Starting phenix.real_space_refine on Tue Sep 24 08:03:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnf_9851/09_2024/6jnf_9851.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnf_9851/09_2024/6jnf_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnf_9851/09_2024/6jnf_9851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnf_9851/09_2024/6jnf_9851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnf_9851/09_2024/6jnf_9851.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnf_9851/09_2024/6jnf_9851.cif" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7271 Number of models: 1 Model: "" Number of chains: 6 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: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'46E': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: F, G, H, I, J Time building chain proxies: 5.17, per 1000 atoms: 0.71 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: 1.64 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.87 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: 1.84 Time building geometry restraints manager: 1.93 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 - 17.79: 3738 17.79 - 35.59: 503 35.59 - 53.38: 90 53.38 - 71.17: 25 71.17 - 88.97: 17 Dihedral angle restraints: 4373 sinusoidal: 1719 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 4370 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 19.860 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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= 0.544 Angle : 1.227 17.959 10053 Z= 0.617 Chirality : 0.063 0.301 1141 Planarity : 0.007 0.072 1272 Dihedral : 17.480 88.966 2653 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.24 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.015 0.002 TRP D 36 HIS 0.007 0.001 HIS I 43 PHE 0.030 0.003 PHE A 92 TYR 0.024 0.002 TYR F 143 ARG 0.003 0.001 ARG F 330 *********************** 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 fitting. rotamer outliers: 8 poor density : 196 time to evaluate : 0.755 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: 0.6500 (p90) cc_final: 0.6296 (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: 0.8979 (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: 0.1936 time to fit residues: 50.9938 Evaluate side-chains 161 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 157 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 74 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN F 65 ASN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2359 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= 0.189 Angle : 0.779 11.998 10053 Z= 0.382 Chirality : 0.045 0.162 1141 Planarity : 0.005 0.054 1272 Dihedral : 8.399 61.396 1003 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 2.05 % Allowed : 24.55 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.25), residues: 888 helix: -3.07 (0.26), residues: 210 sheet: -2.93 (0.25), residues: 366 loop : -3.31 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 36 HIS 0.002 0.001 HIS A 102 PHE 0.011 0.001 PHE A 201 TYR 0.013 0.001 TYR I 30 ARG 0.004 0.000 ARG B 47 *********************** 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 199 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 183 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8352 (p0) cc_final: 0.8070 (p0) REVERT: A 164 MET cc_start: 0.8022 (mpp) cc_final: 0.7685 (mmm) REVERT: A 167 LEU cc_start: 0.8563 (tt) cc_final: 0.7624 (mp) REVERT: A 203 GLN cc_start: 0.7777 (pp30) cc_final: 0.7431 (pp30) REVERT: A 217 TYR cc_start: 0.8301 (t80) cc_final: 0.8059 (t80) REVERT: A 367 LEU cc_start: 0.8296 (tp) cc_final: 0.8081 (tp) REVERT: A 369 MET cc_start: 0.8824 (ttm) cc_final: 0.8424 (ttt) REVERT: B 35 PHE cc_start: 0.9090 (t80) cc_final: 0.8813 (t80) REVERT: C 87 PHE cc_start: 0.6662 (p90) cc_final: 0.6334 (p90) REVERT: C 94 LYS cc_start: 0.8962 (tptt) cc_final: 0.8440 (tppt) REVERT: D 40 MET cc_start: 0.8438 (tpp) cc_final: 0.7957 (tpp) REVERT: D 42 TRP cc_start: 0.8502 (t60) cc_final: 