 207.4761 Evaluate side-chains 421 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 385 time to evaluate : 2.356 ------------------------------------------------------------------------------- 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 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 363 VAL Chi-restraints excluded: chain G residue 325 VAL Chi-restraints excluded: chain G residue 353 CYS 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 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 219 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 24 optimal weight: 30.0000 chunk 105 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 222 optimal weight: 0.9980 chunk 235 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 211 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN G 173 HIS J 15 GLN K 173 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20770 Z= 0.258 Angle : 0.544 6.329 28170 Z= 0.277 Chirality : 0.042 0.208 3224 Planarity : 0.004 0.054 3536 Dihedral : 3.684 17.986 2794 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.84 % Allowed : 25.68 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.40 (0.17), residues: 2448 helix: 2.09 (0.13), residues: 1484 sheet: 0.82 (0.34), residues: 270 loop : -1.70 (0.21), residues: 694 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 0.002 TYR B 146 ARG 0.004 0.000 ARG A 17 *********************** 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 488 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 403 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.6860 (p0) REVERT: A 160 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.6053 (m-80) REVERT: A 201 GLN cc_start: 0.7429 (mm-40) cc_final: 0.6798 (pm20) REVERT: B 145 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.6940 (p0) REVERT: B 184 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8585 (tpt) REVERT: B 201 GLN cc_start: 0.8527 (mp10) cc_final: 0.8207 (mm-40) REVERT: C 31 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8357 (tp30) REVERT: C 61 PHE cc_start: 0.8687 (m-80) cc_final: 0.8294 (m-80) REVERT: C 139 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8555 (mp) REVERT: C 217 ASN cc_start: 0.8881 (t0) cc_final: 0.8645 (t0) REVERT: D 217 ASN cc_start: 0.8913 (t0) cc_final: 0.8556 (t0) REVERT: E 20 TYR cc_start: 0.8312 (m-80) cc_final: 0.8049 (m-80) REVERT: E 36 ASP cc_start: 0.8537 (p0) cc_final: 0.8184 (p0) REVERT: E 179 GLN cc_start: 0.6865 (mm-40) cc_final: 0.6407 (mm-40) REVERT: E 356 TYR cc_start: 0.7819 (t80) cc_final: 0.7421 (t80) REVERT: F 3 MET cc_start: 0.3964 (pmm) cc_final: 0.3088 (pmm) REVERT: F 366 ILE cc_start: 0.9154 (mm) cc_final: 0.8727 (tp) REVERT: H 94 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7583 (mp10) REVERT: I 16 TRP cc_start: 0.7817 (t-100) cc_final: 0.7557 (t-100) REVERT: I 344 ASN cc_start: 0.9195 (m-40) cc_final: 0.8743 (m110) outliers start: 85 outliers final: 47 residues processed: 459 average time/residue: 0.2952 time to fit residues: 211.3245 Evaluate side-chains 443 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 390 time to evaluate : 2.516 ------------------------------------------------------------------------------- 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 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 224 GLU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 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 350 VAL 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 21 LEU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 324 LEU Chi-restraints excluded: chain H residue 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 321 LEU Chi-restraints excluded: chain K residue 326 VAL Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 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 196 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 3 optimal weight: 0.0070 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 120 optimal weight: 0.0470 chunk 211 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 overall best weight: 0.9698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN G 173 HIS I 169 ASN J 15 GLN K 173 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1273 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= 0.171 Angle : 0.514 6.930 28170 Z= 0.260 Chirality : 0.040 0.191 3224 Planarity : 0.003 0.051 3536 