Starting phenix.real_space_refine on Fri Sep 11 04:00:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6jnf_9851/09_2026/6jnf_9851.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jnf_9851/09_2026/6jnf_9851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6jnf_9851/09_2026/6jnf_9851.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6jnf_9851/09_2026/6jnf_9851.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jnf_9851/09_2026/6jnf_9851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jnf_9851/09_2026/6jnf_9851.map" model { file = "/net/cci-nas-00/data/ceres_data/6jnf_9851/09_2026/6jnf_9851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jnf_9851/09_2026/6jnf_9851.cif" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 20 5.16 5 C 4681 2.51 5 N 1215 2.21 5 O 1354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7271 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2363 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 4 Chain: "B" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 336 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "C" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 342 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 292 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "E" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 281 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "F" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2363 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 4 Chain: "G" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 336 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "H" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 342 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "I" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 292 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "J" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 281 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'46E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.88, per 1000 atoms: 0.26 Number of scatterers: 7271 At special positions: 0 Unit cell: (138.19, 114.943, 94.2795, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 1 15.00 O 1354 8.00 N 1215 7.00 C 4681 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 342.0 milliseconds 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1720 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 10 sheets defined 26.4% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 368 through 373 removed outlier: 4.218A pdb=" N GLN A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 373' Processing helix chain 'B' and resid 18 through 26 removed outlier: 3.722A pdb=" N THR B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 43 removed outlier: 3.571A pdb=" N LEU B 37 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B 42 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 54 removed outlier: 3.573A pdb=" N LEU B 53 " --> pdb=" O PHE B 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 102 removed outlier: 3.541A pdb=" N THR C 101 " --> pdb=" O ASN C 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 102 " --> pdb=" O LEU C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 102' Processing helix chain 'C' and resid 110 through 130 removed outlier: 3.710A pdb=" N LEU C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU C 125 " --> pdb=" O GLN C 121 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE C 130 " --> pdb=" O MET C 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 41 removed outlier: 3.608A pdb=" N GLU D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR D 24 " --> pdb=" O GLN D 20 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU D 25 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR D 30 " --> pdb=" O LYS D 26 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL D 31 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP D 36 " --> pdb=" O ALA D 32 " (cutoff:3.500A) Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 44 through 49 removed outlier: 4.051A pdb=" N TRP D 49 " --> pdb=" O VAL D 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 50 removed outlier: 4.205A pdb=" N ILE E 35 " --> pdb=" O PRO E 31 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY E 39 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL E 43 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 57 removed outlier: 3.661A pdb=" N ASP E 55 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET E 56 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU E 57 " --> pdb=" O LEU E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 51 through 57' Processing helix chain 'F' and resid 67 through 72 Processing helix chain 'F' and resid 368 through 373 removed outlier: 4.217A pdb=" N GLN F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY F 373 " --> pdb=" O MET F 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 368 through 373' Processing helix chain 'G' and resid 18 through 26 removed outlier: 3.723A pdb=" N THR G 22 " --> pdb=" O SER G 18 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS G 25 " --> pdb=" O LEU G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 43 removed outlier: 3.572A pdb=" N LEU G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR G 38 " --> pdb=" O PRO G 34 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY G 40 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA G 42 " --> pdb=" O TYR G 38 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS G 43 " --> pdb=" O LEU G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.573A pdb=" N LEU G 53 " --> pdb=" O PHE G 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 102 removed outlier: 3.541A pdb=" N THR H 101 " --> pdb=" O ASN H 97 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU H 102 " --> pdb=" O LEU H 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 97 through 102' Processing helix chain 'H' and resid 110 through 130 removed outlier: 3.709A pdb=" N LEU H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU H 120 " --> pdb=" O SER H 116 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU H 123 " --> pdb=" O ALA H 119 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE H 124 " --> pdb=" O GLU H 120 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU H 125 " --> pdb=" O GLN H 121 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE H 130 " --> pdb=" O MET H 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 41 removed outlier: 3.607A pdb=" N GLU I 22 " --> pdb=" O GLN I 18 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR I 24 " --> pdb=" O GLN I 20 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU I 25 " --> pdb=" O THR I 21 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA I 29 " --> pdb=" O LEU I 25 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR I 30 " --> pdb=" O LYS I 26 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL I 31 " --> pdb=" O GLN I 27 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE I 34 " --> pdb=" O TYR I 30 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) Proline residue: I 39 - end of helix Processing helix chain 'I' and resid 44 through 49 removed outlier: 4.052A pdb=" N TRP I 49 " --> pdb=" O VAL I 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 50 removed outlier: 4.205A pdb=" N ILE J 35 " --> pdb=" O PRO J 31 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY J 39 " --> pdb=" O ILE J 35 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL J 43 " --> pdb=" O GLY J 39 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 57 removed outlier: 3.660A pdb=" N ASP J 55 " --> pdb=" O SER J 51 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET J 56 " --> pdb=" O PRO J 52 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU J 57 " --> pdb=" O LEU J 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 51 through 57' Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121 removed outlier: 3.874A pdb=" N LEU A 119 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN A 99 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA A 121 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 104 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 84 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 85 " --> pdb=" O CYS A 355 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP A 87 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 91 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY A 356 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 338 " --> pdb=" O ARG A 330 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 342 " --> pdb=" O CYS A 326 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 344 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER A 312 " --> pdb=" O TYR A 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 117 removed outlier: 3.616A pdb=" N ILE A 131 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 127 removed outlier: 3.604A pdb=" N PHE A 126 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN A 142 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 137 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 139 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 153 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 166 through 167 removed outlier: 4.071A pdb=" N LEU A 167 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 182 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VAL A 196 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 177 removed outlier: 4.097A pdb=" N GLN A 203 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 234 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER A 258 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 256 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 257 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 259 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 271 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A 274 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 300 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 119 through 121 removed outlier: 3.873A pdb=" N LEU F 119 " --> pdb=" O GLN F 99 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN F 99 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA F 121 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE F 104 " --> pdb=" O ALA F 86 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 84 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG F 85 " --> pdb=" O CYS F 355 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP F 87 " --> pdb=" O LEU F 357 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA F 91 " --> pdb=" O THR F 361 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY F 356 " --> pdb=" O LEU F 339 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL F 338 " --> pdb=" O ARG F 330 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY F 342 " --> pdb=" O CYS F 326 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE F 344 " --> pdb=" O VAL F 324 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER F 312 " --> pdb=" O TYR F 309 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 115 through 117 removed outlier: 3.616A pdb=" N ILE F 131 " --> pdb=" O PHE F 116 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 126 through 127 removed outlier: 3.602A pdb=" N PHE F 126 " --> pdb=" O ASN F 142 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN F 142 " --> pdb=" O PHE F 126 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL F 137 " --> pdb=" O ILE F 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY F 139 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL F 153 " --> pdb=" O LEU F 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 166 through 167 removed outlier: 4.071A pdb=" N LEU F 167 " --> pdb=" O THR F 182 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR F 182 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL F 196 " --> pdb=" O LEU F 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 176 through 177 removed outlier: 4.097A pdb=" N GLN F 203 " --> pdb=" O LEU F 211 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR F 234 " --> pdb=" O GLY F 247 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER F 258 " --> pdb=" O SER F 246 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE F 256 " --> pdb=" O GLN F 248 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA F 257 " --> pdb=" O THR F 273 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU F 259 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE F 271 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR F 274 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER F 300 " --> pdb=" O THR F 274 " (cutoff:3.500A) 204 hydrogen bonds defined for protein. 558 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: 1.01 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1185 1.30 - 1.43: 1964 1.43 - 1.55: 4237 1.55 - 1.68: 4 1.68 - 1.80: 32 Bond restraints: 7422 Sorted by residual: bond pdb=" C21 46E A 401 " pdb=" O21 46E A 401 " ideal model delta sigma weight residual 1.331 1.402 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C31 46E A 401 " pdb=" O31 46E A 401 " ideal model delta sigma weight residual 1.327 1.396 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C SER B 55 " pdb=" N PRO B 56 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 7.94e+00 bond pdb=" C SER G 55 " pdb=" N PRO G 56 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.34e-02 1.83e+03 7.81e+00 bond pdb=" C GLN F 294 " pdb=" N PRO F 295 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.19e+00 ... (remaining 7417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 9838 3.59 - 7.18: 183 7.18 - 10.78: 26 10.78 - 14.37: 3 14.37 - 17.96: 3 Bond angle restraints: 10053 Sorted by residual: angle pdb=" N ILE A 293 " pdb=" CA ILE A 293 " pdb=" C ILE A 293 " ideal model delta sigma weight residual 113.20 106.10 7.10 9.60e-01 1.09e+00 5.46e+01 angle pdb=" N ILE F 293 " pdb=" CA ILE F 293 " pdb=" C ILE F 293 " ideal model delta sigma weight residual 113.20 106.10 7.10 9.60e-01 1.09e+00 5.46e+01 angle pdb=" O11 46E A 401 " pdb=" P 46E A 401 " pdb=" O13 46E A 401 " ideal model delta sigma weight residual 93.37 111.27 -17.90 3.00e+00 1.11e-01 3.56e+01 angle pdb=" C VAL A 205 " pdb=" N THR A 206 " pdb=" CA THR A 206 " ideal model delta sigma weight residual 121.80 135.59 -13.79 2.44e+00 1.68e-01 3.19e+01 angle pdb=" C VAL F 205 " pdb=" N THR F 206 " pdb=" CA THR F 206 " ideal model delta sigma weight residual 121.80 135.50 -13.70 2.44e+00 1.68e-01 3.15e+01 ... (remaining 10048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 3705 17.26 - 34.52: 516 34.52 - 51.78: 100 51.78 - 69.04: 21 69.04 - 86.30: 19 Dihedral angle restraints: 4361 sinusoidal: 1707 harmonic: 2654 Sorted by residual: dihedral pdb=" CA VAL A 205 " pdb=" C VAL A 205 " pdb=" N THR A 206 " pdb=" CA THR A 206 " ideal model delta harmonic sigma weight residual 180.00 151.16 28.84 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA VAL F 205 " pdb=" C VAL F 205 " pdb=" N THR F 206 " pdb=" CA THR F 206 " ideal model delta harmonic sigma weight residual 180.00 151.17 28.83 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ARG B 47 " pdb=" C ARG B 47 " pdb=" N PRO B 48 " pdb=" CA PRO B 48 " ideal model delta harmonic sigma weight residual -180.00 -151.29 -28.71 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 4358 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 822 0.060 - 0.120: 235 0.120 - 0.180: 71 0.180 - 0.241: 9 0.241 - 0.301: 4 Chirality restraints: 1141 Sorted by residual: chirality pdb=" CB VAL F 332 " pdb=" CA VAL F 332 " pdb=" CG1 VAL F 332 " pdb=" CG2 VAL F 332 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB VAL A 332 " pdb=" CA VAL A 332 " pdb=" CG1 VAL A 332 " pdb=" CG2 VAL A 332 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA ASN F 321 " pdb=" N ASN F 321 " pdb=" C ASN F 321 " pdb=" CB ASN F 321 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1138 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 333 " -0.048 5.00e-02 4.00e+02 7.24e-02 8.40e+00 pdb=" N PRO A 334 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 334 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 334 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 333 " 0.048 5.00e-02 4.00e+02 7.20e-02 8.29e+00 pdb=" N PRO F 334 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO F 334 