0.7551 (t60) REVERT: E 41 PHE cc_start: 0.9226 (m-80) cc_final: 0.8950 (m-80) REVERT: F 87 ASP cc_start: 0.8366 (p0) cc_final: 0.8083 (p0) REVERT: F 164 MET cc_start: 0.8060 (mpp) cc_final: 0.7797 (mmm) REVERT: F 167 LEU cc_start: 0.8590 (tt) cc_final: 0.7664 (mp) REVERT: F 203 GLN cc_start: 0.7720 (pp30) cc_final: 0.7340 (pp30) REVERT: G 35 PHE cc_start: 0.9112 (t80) cc_final: 0.8790 (t80) REVERT: J 41 PHE cc_start: 0.9034 (m-80) cc_final: 0.8811 (m-80) outliers start: 16 outliers final: 12 residues processed: 193 average time/residue: 0.1892 time to fit residues: 48.5870 Evaluate side-chains 180 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 168 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 B residue 39 LEU Chi-restraints excluded: chain C residue 88 VAL 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 G residue 39 LEU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain I residue 17 HIS Chi-restraints excluded: chain I residue 40 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 30.0000 chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2633 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= 0.232 Angle : 0.783 11.786 10053 Z= 0.377 Chirality : 0.046 0.187 1141 Planarity : 0.004 0.048 1272 Dihedral : 7.769 67.174 1001 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.95 % Favored : 87.05 % Rotamer: Outliers : 4.22 % Allowed : 25.32 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.27), residues: 888 helix: -1.75 (0.33), residues: 204 sheet: -2.58 (0.26), residues: 366 loop : -2.97 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 260 HIS 0.001 0.000 HIS G 43 PHE 0.014 0.001 PHE A 92 TYR 0.010 0.001 TYR A 79 ARG 0.003 0.000 ARG B 47 *********************** 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 205 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 172 time to evaluate : 0.805 Fit side-chains REVERT: A 164 MET cc_start: 0.7983 (mpp) cc_final: 0.7736 (mmm) REVERT: A 217 TYR cc_start: 0.8324 (t80) cc_final: 0.8117 (t80) REVERT: A 365 GLN cc_start: 0.7812 (pm20) cc_final: 0.7610 (pp30) REVERT: A 369 MET cc_start: 0.8795 (ttm) cc_final: 0.8485 (ttt) REVERT: B 35 PHE cc_start: 0.8998 (t80) cc_final: 0.8707 (t80) REVERT: C 87 PHE cc_start: 0.6493 (p90) cc_final: 0.6083 (p90) REVERT: C 94 LYS cc_start: 0.8955 (tptt) cc_final: 0.8460 (tppt) REVERT: C 121 GLN cc_start: 0.8772 (tp-100) cc_final: 0.8557 (tt0) REVERT: D 18 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8807 (tp40) REVERT: D 42 TRP cc_start: 0.8877 (t60) cc_final: 0.7458 (t60) REVERT: D 44 LEU cc_start: 0.8764 (mm) cc_final: 0.8440 (mm) REVERT: E 25 GLN cc_start: 0.7744 (tp-100) cc_final: 0.6907 (mp10) REVERT: E 41 PHE cc_start: 0.9248 (m-80) cc_final: 0.8961 (m-80) REVERT: F 87 ASP cc_start: 0.8368 (p0) cc_final: 0.8048 (p0) REVERT: F 164 MET cc_start: 0.8002 (mpp) cc_final: 0.7747 (mmm) REVERT: F 203 GLN cc_start: 0.7779 (pp30) cc_final: 0.7567 (pp30) REVERT: F 217 TYR cc_start: 0.8354 (t80) cc_final: 0.8151 (t80) REVERT: F 219 ARG cc_start: 0.8492 (ttt180) cc_final: 0.7844 (ttt-90) REVERT: F 369 MET cc_start: 0.8814 (ttm) cc_final: 0.8500 (ttt) REVERT: G 35 PHE cc_start: 0.9003 (t80) cc_final: 0.8700 (t80) REVERT: H 122 GLN cc_start: 0.8027 (pt0) cc_final: 0.7447 (tt0) REVERT: I 44 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8269 (mm) REVERT: J 41 PHE cc_start: 0.9058 (m-80) cc_final: 0.8666 (m-80) outliers start: 33 outliers final: 27 residues processed: 190 average time/residue: 0.1810 time to fit residues: 46.5360 Evaluate side-chains 191 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 163 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 318 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 THR 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 C residue 114 SER 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 318 LEU Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 351 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 88 VAL Chi-restraints excluded: chain I residue 17 