Starting phenix.real_space_refine on Wed Feb 14 03:00:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvq_22510/02_2024/7jvq_22510_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvq_22510/02_2024/7jvq_22510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvq_22510/02_2024/7jvq_22510.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvq_22510/02_2024/7jvq_22510.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvq_22510/02_2024/7jvq_22510_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvq_22510/02_2024/7jvq_22510_updated.pdb" } resolution = 3.0 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5439 2.51 5 N 1449 2.21 5 O 1541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 23": "NH1" <-> "NH2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "R ARG 52": "NH1" <-> "NH2" Residue "R ARG 55": "NH1" <-> "NH2" Residue "R ARG 216": "NH1" <-> "NH2" Residue "R ARG 219": "NH1" <-> "NH2" Residue "R ARG 226": "NH1" <-> "NH2" Residue "R ARG 233": "NH1" <-> "NH2" Residue "R ARG 266": "NH1" <-> "NH2" Residue "R ARG 338": "NH1" <-> "NH2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 19": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8485 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2273 Classifications: {'peptide': 286} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 10, 'TRANS': 275} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1989 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 214 Unusual residues: {'CLR': 5, 'OR9': 1, 'PLM': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Time building chain proxies: 5.15, per 1000 atoms: 0.61 Number of scatterers: 8485 At special positions: 0 Unit cell: (95.316, 98.358, 121.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1541 8.00 N 1449 7.00 C 5439 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.7 seconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 10 sheets defined 39.4% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'R' and resid 22 through 50 Processing helix chain 'R' and resid 53 through 56 No H-bonds generated for 'chain 'R' and resid 53 through 56' Processing helix chain 'R' and resid 59 through 76 removed outlier: 3.582A pdb=" N SER R 69 " --> pdb=" O LEU R 66 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP R 70 " --> pdb=" O ALA R 67 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL R 75 " --> pdb=" O LEU R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 87 Processing helix chain 'R' and resid 93 through 126 removed outlier: 3.867A pdb=" N ASN R 97 " --> pdb=" O SER R 94 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL R 100 " --> pdb=" O ASN R 97 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET R 105 " --> pdb=" O PHE R 102 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER R 107 " --> pdb=" O ILE R 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR R 108 " --> pdb=" O MET R 105 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA R 109 " --> pdb=" O CYS R 106 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU R 112 " --> pdb=" O ALA R 109 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA R 124 " --> pdb=" O ARG R 121 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE R 125 " --> pdb=" O TYR R 122 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER R 126 " --> pdb=" O TRP R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 134 Processing helix chain 'R' and resid 137 through 161 removed outlier: 4.823A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 192 through 202 Processing helix chain 'R' and resid 204 through 241 Processing helix chain 'R' and resid 265 through 297 Proline residue: R 287 - end of helix removed outlier: 4.092A pdb=" N LEU R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 310 through 332 removed outlier: 4.358A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER R 325 " --> pdb=" O TRP R 321 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU R 326 " --> pdb=" O ALA R 322 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 335 through 345 Processing helix chain 'A' and resid 10 through 39 Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.640A pdb=" N ASN A 101 " --> pdb=" O GLN A 98 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP A 102 " --> pdb=" O CYS A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 