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 334 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 206 " 0.045 5.00e-02 4.00e+02 6.79e-02 7.39e+00 pdb=" N PRO A 207 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " 0.038 5.00e-02 4.00e+02 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2410 2.82 - 3.34: 6024 3.34 - 3.86: 10495 3.86 - 4.38: 11252 4.38 - 4.90: 20355 Nonbonded interactions: 50536 Sorted by model distance: nonbonded pdb=" NE2 GLN F 203 " pdb=" O ILE I 41 " model vdw 2.304 3.120 nonbonded pdb=" O PHE J 27 " pdb=" OG SER J 30 " model vdw 2.306 3.040 nonbonded pdb=" O PHE E 27 " pdb=" OG SER E 30 " model vdw 2.306 3.040 nonbonded pdb=" OG SER A 246 " pdb=" N GLY A 247 " model vdw 2.334 3.120 nonbonded pdb=" OG SER F 246 " pdb=" N GLY F 247 " model vdw 2.335 3.120 ... (remaining 50531 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' and resid 47 through 373) selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.940 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 : 0.009 0.071 7422 Z= 0.379 Angle : 1.227 17.959 10053 Z= 0.617 Chirality : 0.063 0.301 1141 Planarity : 0.007 0.072 1272 Dihedral : 17.143 86.302 2641 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 1.02 % Allowed : 18.41 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.16 (0.22), residues: 888 helix: -4.57 (0.14), residues: 202 sheet: -3.78 (0.22), residues: 366 loop : -3.66 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 330 TYR 0.024 0.002 TYR F 143 PHE 0.030 0.003 PHE A 92 TRP 0.015 0.002 TRP D 36 HIS 0.007 0.001 HIS I 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00855 / 0.38 ( 7422) covalent geometry : angle 1.22736 / 0.62 (10053) hydrogen bonds : bond 0.33245 / 21.85 ( 204) hydrogen bonds : angle 10.46351 / 7.11 ( 558) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 196 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLN cc_start: 0.8420 (pp30) cc_final: 0.7844 (pp30) REVERT: A 217 TYR cc_start: 0.8576 (t80) cc_final: 0.8194 (t80) REVERT: A 219 ARG cc_start: 0.8833 (ttt180) cc_final: 0.8501 (ttp-170) REVERT: B 26 ASN cc_start: 0.7181 (t0) cc_final: 0.6845 (t0) REVERT: C 87 PHE cc_start: 0.6499 (p90) cc_final: 0.6297 (p90) REVERT: C 94 LYS cc_start: 0.9047 (tptt) cc_final: 0.8429 (tppt) REVERT: D 42 TRP cc_start: 0.8507 (t60) cc_final: 0.7847 (t-100) REVERT: E 41 PHE cc_start: 0.9204 (m-80) cc_final: 0.8978 (m-80) REVERT: F 203 GLN cc_start: 0.8300 (pp30) cc_final: 0.7892 (pp30) REVERT: F 214 GLU cc_start: 0.8795 (pp20) cc_final: 0.8585 (pp20) REVERT: F 219 ARG cc_start: 0.8803 (ttt180) cc_final: 0.8572 (ttp-170) REVERT: J 41 PHE cc_start: 0.9164 (m-80) cc_final: 0.8887 (m-80) outliers start: 8 outliers final: 4 residues processed: 202 average time/residue: 0.0890 time to fit residues: 23.8462 Evaluate side-chains 161 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 157 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.172853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127980 restraints weight = 8814.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.125050 restraints weight = 10154.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126611 restraints weight = 9675.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.127666 restraints weight = 5891.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.128326 restraints weight = 5198.526| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7422 Z= 0.210 Angle : 0.839 12.077 10053 Z= 0.415 Chirality : 0.047 0.171 1141 Planarity : 0.005 0.054 1272 Dihedral : 8.132 77.653 991 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.96 % Favored : 86.04 % Rotamer: Outliers : 4.09 % Allowed : 22.76 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.88 (0.26), residues: 888 helix: -2.94 (0.27), residues: 210 sheet: -3.07 (0.25), residues: 366 loop : -3.25 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 315 TYR 0.013 0.002 TYR I 30 PHE 0.019 0.002 PHE F 92 TRP 0.010 0.001 TRP I 36 HIS 0.003 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 ( 7422) covalent geometry : angle 0.83913 / 0.41 (10053) hydrogen bonds : bond 0.05944 / 3.85 ( 204) hydrogen bonds : angle 6.44574 / 4.35 ( 558) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 GLN cc_start: 0.8000 (pp30) cc_final: 0.7659 (pp30) REVERT: A 318 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8386 (pp) REVERT: A 369 MET cc_start: 0.8525 (ttm) cc_final: 0.8136 (ttt) REVERT: C 87 PHE cc_start: 0.6755 (p90) cc_final: 0.6528 (p90) REVERT: C 94 LYS cc_start: 0.8903 (tptt) cc_final: 0.8458 (tppt) REVERT: D 22 GLU cc_start: 0.7599 (pp20) cc_final: 0.7055 (pp20) REVERT: D 42 TRP cc_start: 0.8704 (t60) cc_final: 0.7582 (t60) REVERT: F 203 GLN cc_start: 0.7977 (pp30) cc_final: 0.7702 (pp30) REVERT: F 236 TYR cc_start: 0.8325 (t80) cc_final: 0.7988 (t80) REVERT: F 318 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8405 (pp) REVERT: J 38 ASN cc_start: 0.8571 (m110) cc_final: 0.8364 (m110) REVERT: J 41 PHE cc_start: 0.8944 (m-80) cc_final: 0.8683 (m-80) outliers start: 32 outliers final: 23 residues processed: 188 average time/residue: 0.0787 time to fit residues: 20.1111 Evaluate side-chains 186 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain D residue 17 HIS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 17 HIS Chi-restraints excluded: chain I residue 40 MET Chi-restraints excluded: chain J residue 34 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 13 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 26 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.173624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.129759 restraints weight = 8707.