HIS Chi-restraints excluded: chain I residue 44 LEU 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 79 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 0.0170 chunk 76 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7422 Z= 0.273 Angle : 0.804 11.996 10053 Z= 0.387 Chirality : 0.047 0.197 1141 Planarity : 0.004 0.049 1272 Dihedral : 7.728 74.539 1001 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % Rotamer: Outliers : 5.12 % Allowed : 27.24 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.29), residues: 888 helix: -0.97 (0.36), residues: 202 sheet: -2.32 (0.26), residues: 366 loop : -2.71 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.002 0.000 HIS G 43 PHE 0.017 0.001 PHE F 92 TYR 0.011 0.001 TYR A 79 ARG 0.002 0.000 ARG B 47 *********************** 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 208 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 168 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8614 (tt) cc_final: 0.7772 (mp) REVERT: A 369 MET cc_start: 0.8783 (ttm) cc_final: 0.8478 (ttt) REVERT: B 35 PHE cc_start: 0.8961 (t80) cc_final: 0.8660 (t80) REVERT: C 87 PHE cc_start: 0.6525 (p90) cc_final: 0.6244 (p90) REVERT: C 94 LYS cc_start: 0.8958 (tptt) cc_final: 0.8462 (tppt) REVERT: C 121 GLN cc_start: 0.8771 (tp-100) cc_final: 0.8545 (tt0) REVERT: C 122 GLN cc_start: 0.7988 (pt0) cc_final: 0.7552 (tt0) REVERT: D 18 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8715 (tp40) REVERT: D 42 TRP cc_start: 0.8820 (t60) cc_final: 0.7308 (t60) REVERT: D 44 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8569 (mm) REVERT: E 25 GLN cc_start: 0.7724 (tp-100) cc_final: 0.6942 (mp10) REVERT: E 41 PHE cc_start: 0.9233 (m-80) cc_final: 0.8920 (m-80) REVERT: F 167 LEU cc_start: 0.8628 (tt) cc_final: 0.7810 (mp) REVERT: F 203 GLN cc_start: 0.7801 (pp30) cc_final: 0.7584 (pp30) REVERT: F 219 ARG cc_start: 0.8462 (ttt180) cc_final: 0.7787 (ttt-90) REVERT: F 369 MET cc_start: 0.8794 (ttm) cc_final: 0.8514 (ttt) REVERT: G 35 PHE cc_start: 0.8969 (t80) cc_final: 0.8665 (t80) REVERT: H 122 GLN cc_start: 0.7929 (pt0) cc_final: 0.7512 (tt0) REVERT: I 42 TRP cc_start: 0.8760 (t60) cc_final: 0.7423 (t60) REVERT: J 38 ASN cc_start: 0.8250 (m110) cc_final: 0.8019 (m110) REVERT: J 41 PHE cc_start: 0.9084 (m-80) cc_final: 0.8679 (m-80) outliers start: 40 outliers final: 34 residues processed: 192 average time/residue: 0.1765 time to fit residues: 46.5847 Evaluate side-chains 198 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 351 THR 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 C residue 114 SER Chi-restraints excluded: chain D residue 17 HIS Chi-restraints excluded: chain D residue 44 LEU 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 357 LEU Chi-restraints excluded: chain G residue 22 THR 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 I residue 17 HIS Chi-restraints excluded: chain I residue 43 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 48 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3086 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= 0.254 Angle : 0.803 13.722 10053 Z= 0.385 Chirality : 0.047 0.217 1141 Planarity : 0.004 0.050 1272 Dihedral : 7.460 80.182 1001 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 4.86 % Allowed : 29.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.29), residues: 888 helix: -0.68 (0.37), residues: 214 sheet: -2.09 (0.27), residues: 364 loop : -2.60 (0.39), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 260 HIS 0.001 0.000 HIS G 43 PHE 0.015 0.001 PHE F 92 TYR 0.015 0.001 TYR F 217 ARG 0.002 0.000 ARG G 47 *********************** 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 207 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 169 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8270 (ttt-90) cc_final: 0.7733 (mtp180) REVERT: A 369 MET cc_start: 0.8759 (ttm) cc_final: 0.8474 (ttt) REVERT: B 35 PHE cc_start: 0.8939 (t80) cc_final: 0.8646 (t80) REVERT: C 94 LYS cc_start: 0.8944 (tptt) cc_final: 