98 through 102' Processing helix chain 'A' and resid 116 through 129 removed outlier: 4.077A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 184 through 204 removed outlier: 4.241A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 242 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 3.522A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 removed outlier: 3.947A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing sheet with id= A, first strand: chain 'A' and resid 211 through 215 removed outlier: 7.286A pdb=" N VAL A 139 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N HIS A 214 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU A 141 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 105 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASN A 80 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU A 43 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N HIS A 82 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU A 45 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N PHE A 84 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLY A 47 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL A 86 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.148A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.144A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.896A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.139A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.975A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.731A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.925A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.473A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1038 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: 2.42 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2456 1.34 - 1.46: 2093 1.46 - 1.59: 4046 1.59 - 1.71: 0 1.71 - 1.83: 76 Bond restraints: 8671 Sorted by residual: bond pdb=" C ILE R 205 " pdb=" N PRO R 206 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.28e-02 6.10e+03 3.52e+00 bond pdb=" C MET R 78 " pdb=" N PRO R 79 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.30e-02 5.92e+03 3.46e+00 bond pdb=" C ILE R 157 " pdb=" N PRO R 158 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.23e-02 6.61e+03 2.93e+00 bond pdb=" C THR R 136 " pdb=" N PRO R 137 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.87e+00 bond pdb=" C5 CLR R 502 " pdb=" C6 CLR R 502 " ideal model delta sigma weight residual 1.332 1.300 0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 8666 not shown) Histogram of bond angle deviations from ideal: 100.09 - 107.06: 236 107.06 - 114.03: 4996 114.03 - 121.01: 3967 121.01 - 127.98: 2485 127.98 - 134.96: 76 Bond angle restraints: 11760 Sorted by residual: angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 130.99 -9.45 1.91e+00 2.74e-01 2.45e+01 angle pdb=" C ILE R 294 " pdb=" N LEU R 295 " pdb=" CA LEU R 295 " ideal model delta sigma weight residual 121.62 126.94 -5.32 1.57e+00 4.06e-01 1.15e+01 angle pdb=" N LEU R 286 " pdb=" CA LEU R 286 " pdb=" C LEU R 286 " ideal model delta sigma weight residual 109.81 116.93 -7.12 2.21e+00 2.05e-01 1.04e+01 angle pdb=" N LEU R 295 " pdb=" CA LEU R 295 " pdb=" C LEU R 295 " ideal model delta sigma weight residual 113.77 118.01 -4.24 1.32e+00 5.74e-01 1.03e+01 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 123.93 128.85 -4.92 1.54e+00 4.22e-01 1.02e+01 ... (remaining 11755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.88: 5154 14.88 - 29.75: 223 29.75 - 44.63: 43 44.63 - 59.50: 2 59.50 - 74.38: 3 Dihedral angle restraints: 5425 sinusoidal: 2369 harmonic: 3056 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 163.67 -70.67 1 1.00e+01 1.00e-02 6.42e+01 dihedral pdb=" CA MET R 135 " pdb=" C MET R 135 " pdb=" N THR R 136 " pdb=" CA THR R 136 " ideal model delta harmonic sigma weight residual 180.00 155.08 24.92 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA LEU B 198 " pdb=" C LEU B 198 " pdb=" N PHE B 199 " pdb=" CA PHE B 199 " ideal model delta harmonic sigma weight residual 180.00 156.51 23.49 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 5422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1149 0.084 - 0.168: 148 0.168 - 0.252: 20 0.252 - 0.336: 5 0.336 - 0.420: 6 Chirality restraints: 1328 Sorted by