Starting phenix.real_space_refine on Fri Nov 15 09:52:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zps_60353/11_2024/8zps_60353_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zps_60353/11_2024/8zps_60353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zps_60353/11_2024/8zps_60353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zps_60353/11_2024/8zps_60353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zps_60353/11_2024/8zps_60353_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zps_60353/11_2024/8zps_60353_neut.cif" } resolution = 2.97 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= 0.002 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 53 5.16 5 C 5645 2.51 5 N 1561 2.21 5 O 1589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8848 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1709 Classifications: {'peptide': 208} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 205} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2537 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1698 Classifications: {'peptide': 228} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "G" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 409 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 161 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 3, 'TRANS': 16} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2333 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.72, per 1000 atoms: 0.65 Number of scatterers: 8848 At special positions: 0 Unit cell: (84.872, 119.48, 131.016, 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 53 16.00 O 1589 8.00 N 1561 7.00 C 5645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.2 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 37.3% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.643A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.574A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 246 through 250 removed outlier: 3.649A pdb=" N ARG A 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 268 removed outlier: 3.794A pdb=" N GLU A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.796A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 359 Processing helix chain 'B' and resid 12 through 30 Processing helix chain 'B' and resid 35 through 40 removed outlier: 4.158A pdb=" N ASN B 40 " --> pdb=" O SER B 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.200A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 19 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.663A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'L' and resid 4 through 11 removed outlier: 4.103A pdb=" N TRP L 8 " --> pdb=" O ILE L 4 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER L 11 " --> pdb=" O ALA L 7 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 88 removed outlier: 3.765A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL R 88 " --> pdb=" O VAL R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 92 Processing helix chain 'R' and resid 93 through 123 Proline residue: R 115 - end of helix removed outlier: 3.653A pdb=" N ALA R 119 " --> pdb=" O PRO R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 164 removed outlier: 3.819A pdb=" N LEU R 136 " --> pdb=" O GLY R 132 " (cutoff:3.500A) Proline residue: R 142 - end of helix Processing helix chain 'R' and resid 172 through 198 Proline residue: R 193 - end of helix Processing helix chain 'R' and resid 220 through 255 removed outlier: 3.984A pdb=" N LEU R 224 " --> pdb=" O ARG R 220 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU R 236 " --> pdb=" O VAL R 232 " (cutoff:3.500A) Proline residue: R 237 - end of helix Processing helix chain 'R' and resid 267 through 304 Proline residue: R 293 - end of helix removed outlier: 3.555A pdb=" N ASP R 304 " --> pdb=" O LEU R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 337 removed outlier: 3.820A pdb=" N SER R 327 " --> pdb=" O LEU R 323 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA R 328 " --> pdb=" O ALA R 324 " (cutoff:3.500A) Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 339 through 351 removed outlier: 