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.128714 restraints weight = 10164.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.130340 restraints weight = 9306.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.130653 restraints weight = 5972.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.131172 restraints weight = 5517.822| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7422 Z= 0.178 Angle : 0.809 11.994 10053 Z= 0.392 Chirality : 0.046 0.198 1141 Planarity : 0.005 0.047 1272 Dihedral : 7.603 74.232 991 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.61 % Favored : 87.39 % Rotamer: Outliers : 5.24 % Allowed : 24.17 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.27), residues: 888 helix: -1.82 (0.33), residues: 210 sheet: -2.68 (0.26), residues: 366 loop : -2.98 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 47 TYR 0.013 0.001 TYR A 217 PHE 0.015 0.001 PHE F 92 TRP 0.010 0.001 TRP B 41 HIS 0.002 0.000 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 7422) covalent geometry : angle 0.80878 / 0.39 (10053) hydrogen bonds : bond 0.05073 / 3.30 ( 204) hydrogen bonds : angle 5.98039 / 4.04 ( 558) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8397 (pp) REVERT: A 369 MET cc_start: 0.8310 (ttm) cc_final: 0.8037 (ttt) REVERT: C 94 LYS cc_start: 0.8839 (tptt) cc_final: 0.8477 (tppt) REVERT: D 42 TRP cc_start: 0.8599 (t60) cc_final: 0.7237 (t60) REVERT: E 25 GLN cc_start: 0.7557 (tp-100) cc_final: 0.6624 (mp10) REVERT: F 236 TYR cc_start: 0.8381 (t80) cc_final: 0.8057 (t80) REVERT: F 318 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8406 (pp) REVERT: F 369 MET cc_start: 0.8369 (ttm) cc_final: 0.8049 (ttt) REVERT: J 41 PHE cc_start: 0.8891 (m-80) cc_final: 0.8603 (m-80) outliers start: 41 outliers final: 30 residues processed: 192 average time/residue: 0.0782 time to fit residues: 20.9027 Evaluate side-chains 189 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain D residue 17 HIS Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain F residue 49 HIS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 17 HIS Chi-restraints excluded: chain I residue 40 MET Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 34 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.0170 chunk 80 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.174250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.129148 restraints weight = 8829.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.126489 restraints weight = 9414.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.127769 restraints weight = 9627.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129031 restraints weight = 5644.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.129799 restraints weight = 4971.608| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7422 Z= 0.168 Angle : 0.791 12.042 10053 Z= 0.383 Chirality : 0.047 0.196 1141 Planarity : 0.004 0.047 1272 Dihedral : 7.284 67.614 989 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.29 % Favored : 86.71 % Rotamer: Outliers : 4.60 % Allowed : 28.13 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.29), residues: 888 helix: -1.00 (0.37), residues: 202 sheet: -2.41 (0.26), residues: 366 loop : -2.67 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 47 TYR 0.014 0.001 TYR F 217 PHE 0.025 0.002 PHE B 35 TRP 0.010 0.001 TRP B 41 HIS 0.001 0.000 HIS G 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 7422) covalent geometry : angle 0.79078 / 0.38 (10053) hydrogen bonds : bond 0.04620 / 3.01 ( 204) hydrogen bonds : angle 5.72592 / 3.87 ( 558) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.8008 (mpp) cc_final: 0.7586 (mmm) REVERT: A 219 ARG cc_start: 0.8354 (ttt180) cc_final: 0.8092 (ttt-90) REVERT: A 318 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8346 (pp) REVERT: A 369 MET cc_start: 0.8494 (ttm) cc_final: 0.8238 (ttt) REVERT: C 94 LYS cc_start: 0.8910 (tptt) cc_final: 0.8472 (tppt) REVERT: C 122 GLN cc_start: 0.7793 (pt0) cc_final: 0.7328 (tt0) REVERT: D 42 TRP cc_start: 0.8724 (t60) cc_final: 0.7206 (t60) REVERT: E 25 GLN cc_start: 0.7668 (tp-100) cc_final: 0.6795 (mp10) REVERT: F 155 LEU cc_start: 0.8865 (tt) cc_final: 0.8644 (tt) REVERT: F 236 TYR cc_start: 0.8378 (t80) cc_final: 0.8038 (t80) REVERT: F 318 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8366 (pp) REVERT: F 369 MET cc_start: 0.8545 (ttm) cc_final: 0.8294 (ttt) REVERT: H 122 GLN cc_start: 0.7685 (pt0) cc_final: 0.7219 (tt0) outliers start: 36 outliers final: 29 residues processed: 187 average time/residue: 0.0709 time to fit residues: 18.8001 Evaluate side-chains 197 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain D residue 17 HIS Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain F residue 49 HIS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 17 HIS Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 34 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 26 optimal weight: 0.1980 chunk 47 optimal weight: 0.0980 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 18 GLN ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.179272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.135742 restraints weight = 8746.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.134048 restraints weight = 9695.