residual: chirality pdb=" C14 CLR R 506 " pdb=" C13 CLR R 506 " pdb=" C15 CLR R 506 " pdb=" C8 CLR R 506 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" C14 CLR R 504 " pdb=" C13 CLR R 504 " pdb=" C15 CLR R 504 " pdb=" C8 CLR R 504 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" C14 CLR R 503 " pdb=" C13 CLR R 503 " pdb=" C15 CLR R 503 " pdb=" C8 CLR R 503 " both_signs ideal model delta sigma weight residual False -2.32 -2.71 0.40 2.00e-01 2.50e+01 3.94e+00 ... (remaining 1325 not shown) Planarity restraints: 1462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 207 " 0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C VAL R 207 " -0.068 2.00e-02 2.50e+03 pdb=" O VAL R 207 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA R 208 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 218 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.27e+00 pdb=" C TYR R 218 " -0.053 2.00e-02 2.50e+03 pdb=" O TYR R 218 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG R 219 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 114 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.03e+00 pdb=" C LEU R 114 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU R 114 " -0.018 2.00e-02 2.50e+03 pdb=" N CYS R 115 " -0.017 2.00e-02 2.50e+03 ... (remaining 1459 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1845 2.79 - 3.32: 7504 3.32 - 3.85: 13417 3.85 - 4.37: 15625 4.37 - 4.90: 27685 Nonbonded interactions: 66076 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.268 2.440 nonbonded pdb=" OH TYR A 170 " pdb=" OD2 ASP A 195 " model vdw 2.270 2.440 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.329 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.344 2.440 nonbonded pdb=" NE2 GLN B 75 " pdb=" O VAL B 100 " model vdw 2.358 2.520 ... (remaining 66071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 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: 1.950 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 26.240 Find NCS groups from input model: 0.230 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:14.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 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 : 0.004 0.057 8671 Z= 0.282 Angle : 0.923 9.957 11760 Z= 0.510 Chirality : 0.064 0.420 1328 Planarity : 0.007 0.060 1462 Dihedral : 8.730 74.381 3429 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: -2.33 (0.23), residues: 1031 helix: -1.60 (0.21), residues: 408 sheet: -0.36 (0.34), residues: 219 loop : -2.01 (0.26), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP R 80 HIS 0.011 0.003 HIS R 53 PHE 0.035 0.003 PHE R 141 TYR 0.018 0.002 TYR B 289 ARG 0.009 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8101 (tp30) cc_final: 0.7818 (tm-30) REVERT: A 20 ARG cc_start: 0.7684 (tpt170) cc_final: 0.7189 (ttp-110) REVERT: A 35 GLN cc_start: 0.7724 (mt0) cc_final: 0.7425 (pt0) REVERT: A 145 LYS cc_start: 0.8362 (mttt) cc_final: 0.8147 (mttm) REVERT: A 202 THR cc_start: 0.7396 (m) cc_final: 0.6929 (p) REVERT: A 233 ASP cc_start: 0.8268 (m-30) cc_final: 0.7974 (m-30) REVERT: B 97 SER cc_start: 0.8212 (p) cc_final: 0.7884 (t) REVERT: B 118 ASP cc_start: 0.8247 (p0) cc_final: 0.8002 (p0) REVERT: B 137 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.7078 (ttt180) REVERT: B 163 ASP cc_start: 0.7664 (p0) cc_final: 0.7377 (p0) REVERT: B 181 THR cc_start: 0.7655 (p) cc_final: 0.7234 (t) REVERT: B 239 ASN cc_start: 0.8232 (m-40) cc_final: 0.8031 (m-40) REVERT: B 246 ASP cc_start: 0.7711 (m-30) cc_final: 0.7404 (m-30) REVERT: N 105 ARG cc_start: 0.7686 (mtm180) cc_final: 0.7053 (pmt-80) outliers start: 0 outliers final: 3 residues processed: 216 average time/residue: 1.2646 time to fit residues: 288.9088 Evaluate side-chains 132 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 334 ASN A 23 ASN A 64 HIS B 88 ASN B 259 GLN N 31 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8671 Z= 0.246 Angle : 0.564 9.234 11760 Z= 0.301 Chirality : 0.042 0.149 1328 Planarity : 0.005 0.047 1462 Dihedral : 5.516 35.954 1528 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.77 % Allowed : 10.77 % Favored : 85.46 % 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: -0.34 (0.25), residues: 1031 helix: 0.85 (0.25), residues: 398 sheet: 0.05 (0.33), residues: 225 loop : -1.45 