Dihedral : 3.589 16.600 2794 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.25 % Allowed : 26.58 % Favored : 70.16 % 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: 1.47 (0.17), residues: 2448 helix: 2.15 (0.13), residues: 1486 sheet: 0.84 (0.34), residues: 270 loop : -1.70 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 16 HIS 0.005 0.001 HIS C 65 PHE 0.026 0.001 PHE B 21 TYR 0.018 0.001 TYR B 146 ARG 0.003 0.000 ARG A 17 *********************** 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 473 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 401 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8848 (mtpp) cc_final: 0.8614 (mtpp) REVERT: A 126 TYR cc_start: 0.7199 (OUTLIER) cc_final: 0.5761 (t80) REVERT: A 145 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.6849 (p0) REVERT: A 160 PHE cc_start: 0.6776 (OUTLIER) cc_final: 0.6008 (m-80) REVERT: A 163 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7428 (pttm) REVERT: B 102 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7910 (ptp) REVERT: B 145 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.6904 (p0) REVERT: B 184 MET cc_start: 0.9053 (tpt) cc_final: 0.8598 (tpt) REVERT: B 201 GLN cc_start: 0.8502 (mp10) cc_final: 0.8230 (mm-40) REVERT: C 31 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8399 (tp30) REVERT: C 61 PHE cc_start: 0.8661 (m-80) cc_final: 0.8299 (m-80) REVERT: C 139 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8530 (mp) REVERT: C 217 ASN cc_start: 0.8818 (t0) cc_final: 0.8567 (t0) REVERT: D 110 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: D 139 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8528 (mp) REVERT: D 217 ASN cc_start: 0.8889 (t0) cc_final: 0.8472 (t0) REVERT: E 20 TYR cc_start: 0.8393 (m-80) cc_final: 0.8065 (m-80) REVERT: E 36 ASP cc_start: 0.8497 (p0) cc_final: 0.8180 (p0) REVERT: E 179 GLN cc_start: 0.6853 (mm-40) cc_final: 0.6411 (mm-40) REVERT: E 356 TYR cc_start: 0.7810 (t80) cc_final: 0.7426 (t80) REVERT: F 3 MET cc_start: 0.3856 (pmm) cc_final: 0.2965 (pmm) REVERT: F 366 ILE cc_start: 0.9170 (mm) cc_final: 0.8743 (tp) REVERT: H 94 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7598 (mp10) REVERT: H 322 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7725 (mtmm) REVERT: I 16 TRP cc_start: 0.7810 (t-100) cc_final: 0.7585 (t-100) REVERT: I 36 ASP cc_start: 0.8567 (p0) cc_final: 0.8309 (p0) REVERT: I 86 MET cc_start: 0.8606 (tpp) cc_final: 0.8230 (tpp) REVERT: I 344 ASN cc_start: 0.9190 (m-40) cc_final: 0.8781 (m110) outliers start: 72 outliers final: 43 residues processed: 447 average time/residue: 0.2950 time to fit residues: 205.9081 Evaluate side-chains 447 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 393 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 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 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 93 THR Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 137 ILE 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 94 GLN Chi-restraints excluded: chain H residue 322 LYS Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 326 VAL Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 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 79 optimal weight: 9.9990 chunk 212 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 236 optimal weight: 5.9990 chunk 195 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN G 173 HIS I 15 GLN J 15 GLN K 173 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1321 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= 0.157 Angle : 0.509 6.873 28170 Z= 0.258 Chirality : 0.040 0.192 3224 Planarity : 0.003 0.050 3536 Dihedral : 3.544 16.076 2794 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.07 % Allowed : 27.17 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.52 (0.17), residues: 2448 helix: 2.21 (0.13), residues: 1484 sheet: 0.84 (0.34), residues: 270 loop : -1.70 (0.21), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 16 HIS 0.006 0.001 HIS C 65 PHE 0.021 0.001 PHE D 61 TYR 0.019 0.001 TYR B 146 ARG 0.003 0.000 ARG A 17 *********************** 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 478 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 410 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6994 (tpt) cc_final: 0.6777 (tpp) REVERT: A 89 LYS cc_start: 0.8780 (mtpp) cc_final: 