0.8460 (tppt) REVERT: C 121 GLN cc_start: 0.8839 (tp-100) cc_final: 0.8632 (tt0) REVERT: C 122 GLN cc_start: 0.8018 (pt0) cc_final: 0.7646 (tt0) REVERT: E 25 GLN cc_start: 0.7764 (tp-100) cc_final: 0.7071 (mp10) REVERT: E 38 ASN cc_start: 0.8009 (m110) cc_final: 0.7762 (m110) REVERT: E 41 PHE cc_start: 0.9238 (m-80) cc_final: 0.8919 (m-80) REVERT: F 219 ARG cc_start: 0.8364 (ttt180) cc_final: 0.7877 (ttt-90) REVERT: F 369 MET cc_start: 0.8771 (ttm) cc_final: 0.8453 (ttt) REVERT: G 35 PHE cc_start: 0.8952 (t80) cc_final: 0.8660 (t80) REVERT: H 122 GLN cc_start: 0.7948 (pt0) cc_final: 0.7593 (tt0) REVERT: I 42 TRP cc_start: 0.8681 (t60) cc_final: 0.7348 (t60) REVERT: J 38 ASN cc_start: 0.8172 (m110) cc_final: 0.7921 (m110) REVERT: J 41 PHE cc_start: 0.9181 (m-80) cc_final: 0.8833 (m-80) outliers start: 38 outliers final: 32 residues processed: 193 average time/residue: 0.1737 time to fit residues: 45.2500 Evaluate side-chains 194 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 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 C residue 114 SER 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 357 LEU Chi-restraints excluded: chain G residue 22 THR 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 I residue 17 HIS Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain J residue 32 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 0.0060 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 20.0000 chunk 82 optimal weight: 7.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN E 38 ASN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3326 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= 0.188 Angle : 0.798 17.074 10053 Z= 0.373 Chirality : 0.046 0.225 1141 Planarity : 0.004 0.051 1272 Dihedral : 6.969 80.858 1001 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 4.22 % Allowed : 31.33 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.30), residues: 888 helix: -0.21 (0.39), residues: 200 sheet: -1.78 (0.27), residues: 364 loop : -2.44 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.001 0.000 HIS G 43 PHE 0.014 0.001 PHE A 359 TYR 0.016 0.001 TYR F 217 ARG 0.002 0.000 ARG B 47 *********************** 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 205 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 172 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8208 (p0) cc_final: 0.7886 (p0) REVERT: A 156 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: A 167 LEU cc_start: 0.8548 (tt) cc_final: 0.7700 (mp) REVERT: A 203 GLN cc_start: 0.8174 (pp30) cc_final: 0.7965 (tm-30) REVERT: A 219 ARG cc_start: 0.8214 (ttt-90) cc_final: 0.7705 (mtp180) REVERT: A 369 MET cc_start: 0.8743 (ttm) cc_final: 0.8393 (ttt) REVERT: B 35 PHE cc_start: 0.8921 (t80) cc_final: 0.8679 (t80) REVERT: C 94 LYS cc_start: 0.8917 (tptt) cc_final: 0.8451 (tppt) REVERT: C 121 GLN cc_start: 0.8827 (tp-100) cc_final: 0.8626 (tt0) REVERT: E 25 GLN cc_start: 0.7714 (tp-100) cc_final: 0.7124 (mp10) REVERT: E 38 ASN cc_start: 0.8041 (m-40) cc_final: 0.7796 (m110) REVERT: E 41 PHE cc_start: 0.9253 (m-80) cc_final: 0.8940 (m-80) REVERT: F 87 ASP cc_start: 0.8224 (p0) cc_final: 0.7902 (p0) REVERT: F 156 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: F 167 LEU cc_start: 0.8546 (tt) cc_final: 0.7722 (mp) REVERT: F 369 MET cc_start: 0.8703 (ttm) cc_final: 0.8365 (ttt) REVERT: G 35 PHE cc_start: 0.8937 (t80) cc_final: 0.8675 (t80) REVERT: I 42 TRP cc_start: 0.8689 (t60) cc_final: 0.7376 (t60) REVERT: I 44 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8519 (mm) REVERT: J 38 ASN cc_start: 0.8107 (m110) cc_final: 0.7903 (m110) REVERT: J 41 PHE cc_start: 0.9198 (m-80) cc_final: 0.8963 (m-80) outliers start: 33 outliers final: 23 residues processed: 196 average time/residue: 0.1630 time to fit residues: 44.0202 Evaluate side-chains 190 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 156 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 THR 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 114 SER Chi-restraints