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 133 HIS 0.005 0.002 HIS A 209 PHE 0.013 0.002 PHE B 199 TYR 0.010 0.002 TYR A 163 ARG 0.011 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 278 MET cc_start: 0.6214 (OUTLIER) cc_final: 0.5919 (ttm) REVERT: A 16 GLU cc_start: 0.8069 (tp30) cc_final: 0.7670 (tm-30) REVERT: A 20 ARG cc_start: 0.7703 (tpt170) cc_final: 0.7196 (ttp-110) REVERT: A 32 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8023 (ttpp) REVERT: A 35 GLN cc_start: 0.7617 (mt0) cc_final: 0.7313 (pt0) REVERT: A 42 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.6763 (mpp-170) REVERT: A 102 ASP cc_start: 0.6326 (p0) cc_final: 0.5579 (p0) REVERT: A 167 PHE cc_start: 0.8711 (t80) cc_final: 0.8488 (t80) REVERT: A 169 ARG cc_start: 0.8114 (ttp-110) cc_final: 0.7085 (ttt180) REVERT: A 202 THR cc_start: 0.7432 (m) cc_final: 0.7002 (p) REVERT: A 233 ASP cc_start: 0.8413 (m-30) cc_final: 0.8126 (m-30) REVERT: B 59 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.8029 (t80) REVERT: B 97 SER cc_start: 0.8244 (p) cc_final: 0.8009 (t) REVERT: B 181 THR cc_start: 0.7749 (p) cc_final: 0.7401 (t) REVERT: B 239 ASN cc_start: 0.8218 (m-40) cc_final: 0.7994 (m-40) REVERT: B 246 ASP cc_start: 0.7958 (m-30) cc_final: 0.7625 (m-30) REVERT: B 258 ASP cc_start: 0.7699 (t0) cc_final: 0.7477 (t70) REVERT: N 105 ARG cc_start: 0.7710 (mtm180) cc_final: 0.7067 (pmt-80) outliers start: 34 outliers final: 20 residues processed: 165 average time/residue: 1.0872 time to fit residues: 191.6695 Evaluate side-chains 144 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 278 MET Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 99 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 ASN A 116 ASN B 266 HIS B 268 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 8671 Z= 0.411 Angle : 0.655 7.662 11760 Z= 0.348 Chirality : 0.047 0.169 1328 Planarity : 0.005 0.047 1462 Dihedral : 6.178 42.719 1528 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 6.33 % Allowed : 10.99 % Favored : 82.69 % 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: -0.14 (0.25), residues: 1031 helix: 1.12 (0.25), residues: 389 sheet: -0.05 (0.34), residues: 222 loop : -1.24 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 339 HIS 0.011 0.002 HIS B 54 PHE 0.021 0.002 PHE N 108 TYR 0.015 0.002 TYR N 60 ARG 0.005 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 135 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 23 ARG cc_start: 0.8105 (mtp180) cc_final: 0.7827 (mtm180) REVERT: R 35 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7673 (mm) REVERT: R 165 LYS cc_start: 0.7634 (tptm) cc_final: 0.7140 (ttpt) REVERT: R 342 SER cc_start: 0.7692 (m) cc_final: 0.7468 (p) REVERT: A 20 ARG cc_start: 0.7619 (tpt170) cc_final: 0.7170 (ttp-110) REVERT: A 32 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8177 (ttpp) REVERT: A 42 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7293 (mpp-170) REVERT: A 199 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7525 (ttp-110) REVERT: A 202 THR cc_start: 0.7745 (m) cc_final: 0.7463 (p) REVERT: A 217 CYS cc_start: 0.8456 (m) cc_final: 0.8146 (t) REVERT: A 242 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7648 (tt0) REVERT: A 244 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6970 (tp30) REVERT: B 27 ASP cc_start: 0.6468 (m-30) cc_final: 0.6083 (m-30) REVERT: B 59 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8121 (t80) REVERT: B 96 ARG cc_start: 0.7900 (mtp-110) cc_final: 0.7666 (ttm110) REVERT: B 97 SER cc_start: 0.8187 (p) cc_final: 0.7893 (m) REVERT: B 134 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6788 (mmt-90) REVERT: B 181 THR cc_start: 0.7952 (p) cc_final: 0.7617 (t) REVERT: B 239 ASN cc_start: 0.8279 (m-40) cc_final: 0.8070 (m-40) REVERT: B 246 ASP cc_start: 0.8026 (m-30) cc_final: 0.7695 (m-30) REVERT: B 277 SER cc_start: 0.9142 (t) cc_final: 0.8918 (p) REVERT: N 105 ARG cc_start: 0.7815 (mtm180) cc_final: 0.7011 (pmt-80) outliers start: 57 outliers final: 24 residues processed: 167 average time/residue: 1.1819 time to fit residues: 210.3847 Evaluate side-chains 151 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 0.0370 chunk 43 optimal weight: 0.0040 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.5870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8671 