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.135250 restraints weight = 8040.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.139364 restraints weight = 5625.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.138992 restraints weight = 4558.088| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7422 Z= 0.127 Angle : 0.780 15.301 10053 Z= 0.369 Chirality : 0.046 0.223 1141 Planarity : 0.004 0.054 1272 Dihedral : 6.457 57.481 989 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 3.07 % Allowed : 31.07 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.29), residues: 888 helix: -0.66 (0.37), residues: 202 sheet: -2.02 (0.27), residues: 364 loop : -2.51 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.019 0.001 TYR F 217 PHE 0.013 0.001 PHE A 359 TRP 0.010 0.001 TRP B 41 HIS 0.001 0.000 HIS G 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 7422) covalent geometry : angle 0.77957 / 0.37 (10053) hydrogen bonds : bond 0.03529 / 2.30 ( 204) hydrogen bonds : angle 5.41183 / 3.66 ( 558) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8145 (p0) cc_final: 0.7806 (p0) REVERT: A 167 LEU cc_start: 0.8710 (tt) cc_final: 0.8048 (mp) REVERT: A 369 MET cc_start: 0.8165 (ttm) cc_final: 0.7947 (ttt) REVERT: C 94 LYS cc_start: 0.8812 (tptt) cc_final: 0.8470 (tppt) REVERT: C 122 GLN cc_start: 0.7693 (pt0) cc_final: 0.7372 (tt0) REVERT: D 40 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7665 (tpp) REVERT: E 25 GLN cc_start: 0.7429 (tp-100) cc_final: 0.6699 (mp10) REVERT: E 56 MET cc_start: 0.8145 (tpt) cc_final: 0.7682 (tpt) REVERT: F 87 ASP cc_start: 0.8177 (p0) cc_final: 0.7816 (p0) REVERT: F 164 MET cc_start: 0.7856 (mmm) cc_final: 0.7474 (mpp) REVERT: F 167 LEU cc_start: 0.8776 (tt) cc_final: 0.8095 (mp) REVERT: F 369 MET cc_start: 0.8246 (ttm) cc_final: 0.7994 (ttt) REVERT: H 122 GLN cc_start: 0.7591 (pt0) cc_final: 0.7244 (tt0) outliers start: 24 outliers final: 19 residues processed: 188 average time/residue: 0.0715 time to fit residues: 18.8696 Evaluate side-chains 180 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain D residue 17 HIS Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain F residue 49 HIS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain I residue 17 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 4 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 46 optimal weight: 0.0010 chunk 63 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 57 optimal weight: 0.0370 chunk 6 optimal weight: 4.9990 overall best weight: 0.4464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.181829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.135865 restraints weight = 8716.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.135611 restraints weight = 8708.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.136824 restraints weight = 8180.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.137689 restraints weight = 5094.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.138221 restraints weight = 4680.042| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7422 Z= 0.123 Angle : 0.785 16.830 10053 Z= 0.368 Chirality : 0.045 0.221 1141 Planarity : 0.004 0.054 1272 Dihedral : 5.943 58.960 989 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 4.48 % Allowed : 31.20 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.30), residues: 888 helix: -0.38 (0.38), residues: 202 sheet: -1.73 (0.27), residues: 364 loop : -2.40 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.017 0.001 TYR A 217 PHE 0.013 0.001 PHE A 359 TRP 0.010 0.001 TRP B 41 HIS 0.002 0.000 HIS I 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 7422) covalent geometry : angle 0.78543 / 0.37 (10053) hydrogen bonds : bond 0.03180 / 2.08 ( 204) hydrogen bonds : angle 5.21206 / 3.51 ( 558) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8194 (p0) cc_final: 0.7905 (p0) REVERT: A 164 MET cc_start: 0.7810 (mmm) cc_final: 0.7595 (mpp) REVERT: A 167 LEU cc_start: 0.8706 (tt) cc_final: 0.8044 (mp) REVERT: A 369 MET cc_start: 0.8284 (ttm) cc_final: 0.8074 (ttt) REVERT: C 94 LYS cc_start: 0.8847 (tptt) cc_final: 0.8456 (tppt) REVERT: D 22 GLU cc_start: 0.8058 (pm20) cc_final: 0.7793 (pm20) REVERT: D 40 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7648 (tpp) REVERT: E 25 GLN cc_start: 0.7650 (tp-100) cc_final: 0.7067 (mp10) REVERT: F 87 ASP cc_start: 0.8201 (p0) cc_final: 0.7906 (p0) REVERT: F 167 LEU cc_start: 0.8689 (tt) cc_final: 0.7989 (mp) REVERT: F 369 MET cc_start: 0.8362 (ttm) cc_final: 0.8077 (ttt) outliers start: 35 outliers final: 22 residues processed: 185 average time/residue: 0.0721 time to fit residues: 18.8932 Evaluate side-chains 180 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain F residue 49 HIS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain I residue 17 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 53 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 68 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 chunk 33 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN D 18 GLN ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.182305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.138490 restraints weight = 8700.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.139943 restraints weight = 9272.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140690 restraints weight = 7796.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.140835 restraints weight = 4947.