0.8515 (mtpp) REVERT: A 126 TYR cc_start: 0.7273 (OUTLIER) cc_final: 0.5771 (t80) REVERT: A 145 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.6826 (p0) REVERT: A 160 PHE cc_start: 0.6795 (OUTLIER) cc_final: 0.6001 (m-80) REVERT: A 163 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7434 (pttm) REVERT: A 201 GLN cc_start: 0.7586 (mm-40) cc_final: 0.6722 (pm20) REVERT: B 145 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.6811 (p0) REVERT: B 184 MET cc_start: 0.9050 (tpt) cc_final: 0.8640 (tpt) REVERT: B 201 GLN cc_start: 0.8483 (mp10) cc_final: 0.8223 (mm-40) REVERT: C 31 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8400 (tp30) REVERT: C 61 PHE cc_start: 0.8655 (m-80) cc_final: 0.8288 (m-80) REVERT: C 139 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8523 (mp) REVERT: C 217 ASN cc_start: 0.8807 (t0) cc_final: 0.8514 (t0) REVERT: D 110 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.7966 (mp10) REVERT: D 139 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8554 (mp) REVERT: D 217 ASN cc_start: 0.8884 (t0) cc_final: 0.8455 (t0) REVERT: E 20 TYR cc_start: 0.8433 (m-80) cc_final: 0.8152 (m-80) REVERT: E 36 ASP cc_start: 0.8427 (p0) cc_final: 0.8110 (p0) REVERT: E 344 ASN cc_start: 0.9179 (m-40) cc_final: 0.8870 (m110) REVERT: E 356 TYR cc_start: 0.7821 (t80) cc_final: 0.7409 (t80) REVERT: F 3 MET cc_start: 0.3680 (pmm) cc_final: 0.2850 (pmm) REVERT: F 366 ILE cc_start: 0.9166 (mm) cc_final: 0.8756 (tp) REVERT: G 14 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8688 (mp) REVERT: H 94 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7577 (mp10) REVERT: I 36 ASP cc_start: 0.8529 (p0) cc_final: 0.8269 (p0) REVERT: I 344 ASN cc_start: 0.9194 (m-40) cc_final: 0.8806 (m110) REVERT: J 366 ILE cc_start: 0.9046 (mm) cc_final: 0.8687 (tp) outliers start: 68 outliers final: 43 residues processed: 453 average time/residue: 0.2933 time to fit residues: 208.2004 Evaluate side-chains 448 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 395 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain C residue 60 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 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 14 LEU Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 137 ILE 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 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 90 GLN Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 326 VAL Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 324 LEU Chi-restraints excluded: chain L residue 326 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 131 optimal weight: 20.0000 chunk 235 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN G 173 HIS 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20770 Z= 0.324 Angle : 0.583 7.731 28170 Z= 0.297 Chirality : 0.043 0.239 3224 Planarity : 0.004 0.053 3536 Dihedral : 3.784 18.985 2794 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.75 % Allowed : 26.40 % 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: 1.36 (0.17), residues: 2448 helix: 2.11 (0.13), residues: 1484 sheet: 0.49 (0.32), residues: 302 loop : -1.80 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP I 16 HIS 0.006 0.001 HIS C 65 PHE 0.015 0.001 PHE D 85 TYR 0.023 0.002 TYR J 338 ARG 0.004 0.000 ARG F 340 *********************** 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 487 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 404 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7154 (tpt) cc_final: 0.6927 (tpp) REVERT: A 89 LYS cc_start: 0.8848 (mtpp) cc_final: 0.8559 (mtpp) REVERT: A 126 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.5875 (t80) REVERT: A 145 ASP cc_start: 0.7181 (OUTLIER) cc_final: 0.6562 (p0) REVERT: A 160 PHE cc_start: 0.6818 (OUTLIER) cc_final: 0.6017 (m-80) REVERT: B 145 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.6904 (p0) REVERT: B 160 PHE cc_start: 0.6547 (OUTLIER) cc_final: 0.5881 (m-80) REVERT: B 201 GLN cc_start: 0.8500 (mp10) cc_final: 0.8241 (mm-40) REVERT: C 31 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8421 (tp30) REVERT: C 61 PHE cc_start: 0.8627 (m-80) cc_final: 0.8247 (m-80) REVERT: C 139 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8580 (mp) REVERT: C 217 ASN cc_start: 0.8930 (t0) cc_final: 0.8706 (t0) REVERT: D 39 ARG cc_start: 0.6724 (OUTLIER) cc_final: 0.6070 (tpt-90) REVERT: D 110 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8111 (mp10) REVERT: D 217 ASN cc_start: 0.8948 (t0) cc_final: 0.8581 (t0) REVERT: E 20 TYR cc_start: 0.8527 (m-80) cc_final: 0.8159 (m-80) REVERT: E 36 ASP cc_start: 0.8506 (p0) cc_final: 0.8170 (p0) REVERT: E 179 GLN cc_start: 0.6447 (mm-40) cc_final: 0.6124 (mm-40) REVERT: F 366 ILE cc_start: 0.9163 (mm) cc_final: 0.8743 (tp) REVERT: G 14 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8767 (mp) REVERT: I 86 MET cc_start: 0.8685 (tpp) cc_final: 0.8334 (tpp) REVERT: K 14 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8762 (mp) outliers start: 83 outliers final: 52 residues processed: 455 average time/residue: 0.2926 time to fit residues: 207.3063 Evaluate side-chains 460 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 398 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 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 14 LEU 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 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 14 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 45 optimal weight: 0.0010 chunk 149 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 21 optimal weight: 20.0000 chunk 184 optimal weight: 0.0170 overall best weight: 0.5826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN F 15 GLN G 173 HIS J 15 GLN K 173 HIS L 94 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1423 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= 0.145 Angle : 0.525 8.232 28170 Z= 0.266 Chirality : 0.040 0.201 3224 Planarity : 0.003 0.050 3536 Dihedral : 3.600 16.670 2794 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.49 % Allowed : 27.53 % 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: 1.47 (0.17), residues: 2448 helix: 2.16 (0.13), residues: 1488 sheet: 0.69 (0.33), residues: 280 loop : -1.68 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 16 HIS 0.007 0.001 HIS C 65 PHE 0.022 0.001 PHE D 61 TYR 0.019 0.001 TYR G 343 ARG 0.005 0.000 ARG L 177 *********************** 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 472 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 417 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6872 (tpt) cc_final: 0.6640 (tpp) REVERT: A 89 LYS cc_start: 0.8776 (mtpp) cc_final: 0.8518 (mtpp) REVERT: A 145 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6467 (p0) REVERT: A 160 PHE cc_start: 0.6730 (OUTLIER) cc_final: 0.5904 (m-80) REVERT: B 160 PHE cc_start: 0.6493 (OUTLIER) cc_final: 0.5914 (m-80) REVERT: B 177 MET cc_start: 0.8304 (tmm) cc_final: 0.8067 (tmm) REVERT: B 184 MET cc_start: 0.8922 (tpt) cc_final: 0.8628 (tpt) REVERT: B 201 GLN cc_start: 0.8509 (mp10) cc_final: 0.8252 (mm-40) REVERT: C 31 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8426 (tp30) REVERT: C 61 PHE cc_start: 0.8663 (m-80) cc_final: 0.8287 (m-80) REVERT: C 139 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8519 (mp) REVERT: C 217 ASN cc_start: 0.8814 (t0) cc_final: 0.8521 (t0) REVERT: D 100 ASP cc_start: 0.8272 (p0) cc_final: 0.8013 (p0) REVERT: D 110 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8031 (mp10) REVERT: D 139 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8536 (mp) REVERT: D 217 ASN cc_start: 0.8882 (t0) cc_final: 0.8454 (t0) REVERT: E 20 TYR cc_start: 0.8602 (m-80) cc_final: 0.8003 (m-80) REVERT: E 36 ASP cc_start: 0.8422 (p0) cc_final: 0.8110 (p0) REVERT: E 179 GLN cc_start: 0.6440 (mm-40) cc_final: 0.6081 (mm-40) REVERT: E 344 ASN cc_start: 0.9189 (m-40) cc_final: 0.8900 (m110) REVERT: E 356 TYR cc_start: 0.7830 (t80) cc_final: 0.7441 (t80) REVERT: F 366 ILE cc_start: 0.9193 (mm) cc_final: 0.8794 (tp) REVERT: G 14 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8777 (mp) REVERT: I 36 ASP cc_start: 0.8527 (p0) cc_final: 0.8271 (p0) REVERT: I 86 MET cc_start: 0.8601 (tpp) cc_final: 0.8221 (tpp) REVERT: I 344 ASN cc_start: 0.9173 (m-40) cc_final: 0.8770 (m110) REVERT: J 366 ILE cc_start: 0.9019 (mm) cc_final: 0.8683 (tp) REVERT: K 14 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8708 (mp) outliers start: 55 outliers final: 33 residues processed: 453 average time/residue: 0.2935 time to fit residues: 206.8953 Evaluate side-chains 446 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 405 time to evaluate : 2.330 ------------------------------------------------------------------------------- 