3.838A pdb=" N ARG R 343 " --> pdb=" O HIS R 339 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU R 345 " --> pdb=" O SER R 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.449A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.884A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.451A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.722A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 85 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS B 96 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 3.698A pdb=" N SER B 127 " --> pdb=" O CYS B 119 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 153 through 156 removed outlier: 3.584A pdb=" N ALA B 172 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.925A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 208 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 4.066A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 4.680A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN B 300 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 311 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.485A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.508A pdb=" N THR E 141 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG E 160 " --> pdb=" O THR E 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 194 through 195 removed outlier: 6.848A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 199 through 200 424 hydrogen bonds defined for protein. 1197 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: 2.47 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2467 1.33 - 1.45: 1566 1.45 - 1.57: 4930 1.57 - 1.69: 0 1.69 - 1.81: 73 Bond restraints: 9036 Sorted by residual: bond pdb=" N LYS A 352 " pdb=" CA LYS A 352 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.23e-02 6.61e+03 9.07e+00 bond pdb=" N VAL R 201 " pdb=" CA VAL R 201 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.88e+00 bond pdb=" N VAL R 208 " pdb=" CA VAL R 208 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.07e-02 8.73e+03 8.58e+00 bond pdb=" N GLU E 6 " pdb=" CA GLU E 6 " ideal model delta sigma weight residual 1.454 1.491 -0.036 1.27e-02 6.20e+03 8.12e+00 bond pdb=" N SER E 7 " pdb=" CA SER E 7 " ideal model delta sigma weight residual 1.455 1.489 -0.035 1.29e-02 6.01e+03 7.20e+00 ... (remaining 9031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 11889 1.28 - 2.56: 265 2.56 - 3.84: 83 3.84 - 5.12: 21 5.12 - 6.41: 9 Bond angle restraints: 12267 Sorted by residual: angle pdb=" CA VAL R 208 " pdb=" C VAL R 208 " pdb=" O VAL R 208 " ideal model delta sigma weight residual 121.09 117.17 3.92 8.20e-01 1.49e+00 2.28e+01 angle pdb=" C HIS R 206 " pdb=" N ASP R 207 " pdb=" CA ASP R 207 " ideal model delta sigma weight residual 122.42 116.19 6.23 1.33e+00 5.65e-01 2.20e+01 angle pdb=" N GLY A 359 " pdb=" CA GLY A 359 " pdb=" C GLY A 359 " ideal model delta sigma weight residual 115.30 108.89 6.41 1.39e+00 5.18e-01 2.12e+01 angle pdb=" N THR R 117 " pdb=" CA THR R 117 " pdb=" C THR R 117 " ideal model delta sigma weight residual 112.54 106.93 5.61 1.22e+00 6.72e-01 2.12e+01 angle pdb=" N MET A 353 " pdb=" CA MET A 353 " pdb=" C MET A 353 " ideal model delta sigma weight residual 111.28 106.70 4.58 1.09e+00 8.42e-01 1.77e+01 ... (remaining 12262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.62: 4989 13.62 - 27.24: 230 27.24 - 40.87: 76 40.87 - 54.49: 23 54.49 - 68.11: 6 Dihedral angle restraints: 5324 sinusoidal: 2038 harmonic: 3286 Sorted by residual: dihedral pdb=" CA CYS R 113 " pdb=" C CYS R 113 " pdb=" N VAL R 114 " pdb=" CA VAL R 114 " ideal model delta harmonic sigma weight residual -180.00 -164.32 -15.68 0 5.00e+00 4.00e-02 9.84e+00 dihedral pdb=" N LEU A 355 " pdb=" CA LEU A 355 " pdb=" CB LEU A 355 " pdb=" CG LEU A 355 " ideal model delta sinusoidal sigma weight residual -60.00 -118.48 58.48 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N MET A 353 " pdb=" CA MET A 353 " pdb=" CB MET A 353 " pdb=" CG MET A 353 " ideal model delta sinusoidal sigma weight residual 60.00 117.77 -57.77 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 