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.141455 restraints weight = 4569.542| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7422 Z= 0.122 Angle : 0.788 18.718 10053 Z= 0.364 Chirality : 0.045 0.197 1141 Planarity : 0.004 0.054 1272 Dihedral : 5.670 58.672 989 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 3.20 % Allowed : 31.59 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.30), residues: 888 helix: -0.11 (0.39), residues: 200 sheet: -1.50 (0.28), residues: 364 loop : -2.38 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 47 TYR 0.021 0.001 TYR A 217 PHE 0.014 0.001 PHE A 359 TRP 0.011 0.001 TRP B 41 HIS 0.001 0.000 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 7422) covalent geometry : angle 0.78843 / 0.36 (10053) hydrogen bonds : bond 0.03030 / 1.97 ( 204) hydrogen bonds : angle 5.06946 / 3.42 ( 558) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8246 (p0) cc_final: 0.7981 (p0) REVERT: A 167 LEU cc_start: 0.8627 (tt) cc_final: 0.7924 (mp) REVERT: A 369 MET cc_start: 0.8283 (ttm) cc_final: 0.7984 (ttt) REVERT: C 94 LYS cc_start: 0.8862 (tptt) cc_final: 0.8412 (tppt) REVERT: D 22 GLU cc_start: 0.8073 (pm20) cc_final: 0.7868 (pm20) REVERT: E 25 GLN cc_start: 0.7573 (tp-100) cc_final: 0.7022 (mp10) REVERT: E 56 MET cc_start: 0.8208 (tpt) cc_final: 0.7763 (tpt) REVERT: F 87 ASP cc_start: 0.8274 (p0) cc_final: 0.7999 (p0) REVERT: F 167 LEU cc_start: 0.8641 (tt) cc_final: 0.7959 (mp) REVERT: F 168 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7395 (mt-10) REVERT: F 369 MET cc_start: 0.8264 (ttm) cc_final: 0.7978 (ttt) REVERT: J 56 MET cc_start: 0.8219 (tpt) cc_final: 0.7751 (tpt) outliers start: 25 outliers final: 19 residues processed: 176 average time/residue: 0.0761 time to fit residues: 18.7403 Evaluate side-chains 174 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain F residue 49 HIS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain I residue 17 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.171501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.129698 restraints weight = 8991.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.128529 restraints weight = 12126.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.129471 restraints weight = 11451.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.130260 restraints weight = 6541.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.130854 restraints weight = 5798.522| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 7422 Z= 0.287 Angle : 0.899 14.757 10053 Z= 0.433 Chirality : 0.051 0.259 1141 Planarity : 0.005 0.051 1272 Dihedral : 6.639 48.234 987 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.30 % Favored : 85.70 % Rotamer: Outliers : 4.48 % Allowed : 31.71 % Favored : 63.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.30), residues: 888 helix: 0.04 (0.39), residues: 202 sheet: -1.96 (0.27), residues: 366 loop : -2.41 (0.39), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 85 TYR 0.016 0.002 TYR A 79 PHE 0.022 0.002 PHE F 92 TRP 0.009 0.002 TRP F 145 HIS 0.002 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.29 ( 7422) covalent geometry : angle 0.89910 / 0.43 (10053) hydrogen bonds : bond 0.05115 / 3.37 ( 204) hydrogen bonds : angle 5.55788 / 3.74 ( 558) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8289 (ttm) cc_final: 0.7965 (ttt) REVERT: C 94 LYS cc_start: 0.8926 (tptt) cc_final: 0.8545 (tppt) REVERT: E 25 GLN cc_start: 0.7550 (tp-100) cc_final: 0.6843 (mp10) REVERT: F 156 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8031 (tt0) REVERT: F 369 MET cc_start: 0.8334 (ttm) cc_final: 0.8011 (ttt) REVERT: J 38 ASN cc_start: 0.8354 (m-40) cc_final: 0.8059 (m110) outliers start: 35 outliers final: 26 residues processed: 173 average time/residue: 0.0713 time to fit residues: 17.6329 Evaluate side-chains 174 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain F residue 49 HIS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 156 GLN Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain I residue 17 HIS Chi-restraints excluded: chain I residue 43 HIS Chi-restraints excluded: chain I residue 45 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 46 optimal weight: 0.0470 chunk 60 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 72 optimal weight: 0.1980 chunk 17 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 77 optimal weight: 0.0050 chunk 55 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 overall best weight: 0.6094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.179102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.135153 restraints weight = 8640.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.132528 restraints weight = 10645.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.134371 restraints weight = 9831.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.135369 restraints weight = 5867.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.135903 restraints weight = 5201.464| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7422 Z= 0.132 Angle : 0.834 14.273 10053 Z= 0.386 Chirality : 0.046 0.187 1141 Planarity : 0.004 0.054 1272 Dihedral : 5.698 39.890 987 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 2.94 % Allowed : 33.63 % Favored : 63.