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 109 VAL Chi-restraints excluded: chain B residue 140 MET 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 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 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 137 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 325 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 67 optimal weight: 0.0050 chunk 198 optimal weight: 0.5980 chunk 207 optimal weight: 5.9990 chunk 218 optimal weight: 0.6980 overall best weight: 0.8596 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20770 Z= 0.170 Angle : 0.538 7.601 28170 Z= 0.273 Chirality : 0.041 0.201 3224 Planarity : 0.003 0.050 3536 Dihedral : 3.589 16.790 2794 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.31 % Allowed : 27.76 % 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: 1.48 (0.17), residues: 2448 helix: 2.18 (0.13), residues: 1488 sheet: 0.62 (0.32), residues: 302 loop : -1.75 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 16 HIS 0.012 0.001 HIS C 65 PHE 0.014 0.001 PHE C 85 TYR 0.026 0.001 TYR C 194 ARG 0.010 0.000 ARG L 177 *********************** 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 455 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 404 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6877 (tpt) cc_final: 0.6646 (tpp) REVERT: A 89 LYS cc_start: 0.8687 (mtpp) cc_final: 0.8390 (mtpp) REVERT: A 145 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6545 (p0) REVERT: A 160 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.5895 (m-80) REVERT: B 102 MET cc_start: 0.8193 (ptp) cc_final: 0.7770 (ptt) REVERT: B 160 PHE cc_start: 0.6390 (OUTLIER) cc_final: 0.5705 (m-80) REVERT: B 177 MET cc_start: 0.8328 (tmm) cc_final: 0.8102 (tmm) REVERT: B 184 MET cc_start: 0.8931 (tpt) cc_final: 0.8596 (tpt) REVERT: B 201 GLN cc_start: 0.8510 (mp10) cc_final: 0.8245 (mm-40) REVERT: C 31 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8440 (tp30) REVERT: C 61 PHE cc_start: 0.8622 (m-80) cc_final: 0.8228 (m-80) REVERT: C 139 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8539 (mp) REVERT: C 217 ASN cc_start: 0.8831 (t0) cc_final: 0.8572 (t0) REVERT: D 110 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8076 (mp10) REVERT: D 139 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8534 (mp) REVERT: D 217 ASN cc_start: 0.8900 (t0) cc_final: 0.8472 (t0) REVERT: E 20 TYR cc_start: 0.8636 (m-80) cc_final: 0.8106 (m-80) REVERT: E 36 ASP cc_start: 0.8404 (p0) cc_final: 0.8090 (p0) REVERT: E 179 GLN cc_start: 0.6404 (mm-40) cc_final: 0.6009 (mm-40) REVERT: E 344 ASN cc_start: 0.9180 (m-40) cc_final: 0.8849 (m110) REVERT: E 356 TYR cc_start: 0.7803 (t80) cc_final: 0.7412 (t80) REVERT: F 366 ILE cc_start: 0.9172 (mm) cc_final: 0.8771 (tp) REVERT: G 14 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8783 (mp) REVERT: I 23 MET cc_start: 0.8965 (mmm) cc_final: 0.8649 (mmm) REVERT: I 36 ASP cc_start: 0.8512 (p0) cc_final: 0.8257 (p0) REVERT: I 86 MET cc_start: 0.8622 (tpp) cc_final: 0.8220 (tpp) REVERT: I 344 ASN cc_start: 0.9189 (m-40) cc_final: 0.8776 (m110) REVERT: J 366 ILE cc_start: 0.9027 (mm) cc_final: 0.8675 (tp) REVERT: K 14 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8706 (mp) outliers start: 51 outliers final: 41 residues processed: 438 average time/residue: 0.2927 time to fit residues: 200.5590 Evaluate side-chains 448 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 399 time to evaluate : 2.386 ------------------------------------------------------------------------------- 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 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 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 F residue 9 LEU Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 325 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain 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 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 143 optimal weight: 0.6980 chunk 231 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 243 optimal weight: 5.9990 chunk 223 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 149 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1500 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= 0.188 Angle : 0.552 8.107 28170 Z= 0.279 Chirality : 0.041 0.203 3224 Planarity : 0.004 0.050 3536 Dihedral : 