Z= 0.142 Angle : 0.488 9.634 11760 Z= 0.257 Chirality : 0.040 0.138 1328 Planarity : 0.004 0.046 1462 Dihedral : 5.558 36.592 1526 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.22 % Allowed : 15.21 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1031 helix: 1.74 (0.26), residues: 388 sheet: -0.07 (0.33), residues: 219 loop : -1.03 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 133 HIS 0.004 0.001 HIS A 209 PHE 0.012 0.001 PHE B 199 TYR 0.022 0.001 TYR N 60 ARG 0.008 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 23 ARG cc_start: 0.8007 (mtp180) cc_final: 0.7739 (mtm180) REVERT: R 35 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7839 (mm) REVERT: R 342 SER cc_start: 0.7654 (m) cc_final: 0.7434 (p) REVERT: A 93 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7652 (ptp-170) REVERT: A 167 PHE cc_start: 0.8914 (t80) cc_final: 0.8649 (t80) REVERT: A 169 ARG cc_start: 0.7964 (ttp-110) cc_final: 0.6974 (ttt180) REVERT: A 202 THR cc_start: 0.7553 (m) cc_final: 0.7244 (p) REVERT: A 206 ASP cc_start: 0.6524 (m-30) cc_final: 0.6224 (m-30) REVERT: A 217 CYS cc_start: 0.8423 (m) cc_final: 0.8085 (t) REVERT: A 242 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7721 (tt0) REVERT: B 27 ASP cc_start: 0.6475 (m-30) cc_final: 0.6222 (m-30) REVERT: B 59 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.7964 (t80) REVERT: B 96 ARG cc_start: 0.7813 (mtp-110) cc_final: 0.7593 (ttm110) REVERT: B 97 SER cc_start: 0.8085 (p) cc_final: 0.7779 (m) REVERT: B 134 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6665 (pmt170) REVERT: B 181 THR cc_start: 0.7922 (p) cc_final: 0.7547 (t) REVERT: B 239 ASN cc_start: 0.8313 (m-40) cc_final: 0.8068 (m-40) REVERT: B 246 ASP cc_start: 0.7965 (m-30) cc_final: 0.7645 (m-30) REVERT: B 277 SER cc_start: 0.9037 (t) cc_final: 0.8833 (p) REVERT: B 303 ASP cc_start: 0.8157 (m-30) cc_final: 0.7937 (m-30) REVERT: N 105 ARG cc_start: 0.7735 (mtm180) cc_final: 0.6920 (pmt-80) REVERT: N 109 ASP cc_start: 0.7461 (p0) cc_final: 0.7230 (p0) outliers start: 29 outliers final: 13 residues processed: 148 average time/residue: 1.1383 time to fit residues: 180.1871 Evaluate side-chains 137 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.0040 chunk 87 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN N 31 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8671 Z= 0.202 Angle : 0.518 10.514 11760 Z= 0.272 Chirality : 0.041 0.155 1328 Planarity : 0.004 0.049 1462 Dihedral : 5.467 39.542 1524 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.22 % Allowed : 14.87 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1031 helix: 1.88 (0.26), residues: 382 sheet: -0.09 (0.33), residues: 223 loop : -0.95 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.016 0.001 PHE R 51 TYR 0.019 0.001 TYR N 60 ARG 0.004 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 128 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 23 ARG cc_start: 0.7980 (mtp180) cc_final: 0.7705 (mtm180) REVERT: R 35 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7788 (mm) REVERT: R 94 SER cc_start: 0.8527 (p) cc_final: 0.8163 (t) REVERT: A 32 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8049 (ttpp) REVERT: A 93 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7670 (ptp-170) REVERT: A 169 ARG cc_start: 0.7943 (ttp-110) cc_final: 0.6898 (ttt180) REVERT: A 202 THR cc_start: 0.7763 (m) cc_final: 0.7490 (p) REVERT: A 206 ASP cc_start: 0.6358 (m-30) cc_final: 0.6079 (m-30) REVERT: A 217 CYS cc_start: 0.8400 (m) cc_final: 0.8059 (t) REVERT: A 242 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7754 (tt0) REVERT: A 244 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: B 59 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.8038 (t80) REVERT: B 96 ARG cc_start: 0.7824 (mtp-110) cc_final: 0.7587 (ttm110) REVERT: B 134 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6800 (pmt170) REVERT: B 181 THR cc_start: 0.7862 (p) cc_final: 0.7476 (t) REVERT: B 186 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7324 (m-30) REVERT: B 239 ASN cc_start: 0.8344 (m-40) cc_final: 0.8098 (m-40) REVERT: B 246 ASP cc_start: 0.7982 (m-30) cc_final: 0.7631 (m-30) REVERT: B 303 ASP cc_start: 0.8132 (m-30) cc_final: 0.7890 (m-30) REVERT: G 51 LEU cc_start: 0.8281 (tp) cc_final: 0.8008 (mt) REVERT: N 105 ARG cc_start: 0.7668 (mtm180) cc_final: 0.6809 (pmt-80) outliers start: 38 outliers final: 24 residues processed: 147 average time/residue: 1.0489 time to fit residues: 165.7412 Evaluate side-chains 149 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 118 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 24 optimal weight: 0.0570 chunk 97 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 51 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 91 HIS ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8671 Z= 0.141 Angle : 0.470 8.887 11760 Z= 0.247 Chirality : 0.039 0.133 1328 Planarity : 0.003 0.049 1462 Dihedral : 5.114 36.559 1524 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.00 % Allowed : 15.76 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.26), residues: 1031 helix: 2.03 (0.26), residues: 386 sheet: -0.19 (0.32), residues: 223 loop : -0.88 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 209 PHE 0.010 0.001 PHE B 199 TYR 0.019 0.001 TYR N 60 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7916 (mm) REVERT: R 94 SER cc_start: 0.8480 (p) cc_final: 0.8128 (t) REVERT: A 20 ARG cc_start: 0.7562 (tpt170) cc_final: 0.7167 (ttp-110) REVERT: A 42 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7036 (mpp-170) REVERT: A 60 MET cc_start: 0.4685 (OUTLIER) cc_final: 0.4402 (pmt) REVERT: A 82 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7817 (t-90) REVERT: A 93 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7675 (ptp-170) REVERT: A 169 ARG cc_start: 0.7842 (ttp-110) cc_final: 0.6829 (ttt180) REVERT: A 202 THR cc_start: 0.7693 (m) cc_final: 0.7424 (p) REVERT: A 206 ASP cc_start: 0.6305 (m-30) cc_final: 0.6076 (m-30) REVERT: A 217 CYS cc_start: 0.8346 (m) cc_final: 0.8037 (t) REVERT: A 242 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7760 (tt0) REVERT: A 244 GLU cc_start: 0.7157 (tp30) cc_final: 0.6828 (mp0) REVERT: B 27 ASP cc_start: 0.6479 (m-30) cc_final: 0.6270 (p0) REVERT: B 59 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.7958 (t80) REVERT: B 96 ARG cc_start: 0.7785 (mtp-110) cc_final: 0.7567 (ttm110) REVERT: B 134 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6691 (pmt170) REVERT: B 181 THR cc_start: 0.7717 (p) cc_final: 0.7324 (t) REVERT: B 239 ASN cc_start: 0.8307 (m-40) cc_final: 0.8086 (m-40) REVERT: B 246 ASP cc_start: 0.7986 (m-30) cc_final: 0.7632 (m-30) REVERT: B 280 LYS cc_start: 0.8635 (tttp) cc_final: 0.8278 (ttpp) REVERT: B 303 ASP cc_start: 0.7991 (m-30) cc_final: 0.7749 (m-30) REVERT: N 105 ARG cc_start: 0.7580 (mtm180) cc_final: 0.6727 (pmt-80) outliers start: 36 outliers final: 18 residues processed: 150 average time/residue: 1.1279 time to fit residues: 180.7937 Evaluate side-chains 142 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 0.0980 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 0.0970 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8671 Z= 0.163 Angle : 0.488 7.896 11760 Z= 0.254 Chirality : 0.040 0.156 1328 Planarity : 0.003 0.046 1462 Dihedral : 5.066 35.203 1524 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.66 % Allowed : 17.20 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1031 helix: 2.05 (0.26), residues: 385 sheet: -0.24 (0.32), residues: 225 loop : -0.90 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 PHE 0.020 0.001 PHE R 102 TYR 0.020 0.001 TYR N 60 ARG 0.007 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7854 (mm) REVERT: R 94 SER cc_start: 0.8477 (p) cc_final: 0.8139 (t) REVERT: A 20 ARG cc_start: 0.7567 (tpt170) cc_final: 0.7144 (ttp-110) REVERT: A 42 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7042 (mpp-170) REVERT: A 60 MET cc_start: 0.4606 (OUTLIER) cc_final: 0.4332 (pmt) REVERT: A 82 HIS cc_start: 0.8216 (OUTLIER) cc_final: 0.7860 (t-90) REVERT: A 93 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7685 (ptp-170) REVERT: A 169 ARG cc_start: 0.7837 (ttp-110) cc_final: 0.6822 (ttt180) REVERT: A 202 THR cc_start: 0.7705 (m) cc_final: 0.7463 (p) REVERT: A 206 ASP cc_start: 0.6083 (m-30) cc_final: 0.5847 (m-30) REVERT: A 217 CYS cc_start: 0.8364 (m) cc_final: 0.8037 (t) REVERT: A 242 GLN cc_start: 0.8092 (tm-30) cc_final: 0.7718 (tt0) REVERT: A 244 GLU cc_start: 0.7217 (tp30) cc_final: 0.6881 (mp0) REVERT: B 13 GLN cc_start: 0.7346 (tp40) cc_final: 0.6779 (pt0) REVERT: B 59 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.7977 (t80) REVERT: B 96 ARG cc_start: 0.7827 (mtp-110) cc_final: 0.7598 (ttm110) REVERT: B 134 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6722 (pmt170) REVERT: B 181 THR cc_start: 0.7792 (p) cc_final: 0.7379 (t) REVERT: B 186 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7304 (m-30) REVERT: B 239 ASN cc_start: 0.8339 (m-40) cc_final: 0.8069 (m-40) REVERT: B 246 ASP cc_start: 0.7970 (m-30) cc_final: 0.7636 (m-30) REVERT: B 303 ASP cc_start: 0.7996 (m-30) cc_final: 0.7757 (m-30) REVERT: N 105 ARG cc_start: 0.7648 (mtm180) cc_final: 0.6755 (pmt-80) outliers start: 33 outliers final: 18 residues processed: 137 average time/residue: 1.1981 time to fit residues: 175.1661 Evaluate side-chains 140 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8671 Z= 0.182 Angle : 0.490 7.207 11760 Z= 0.257 Chirality : 0.040 0.171 1328 Planarity : 0.004 0.045 1462 Dihedral : 5.027 33.888 1524 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.88 % Allowed : 17.54 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1031 helix: 2.07 (0.26), residues: 385 sheet: -0.18 (0.32), residues: 224 loop : -0.91 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 PHE 0.014 0.001 PHE R 51 TYR 0.017 0.001 TYR A 163 ARG 0.008 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 117 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7758 (mm) REVERT: R 94 SER cc_start: 0.8483 (p) cc_final: 0.8159 (t) REVERT: A 20 ARG cc_start: 0.7515 (tpt170) cc_final: 0.7129 (ttp-110) REVERT: A 42 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7101 (mpp-170) REVERT: A 60 MET cc_start: 0.4661 (OUTLIER) cc_final: 0.4402 (pmt) REVERT: A 169 ARG cc_start: 0.7811 (ttp-110) cc_final: 0.7352 (ptm160) REVERT: A 202 THR cc_start: 0.7725 (m) cc_final: 0.7515 (p) REVERT: A 206 ASP cc_start: 0.6095 (m-30) cc_final: 0.5875 (m-30) REVERT: A 217 CYS cc_start: 0.8379 (m) cc_final: 0.8046 (t) REVERT: A 242 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7716 (tt0) REVERT: A 244 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: B 13 GLN cc_start: 0.7478 (tp40) cc_final: 0.6892 (pt0) REVERT: B 27 ASP cc_start: 0.6553 (m-30) cc_final: 0.6307 (p0) REVERT: B 59 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.7991 (t80) REVERT: B 96 ARG cc_start: 0.7830 (mtp-110) cc_final: 0.7599 (ttm110) REVERT: B 134 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6767 (pmt170) REVERT: B 181 THR cc_start: 0.7717 (p) cc_final: 0.7318 (t) REVERT: B 239 ASN cc_start: 0.8309 (m-40) cc_final: 0.8038 (m-40) REVERT: B 246 ASP cc_start: 0.7982 (m-30) cc_final: 0.7651 (m-30) REVERT: B 303 ASP cc_start: 0.8018 (m-30) cc_final: 0.7797 (m-30) REVERT: N 7 SER cc_start: 0.7668 (OUTLIER) cc_final: 0.7466 (p) REVERT: N 105 ARG cc_start: 0.7679 (mtm180) cc_final: 0.6757 (pmt-80) outliers start: 35 outliers final: 21 residues processed: 138 average time/residue: 1.1221 time to fit residues: 165.9592 Evaluate side-chains 141 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 59 optimal weight: 0.0970 chunk 95 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS B 36 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8671 Z= 0.158 Angle : 0.483 7.823 11760 Z= 0.252 Chirality : 0.040 0.166 1328 Planarity : 0.003 0.045 1462 Dihedral : 4.906 33.127 1524 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.55 % Allowed : 18.09 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.26), residues: 1031 helix: 2.18 (0.26), residues: 385 sheet: -0.27 (0.32), residues: 228 loop : -0.83 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 PHE 0.009 0.001 PHE B 199 TYR 0.021 0.001 TYR N 60 ARG 0.006 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 115 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7869 (mm) REVERT: R 94 SER cc_start: 0.8472 (p) cc_final: 0.8155 (t) REVERT: A 20 ARG cc_start: 0.7489 (tpt170) cc_final: 0.7084 (ttp-110) REVERT: A 42 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7105 (mpp-170) REVERT: A 60 MET cc_start: 0.4613 (OUTLIER) cc_final: 0.4328 (pmt) REVERT: A 169 ARG cc_start: 0.7770 (ttp-110) cc_final: 0.7338 (ptm160) REVERT: A 202 THR cc_start: 0.7704 (m) cc_final: 0.7489 (p) REVERT: A 206 ASP cc_start: 0.6076 (m-30) cc_final: 0.5849 (m-30) REVERT: A 217 CYS cc_start: 0.8349 (m) cc_final: 0.8033 (t) REVERT: A 242 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7698 (tt0) REVERT: A 244 GLU cc_start: 0.7232 (tp30) cc_final: 0.6925 (mp0) REVERT: B 13 GLN cc_start: 0.7640 (tp40) cc_final: 0.7049 (pt0) REVERT: B 27 ASP cc_start: 0.6601 (m-30) cc_final: 0.6343 (p0) REVERT: B 59 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.7980 (t80) REVERT: B 96 ARG cc_start: 0.7804 (mtp-110) cc_final: 0.7576 (ttm110) REVERT: B 134 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6783 (pmt170) REVERT: B 181 THR cc_start: 0.7770 (p) cc_final: 0.7356 (t) REVERT: B 186 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7384 (m-30) REVERT: B 239 ASN cc_start: 0.8315 (m-40) cc_final: 0.8015 (m-40) REVERT: B 246 ASP cc_start: 0.7973 (m-30) cc_final: 0.7637 (m-30) REVERT: B 303 ASP cc_start: 0.7981 (m-30) cc_final: 0.7750 (m-30) REVERT: N 7 SER cc_start: 0.7617 (OUTLIER) cc_final: 0.7410 (p) REVERT: N 105 ARG cc_start: 0.7654 (mtm180) cc_final: 0.6777 (pmt-80) outliers start: 32 outliers final: 21 residues processed: 136 average time/residue: 1.1472 time to fit residues: 166.8011 Evaluate side-chains 140 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 24 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 82 HIS B 36 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8671 Z= 0.159 Angle : 0.483 7.149 11760 Z= 0.253 Chirality : 0.040 0.168 1328 Planarity : 0.003 0.045 1462 Dihedral : 4.836 32.400 1524 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.11 % Allowed : 18.87 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1031 helix: 2.21 (0.26), residues: 385 sheet: -0.26 (0.32), residues: 228 loop : -0.79 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 PHE 0.009 0.001 PHE B 199 TYR 0.020 0.001 TYR N 60 ARG 0.007 0.000 ARG A 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7813 (mm) REVERT: R 94 SER cc_start: 0.8470 (p) cc_final: 0.8155 (t) REVERT: A 20 ARG cc_start: 0.7587 (tpt170) cc_final: 0.7209 (ttp-110) REVERT: A 42 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7089 (mpp-170) REVERT: A 169 ARG cc_start: 0.7755 (ttp-110) cc_final: 0.7420 (ptm160) REVERT: A 202 THR cc_start: 0.7702 (m) cc_final: 0.7496 (p) REVERT: A 206 ASP cc_start: 0.5964 (m-30) cc_final: 0.5746 (m-30) REVERT: A 217 CYS cc_start: 0.8368 (m) cc_final: 0.8033 (t) REVERT: A 242 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7695 (tt0) REVERT: A 244 GLU cc_start: 0.7234 (tp30) cc_final: 0.6938 (mp0) REVERT: B 27 ASP cc_start: 0.6598 (m-30) cc_final: 0.6268 (p0) REVERT: B 59 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.7983 (t80) REVERT: B 96 ARG cc_start: 0.7806 (mtp-110) cc_final: 0.7568 (ttm110) REVERT: B 134 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6774 (pmt170) REVERT: B 181 THR cc_start: 0.7746 (p) cc_final: 0.7335 (t) REVERT: B 239 ASN cc_start: 0.8307 (m-40) cc_final: 0.8011 (m-40) REVERT: B 246 ASP cc_start: 0.7985 (m-30) cc_final: 0.7651 (m-30) REVERT: B 303 ASP cc_start: 0.7982 (m-30) cc_final: 0.7750 (m-30) REVERT: N 7 SER cc_start: 0.7601 (OUTLIER) cc_final: 0.7384 (p) REVERT: N 105 ARG cc_start: 0.7662 (mtm180) cc_final: 0.6780 (pmt-80) outliers start: 28 outliers final: 20 residues processed: 135 average time/residue: 1.0804 time to fit residues: 156.3629 Evaluate side-chains 139 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.1980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 334 ASN A 82 HIS B 36 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.191343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.144581 restraints weight = 8458.269| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.31 r_work: 0.3388 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8671 Z= 0.190 Angle : 0.508 8.069 11760 Z= 0.265 Chirality : 0.040 0.175 1328 Planarity : 0.004 0.045 1462 Dihedral : 4.927 32.393 1524 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.44 % Allowed : 18.87 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1031 helix: 2.04 (0.26), residues: 390 sheet: -0.26 (0.32), residues: 228 loop : -0.76 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 PHE 0.010 0.001 PHE B 199 TYR 0.013 0.001 TYR B 111 ARG 0.007 0.000 ARG A 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3640.80 seconds wall clock time: 65 minutes 34.50 seconds (3934.50 seconds total)