excluded: chain D residue 17 HIS 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 156 GLN 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 Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain J residue 34 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3483 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= 0.206 Angle : 0.827 18.926 10053 Z= 0.379 Chirality : 0.046 0.211 1141 Planarity : 0.004 0.051 1272 Dihedral : 6.792 80.778 1001 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 4.86 % Allowed : 30.69 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.30), residues: 888 helix: -0.11 (0.38), residues: 208 sheet: -1.65 (0.27), residues: 378 loop : -2.39 (0.39), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 260 HIS 0.001 0.000 HIS G 43 PHE 0.014 0.001 PHE A 359 TYR 0.017 0.001 TYR F 217 ARG 0.002 0.000 ARG G 47 *********************** 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 206 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 168 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8272 (p0) cc_final: 0.7950 (p0) REVERT: A 156 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: A 167 LEU cc_start: 0.8546 (tt) cc_final: 0.7697 (mp) REVERT: A 203 GLN cc_start: 0.7995 (pp30) cc_final: 0.7729 (tm-30) REVERT: A 219 ARG cc_start: 0.8182 (ttt-90) cc_final: 0.7716 (mtp180) REVERT: A 369 MET cc_start: 0.8688 (ttm) cc_final: 0.8337 (ttt) REVERT: B 35 PHE cc_start: 0.8812 (t80) cc_final: 0.8529 (t80) REVERT: C 94 LYS cc_start: 0.8904 (tptt) cc_final: 0.8446 (tppt) REVERT: D 18 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8316 (tp40) REVERT: E 25 GLN cc_start: 0.7690 (tp-100) cc_final: 0.7145 (mp10) REVERT: E 41 PHE cc_start: 0.9263 (m-80) cc_final: 0.8953 (m-80) REVERT: F 87 ASP cc_start: 0.8281 (p0) cc_final: 0.7955 (p0) REVERT: F 167 LEU cc_start: 0.8549 (tt) cc_final: 0.7731 (mp) REVERT: F 219 ARG cc_start: 0.8436 (ttt-90) cc_final: 0.8137 (mtp180) REVERT: F 369 MET cc_start: 0.8683 (ttm) cc_final: 0.8339 (ttt) REVERT: G 35 PHE cc_start: 0.8823 (t80) cc_final: 0.8525 (t80) REVERT: I 42 TRP cc_start: 0.8723 (t60) cc_final: 0.7418 (t60) REVERT: J 38 ASN cc_start: 0.7969 (m110) cc_final: 0.7768 (m110) REVERT: J 41 PHE cc_start: 0.9222 (m-80) cc_final: 0.8899 (m-80) outliers start: 38 outliers final: 29 residues processed: 194 average time/residue: 0.1714 time to fit residues: 44.9626 Evaluate side-chains 192 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 119 LEU Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 318 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 93 THR Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain D residue 17 HIS Chi-restraints excluded: chain D residue 18 GLN 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 119 LEU Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 318 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 88 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain I residue 17 HIS Chi-restraints excluded: chain J residue 34 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 74 optimal weight: 30.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7422 Z= 0.271 Angle : 0.864 20.051 10053 Z= 0.402 Chirality : 0.047 0.239 1141 Planarity : 0.004 0.051 1272 Dihedral : 7.029 80.031 1000 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.30), residues: 888 helix: -0.08 (0.39), residues: 206 sheet: -1.73 (0.27), residues: 380 loop : -2.32 (0.40), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 260 HIS 0.002 0.000 HIS G 43 PHE 0.016 0.002 PHE F 92 TYR 0.017 0.002 TYR A 217 ARG 0.004 0.000 ARG G 47 *********************** 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 203 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 168 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: A 167 LEU cc_start: 0.8415 (tt) cc_final: 0.7608 (mp) REVERT: A 203 GLN cc_start: 0.8037 (pp30) cc_final: 0.7760 (tm-30) REVERT: A 219 ARG cc_start: 0.8218 (ttt-90) cc_final: 0.7724 (mtp180) REVERT: A 369 MET cc_start: 0.8686 (ttm) cc_final: 0.8312 (ttt) REVERT: B 35 PHE cc_start: 0.8804 (t80) cc_final: 0.8504 (t80) REVERT: C 94 LYS cc_start: 0.8976 (tptt) cc_final: 0.8482 (tppt) REVERT: D 18 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8351 (tp40) REVERT: D 22 GLU cc_start: 0.8684 (pm20) cc_final: 0.8388 (pm20) REVERT: D 40 MET cc_start: 0.8521 (tpp) cc_final: 0.8262 (tmm) REVERT: E 25 GLN cc_start: 0.7704 (tp-100) cc_final: 0.7176 (mp10) REVERT: E 41 PHE cc_start: 0.9251 (m-80) cc_final: 0.8957 (m-80) REVERT: F 167 LEU cc_start: 0.8491 (tt) cc_final: 0.7721 (mp) REVERT: F 369 MET cc_start: 0.8694 (ttm) cc_final: 0.8328 (ttt) REVERT: G 35 PHE cc_start: 0.8816 (t80) cc_final: 0.8502 (t80) REVERT: I 42 TRP cc_start: 0.8715 (t60) cc_final: 0.7235 (t60) REVERT: J 38 ASN cc_start: 0.8025 (m110) cc_final: 0.7796 (m110) REVERT: J 41 PHE cc_start: 0.9227 (m-80) cc_final: 0.8938 (m-80) outliers start: 35 outliers final: 31 residues processed: 190 average time/residue: 0.1680 time to fit residues: 43.5332 Evaluate side-chains 194 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 161 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 119 LEU Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 318 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 93 THR Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain D residue 17 HIS Chi-restraints excluded: chain D residue 18 GLN 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 119 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 357 LEU Chi-restraints excluded: chain G residue 22 THR 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 I residue 17 HIS Chi-restraints excluded: chain J residue 34 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 30.0000 chunk 78 optimal weight: 0.0040 chunk 51 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3640 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= 0.199 Angle : 0.839 18.649 10053 Z= 0.388 Chirality : 0.046 0.201 1141 Planarity : 0.004 0.051 1272 Dihedral : 6.696 80.219 1000 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 3.96 % Allowed : 32.10 % Favored : 63.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.30), residues: 888 helix: -0.02 (0.38), residues: 206 sheet: -1.50 (0.27), residues: 380 loop : -2.31 (0.39), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.001 0.000 HIS A 102 PHE 0.014 0.001 PHE A 359 TYR 0.024 0.001 TYR F 217 ARG 0.004 0.000 ARG G 47 *********************** 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 197 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 166 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8194 (p0) cc_final: 0.7878 (p0) REVERT: A 167 LEU cc_start: 0.8431 (tt) cc_final: 0.7695 (mp) REVERT: A 219 ARG cc_start: 0.8144 (ttt-90) cc_final: 0.7672 (mtp180) REVERT: A 369 MET cc_start: 0.8645 (ttm) cc_final: 0.8283 (ttt) REVERT: B 35 PHE cc_start: 0.8796 (t80) cc_final: 0.8523 (t80) REVERT: C 94 LYS cc_start: 0.8956 (tptt) cc_final: 0.8466 (tppt) REVERT: D 18 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8341 (tp40) REVERT: D 22 GLU cc_start: 0.8670 (pm20) cc_final: 0.7867 (pm20) REVERT: D 40 MET cc_start: 0.8486 (tpp) cc_final: 0.8247 (tmm) REVERT: E 25 GLN cc_start: 0.7744 (tp-100) cc_final: 0.7274 (mp10) REVERT: E 41 PHE cc_start: 0.9241 (m-80) cc_final: 0.8942 (m-80) REVERT: F 87 ASP cc_start: 0.8184 (p0) cc_final: 0.7875 (p0) REVERT: F 167 LEU cc_start: 0.8443 (tt) cc_final: 0.7732 (mp) REVERT: F 203 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: F 369 MET cc_start: 0.8670 (ttm) cc_final: 0.8306 (ttt) REVERT: G 35 PHE cc_start: 0.8805 (t80) cc_final: 0.8536 (t80) REVERT: J 41 PHE cc_start: 0.9225 (m-80) cc_final: 0.8978 (m-80) outliers start: 31 outliers final: 27 residues processed: 188 average time/residue: 0.1555 time to fit residues: 39.9415 Evaluate side-chains 191 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 119 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 318 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 93 THR Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain D residue 18 GLN 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 88 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 318 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 J residue 34 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 GLN ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7422 Z= 0.310 Angle : 0.871 17.146 10053 Z= 0.410 Chirality : 0.048 0.208 1141 Planarity : 0.004 0.050 1272 Dihedral : 6.994 79.586 999 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.18 % Favored : 86.