3.607 16.592 2794 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.40 % Allowed : 27.94 % Favored : 69.67 % 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: 2.10 (0.13), residues: 1500 sheet: 0.59 (0.32), residues: 302 loop : -1.76 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 16 HIS 0.013 0.001 HIS D 65 PHE 0.023 0.001 PHE D 61 TYR 0.022 0.001 TYR C 194 ARG 0.009 0.000 ARG L 177 ********************** 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 457 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 404 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6893 (tpt) cc_final: 0.6650 (tpp) REVERT: A 89 LYS cc_start: 0.8690 (mtpp) cc_final: 0.8400 (mtpp) REVERT: A 145 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6538 (p0) REVERT: A 160 PHE cc_start: 0.6709 (OUTLIER) cc_final: 0.5867 (m-80) REVERT: B 102 MET cc_start: 0.8194 (ptp) cc_final: 0.7830 (ptt) REVERT: B 160 PHE cc_start: 0.6500 (OUTLIER) cc_final: 0.5835 (m-80) REVERT: B 177 MET cc_start: 0.8307 (tmm) cc_final: 0.7833 (tmm) REVERT: B 184 MET cc_start: 0.8938 (tpt) cc_final: 0.8601 (tpt) REVERT: B 201 GLN cc_start: 0.8514 (mp10) cc_final: 0.8261 (mm-40) REVERT: C 31 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8447 (tp30) REVERT: C 57 MET cc_start: 0.8899 (mmt) cc_final: 0.8668 (mpp) REVERT: C 61 PHE cc_start: 0.8686 (m-80) cc_final: 0.8289 (m-80) REVERT: C 100 ASP cc_start: 0.8267 (p0) cc_final: 0.8067 (p0) REVERT: C 139 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8541 (mp) REVERT: C 217 ASN cc_start: 0.8844 (t0) cc_final: 0.8589 (t0) REVERT: D 110 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8140 (mp10) REVERT: D 139 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8534 (mp) REVERT: D 217 ASN cc_start: 0.8892 (t0) cc_final: 0.8508 (t0) REVERT: E 20 TYR cc_start: 0.8665 (m-80) cc_final: 0.8081 (m-80) REVERT: E 36 ASP cc_start: 0.8408 (p0) cc_final: 0.8090 (p0) REVERT: E 179 GLN cc_start: 0.6515 (mm-40) cc_final: 0.6118 (mm-40) REVERT: E 344 ASN cc_start: 0.9191 (m-40) cc_final: 0.8861 (m110) REVERT: E 356 TYR cc_start: 0.7808 (t80) cc_final: 0.7425 (t80) REVERT: F 366 ILE cc_start: 0.9173 (mm) cc_final: 0.8776 (tp) REVERT: I 23 MET cc_start: 0.9000 (mmm) cc_final: 0.8680 (mmm) REVERT: I 36 ASP cc_start: 0.8521 (p0) cc_final: 0.8264 (p0) REVERT: I 320 LYS cc_start: 0.7549 (tppt) cc_final: 0.7229 (tptp) REVERT: I 344 ASN cc_start: 0.9209 (m-40) cc_final: 0.8793 (m110) REVERT: J 366 ILE cc_start: 0.9026 (mm) cc_final: 0.8680 (tp) outliers start: 53 outliers final: 43 residues processed: 440 average time/residue: 0.2934 time to fit residues: 201.2407 Evaluate side-chains 446 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 397 time to evaluate : 2.487 ------------------------------------------------------------------------------- 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 160 PHE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 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 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 46 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 325 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 324 LEU Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 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 153 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 199 optimal weight: 0.7980 chunk 24 optimal weight: 40.0000 chunk 35 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.143601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.101878 restraints weight = 39479.711| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.60 r_work: 0.3283 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1527 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= 0.216 Angle : 0.560 8.141 28170 Z= 0.283 Chirality : 0.041 0.207 3224 Planarity : 0.004 0.049 3536 Dihedral : 3.667 17.334 2794 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.49 % Allowed : 27.67 % 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: 1.41 (0.17), residues: 2448 helix: 2.10 (0.13), residues: 1498 sheet: 0.55 (0.32), residues: 302 loop : -1.76 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 16 HIS 0.013 0.001 HIS D 65 PHE 0.018 0.001 PHE A 21 TYR 0.023 0.001 TYR G 78 ARG 0.009 0.000 ARG L 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5004.79 seconds wall clock time: 89 minutes 8.35 seconds (5348.35 seconds total)