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.30), residues: 888 helix: 0.20 (0.40), residues: 202 sheet: -1.70 (0.27), residues: 380 loop : -2.24 (0.39), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 310 TYR 0.015 0.001 TYR A 217 PHE 0.014 0.001 PHE A 359 TRP 0.013 0.001 TRP B 41 HIS 0.002 0.000 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 7422) covalent geometry : angle 0.83439 / 0.39 (10053) hydrogen bonds : bond 0.03129 / 2.04 ( 204) hydrogen bonds : angle 5.19952 / 3.53 ( 558) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8115 (p0) cc_final: 0.7859 (p0) REVERT: A 167 LEU cc_start: 0.8712 (tt) cc_final: 0.8052 (mp) REVERT: A 369 MET cc_start: 0.8311 (ttm) cc_final: 0.7987 (ttt) REVERT: C 94 LYS cc_start: 0.8930 (tptt) cc_final: 0.8499 (tppt) REVERT: E 25 GLN cc_start: 0.7636 (tp-100) cc_final: 0.7034 (mp10) REVERT: F 87 ASP cc_start: 0.8109 (p0) cc_final: 0.7854 (p0) REVERT: F 156 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: F 167 LEU cc_start: 0.8625 (tt) cc_final: 0.7955 (mp) REVERT: F 369 MET cc_start: 0.8387 (ttm) cc_final: 0.8067 (ttt) REVERT: G 47 ARG cc_start: 0.7255 (mpp80) cc_final: 0.7033 (mpp80) REVERT: J 56 MET cc_start: 0.8374 (tpt) cc_final: 0.8122 (tpt) outliers start: 23 outliers final: 21 residues processed: 175 average time/residue: 0.0729 time to fit residues: 18.2570 Evaluate side-chains 180 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain F residue 49 HIS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 156 GLN Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain I residue 17 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 84 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 50 optimal weight: 0.0770 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 78 optimal weight: 0.0870 chunk 63 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.181988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136993 restraints weight = 8720.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.137160 restraints weight = 9063.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.138226 restraints weight = 8652.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.138879 restraints weight = 5150.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.139306 restraints weight = 4816.149| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7422 Z= 0.125 Angle : 0.803 13.783 10053 Z= 0.371 Chirality : 0.045 0.193 1141 Planarity : 0.004 0.053 1272 Dihedral : 5.112 25.981 987 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 2.56 % Allowed : 33.76 % Favored : 63.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.30), residues: 888 helix: 0.35 (0.40), residues: 202 sheet: -1.49 (0.27), residues: 378 loop : -2.20 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.017 0.001 TYR A 217 PHE 0.015 0.001 PHE A 359 TRP 0.015 0.001 TRP B 41 HIS 0.001 0.000 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 7422) covalent geometry : angle 0.80280 / 0.37 (10053) hydrogen bonds : bond 0.02739 / 1.78 ( 204) hydrogen bonds : angle 4.94238 / 3.34 ( 558) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8258 (p0) cc_final: 0.7973 (p0) REVERT: A 167 LEU cc_start: 0.8616 (tt) cc_final: 0.8012 (mp) REVERT: A 369 MET cc_start: 0.8105 (ttm) cc_final: 0.7888 (ttt) REVERT: C 94 LYS cc_start: 0.8899 (tptt) cc_final: 0.8384 (tppt) REVERT: D 22 GLU cc_start: 0.8418 (pm20) cc_final: 0.8135 (pm20) REVERT: E 25 GLN cc_start: 0.7653 (tp-100) cc_final: 0.7112 (mp10) REVERT: E 56 MET cc_start: 0.8051 (tpt) cc_final: 0.7653 (tpt) REVERT: F 87 ASP cc_start: 0.8267 (p0) cc_final: 0.7974 (p0) REVERT: F 167 LEU cc_start: 0.8614 (tt) cc_final: 0.7960 (mp) REVERT: F 369 MET cc_start: 0.8165 (ttm) cc_final: 0.7878 (ttt) REVERT: J 56 MET cc_start: 0.8405 (tpt) cc_final: 0.8017 (tpt) outliers start: 20 outliers final: 20 residues processed: 173 average time/residue: 0.0710 time to fit residues: 17.2952 Evaluate side-chains 170 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain F residue 49 HIS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain I residue 17 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 11 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 47 optimal weight: 0.0770 chunk 34 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 0.2980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.181219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.136925 restraints weight = 8682.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.139565 restraints weight = 9444.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.139572 restraints weight = 7789.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.139753 restraints weight = 4730.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.140441 restraints weight = 4300.390| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7422 Z= 0.130 Angle : 0.805 13.577 10053 Z= 0.375 Chirality : 0.045 0.180 1141 Planarity : 0.004 0.052 1272 Dihedral : 5.115 24.865 987 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 2.69 % Allowed : 33.25 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.30), residues: 888 helix: 0.38 (0.40), residues: 200 sheet: -1.38 (0.27), residues: 380 loop : -2.07 (0.39), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 47 TYR 0.016 0.001 TYR A 217 PHE 0.015 0.001 PHE A 359 TRP 0.014 0.001 TRP B 41 HIS 0.001 0.000 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 7422) covalent geometry : angle 0.80481 / 0.37 (10053) hydrogen bonds : bond 0.02909 / 1.89 ( 204) hydrogen bonds : angle 4.94750 / 3.34 ( 558) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1283.25 seconds wall clock time: 22 minutes 49.44 seconds (1369.44 seconds total)