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.30), residues: 888 helix: 0.08 (0.39), residues: 206 sheet: -1.76 (0.27), residues: 380 loop : -2.23 (0.40), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.001 0.000 HIS G 43 PHE 0.018 0.002 PHE F 92 TYR 0.017 0.002 TYR F 217 ARG 0.005 0.000 ARG G 47 ********************** 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 196 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 161 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8462 (tt) REVERT: A 219 ARG cc_start: 0.8215 (ttt-90) cc_final: 0.7753 (mtp180) REVERT: A 369 MET cc_start: 0.8653 (ttm) cc_final: 0.8271 (ttt) REVERT: B 35 PHE cc_start: 0.8809 (t80) cc_final: 0.8493 (t80) REVERT: C 94 LYS cc_start: 0.8974 (tptt) cc_final: 0.8482 (tppt) REVERT: D 18 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8299 (tp40) REVERT: D 22 GLU cc_start: 0.8623 (pm20) cc_final: 0.7866 (pm20) REVERT: D 40 MET cc_start: 0.8456 (tpp) cc_final: 0.8245 (tmm) REVERT: E 25 GLN cc_start: 0.7725 (tp-100) cc_final: 0.7183 (mp10) REVERT: E 41 PHE cc_start: 0.9256 (m-80) cc_final: 0.8965 (m-80) REVERT: F 167 LEU cc_start: 0.8446 (tt) cc_final: 0.7644 (mp) REVERT: F 203 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: F 369 MET cc_start: 0.8691 (ttm) cc_final: 0.8281 (ttt) REVERT: G 35 PHE cc_start: 0.8826 (t80) cc_final: 0.8521 (t80) REVERT: J 38 ASN cc_start: 0.8025 (m110) cc_final: 0.7796 (m110) REVERT: J 41 PHE cc_start: 0.9241 (m-80) cc_final: 0.9007 (m-80) outliers start: 35 outliers final: 32 residues processed: 182 average time/residue: 0.1648 time to fit residues: 41.3191 Evaluate side-chains 195 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 160 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 119 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 318 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 93 THR Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 43 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 88 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 203 GLN 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 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 88 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain I residue 17 HIS Chi-restraints excluded: chain J residue 34 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 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 = 0.4129 r_free = 0.4129 target = 0.174713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128226 restraints weight = 8885.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.125449 restraints weight = 10389.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.127623 restraints weight = 9342.050| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.155 7422 Z= 0.304 Angle : 1.187 59.187 10053 Z= 0.649 Chirality : 0.049 0.386 1141 Planarity : 0.006 0.148 1272 Dihedral : 7.003 79.593 999 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.06 % Favored : 86.94 % Rotamer: Outliers : 4.73 % Allowed : 31.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.30), residues: 888 helix: 0.11 (0.39), residues: 206 sheet: -1.76 (0.27), residues: 380 loop : -2.23 (0.40), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 260 HIS 0.002 0.001 HIS D 17 PHE 0.017 0.002 PHE F 92 TYR 0.013 0.002 TYR F 217 ARG 0.005 0.000 ARG G 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1656.68 seconds wall clock time: 30 minutes 7.12 seconds (1807.12 seconds total)