5321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1154 0.049 - 0.099: 201 0.099 - 0.148: 46 0.148 - 0.198: 2 0.198 - 0.247: 2 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CA VAL R 208 " pdb=" N VAL R 208 " pdb=" C VAL R 208 " pdb=" CB VAL R 208 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA VAL E 5 " pdb=" N VAL E 5 " pdb=" C VAL E 5 " pdb=" CB VAL E 5 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA LEU A 360 " pdb=" N LEU A 360 " pdb=" C LEU A 360 " pdb=" CB LEU A 360 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.15e-01 ... (remaining 1402 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 351 " 0.026 2.00e-02 2.50e+03 5.10e-02 2.60e+01 pdb=" C ILE A 351 " -0.088 2.00e-02 2.50e+03 pdb=" O ILE A 351 " 0.033 2.00e-02 2.50e+03 pdb=" N LYS A 352 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 4 " 0.022 2.00e-02 2.50e+03 4.54e-02 2.06e+01 pdb=" C LEU E 4 " -0.079 2.00e-02 2.50e+03 pdb=" O LEU E 4 " 0.030 2.00e-02 2.50e+03 pdb=" N VAL E 5 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 208 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C VAL R 208 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL R 208 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG R 209 " 0.010 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.38: 14 2.38 - 3.01: 4718 3.01 - 3.64: 13013 3.64 - 4.27: 19335 4.27 - 4.90: 32934 Nonbonded interactions: 70014 Sorted by model distance: nonbonded pdb=" OG SER E 7 " pdb=" OG SER E 21 " model vdw 1.744 3.040 nonbonded pdb=" O LEU B 35 " pdb=" OG1 THR B 39 " model vdw 2.272 3.040 nonbonded pdb=" OG SER B 152 " pdb=" O MET B 193 " model vdw 2.274 3.040 nonbonded pdb=" OG SER B 336 " pdb=" OD1 ASP B 338 " model vdw 2.281 3.040 nonbonded pdb=" ND2 ASN R 93 " pdb=" OD1 ASN R 96 " model vdw 2.285 3.120 ... (remaining 70009 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 ========== 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: 2.540 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: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.630 Find NCS groups from input model: 0.130 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:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 39.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 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 : 0.002 0.037 9036 Z= 0.156 Angle : 0.537 6.406 12267 Z= 0.331 Chirality : 0.040 0.247 1405 Planarity : 0.003 0.051 1548 Dihedral : 9.774 68.111 3199 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.06 % Allowed : 7.77 % Favored : 91.17 % 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: 1.49 (0.26), residues: 1111 helix: 2.74 (0.26), residues: 379 sheet: 1.54 (0.33), residues: 254 loop : -0.84 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 174 HIS 0.003 0.001 HIS A 324 PHE 0.006 0.001 PHE B 204 TYR 0.006 0.001 TYR E 95 ARG 0.002 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 196 time to evaluate : 1.009 Fit side-chains REVERT: A 192 ASP cc_start: 0.6767 (p0) cc_final: 0.6535 (m-30) REVERT: A 198 MET cc_start: 0.8634 (ttp) cc_final: 0.8361 (ttp) REVERT: A 208 ARG cc_start: 0.6847 (ptp-110) cc_final: 0.6480 (ttm110) REVERT: A 309 ARG cc_start: 0.4397 (mtp-110) cc_final: 0.3971 (tmm-80) REVERT: A 330 PHE cc_start: 0.5931 (m-10) cc_final: 0.4135 (t80) REVERT: B 20 LYS cc_start: 0.5740 (mptm) cc_final: 0.5450 (mmtm) REVERT: B 103 SER cc_start: 0.6905 (m) cc_final: 0.6634 (p) REVERT: B 105 VAL cc_start: 0.7293 (m) cc_final: 0.6987 (p) REVERT: B 142 ARG cc_start: 0.6466 (tpp-160) cc_final: 0.6116 (tpp80) REVERT: B 219 ARG cc_start: 0.5850 (mtm110) cc_final: 0.5377 (mpt180) REVERT: B 261 ARG cc_start: 0.6994 (mtm180) cc_final: 0.6405 (mmt90) REVERT: B 272 ASP cc_start: 0.7225 (m-30) cc_final: 0.6737 (p0) REVERT: B 285 LYS cc_start: 0.7446 (tttm) cc_final: 0.7225 (tttm) REVERT: E 155 VAL cc_start: 0.7549 (p) cc_final: 0.7341 (p) REVERT: E 234 GLU cc_start: 0.6534 (mt-10) cc_final: 0.6278 (mp0) REVERT: G 16 VAL cc_start: 0.5479 (t) cc_final: 0.4962 (m) REVERT: R 277 PHE cc_start: 0.4980 (m-10) cc_final: 0.4553 (t80) REVERT: R 279 LEU cc_start: 0.6792 (tm) cc_final: 0.6210 (mt) REVERT: R 322 TRP cc_start: 0.5930 (t60) cc_final: 0.5713 (t60) outliers start: 10 outliers final: 3 residues processed: 203 average time/residue: 0.9684 time to fit residues: 212.8845 Evaluate side-chains 122 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain R residue 276 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 33 optimal weight: 0.0980 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 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 190 GLN A 246 ASN B 21 ASN ** B 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS E 3 GLN E 82 GLN L 5 ASN R 96 ASN R 141 GLN R 165 HIS R 223 GLN R 331 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9036 Z= 0.268 Angle : 0.619 6.444 12267 Z= 0.320 Chirality : 0.044 0.189 1405 Planarity : 0.005 0.044 1548 Dihedral : 4.665 58.533 1245 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.40 % Allowed : 13.19 % Favored : 83.40 % 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: 1.37 (0.26), residues: 1111 helix: 2.48 (0.26), residues: 386 sheet: 1.31 (0.31), residues: 270 loop : -0.77 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 216 HIS 0.010 0.002 HIS A 324 PHE 0.021 0.002 PHE B 239 TYR 0.015 0.002 TYR B 64 ARG 0.007 0.001 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.967 Fit side-chains REVERT: A 20 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6248 (mm-30) REVERT: A 21 LYS cc_start: 0.6469 (mttt) cc_final: 0.6120 (mttm) REVERT: A 195 ASN cc_start: 0.7577 (OUTLIER) cc_final: 0.7053 (m110) REVERT: A 198 MET cc_start: 0.8635 (ttp) cc_final: 0.8338 (ttp) REVERT: A 208 ARG cc_start: 0.7147 (ptp-110) cc_final: 0.6676 (ttm110) REVERT: A 309 ARG cc_start: 0.4930 (mtp-110) cc_final: 0.4288 (tmm-80) REVERT: A 311 GLU cc_start: 0.3954 (mm-30) cc_final: 0.3706 (mm-30) REVERT: B 64 TYR cc_start: 0.7814 (m-80) cc_final: 0.7527 (m-80) REVERT: B 103 SER cc_start: 0.7341 (m) cc_final: 0.6917 (p) REVERT: B 154 CYS cc_start: 0.7622 (m) cc_final: 0.7132 (p) REVERT: B 180 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6616 (pp30) REVERT: B 194 SER cc_start: 0.8710 (p) cc_final: 0.8127 (t) REVERT: B 219 ARG cc_start: 0.6320 (mtm110) cc_final: 0.5944 (mpt180) REVERT: B 260 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7516 (mp) REVERT: B 261 ARG cc_start: 0.7254 (mtm180) cc_final: 0.7017 (mtm180) REVERT: B 264 GLN cc_start: 0.6828 (mt0) cc_final: 0.6558 (mt0) REVERT: B 272 ASP cc_start: 0.7114 (m-30) cc_final: 0.6683 (p0) REVERT: B 285 LYS cc_start: 0.7421 (tttm) cc_final: 0.7134 (tttm) REVERT: E 234 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6744 (mm-30) REVERT: G 16 VAL cc_start: 0.5655 (t) cc_final: 0.5216 (m) REVERT: G 22 GLU cc_start: 0.5142 (mt-10) cc_final: 0.4886 (mt-10) REVERT: R 247 ARG cc_start: 0.5438 (mmm-85) cc_final: 0.5014 (tpt170) REVERT: R 277 PHE cc_start: 0.5257 (m-10) cc_final: 0.4613 (t80) REVERT: R 322 TRP cc_start: 0.6116 (t60) cc_final: 0.5791 (t60) outliers start: 32 outliers final: 11 residues processed: 156 average time/residue: 1.1713 time to fit residues: 195.5053 Evaluate side-chains 119 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 319 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 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 216 ASN B 59 HIS G 59 ASN R 96 ASN R 141 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9036 Z= 0.262 Angle : 0.608 8.524 12267 Z= 0.315 Chirality : 0.044 0.238 1405 Planarity : 0.005 0.033 1548 Dihedral : 4.724 50.058 1244 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.83 % Allowed : 16.70 % Favored : 79.47 % 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: 1.17 (0.26), residues: 1111 helix: 2.35 (0.26), residues: 384 sheet: 1.16 (0.31), residues: 262 loop : -0.84 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 104 HIS 0.013 0.002 HIS B 59 PHE 0.015 0.002 PHE B 156 TYR 0.013 0.002 TYR E 95 ARG 0.010 0.001 ARG A 250 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.992 Fit side-chains REVERT: A 20 GLU cc_start: 0.6827 (mt-10) cc_final: 0.6260 (mm-30) REVERT: A 21 LYS cc_start: 0.6652 (mttt) cc_final: 0.6247 (mttt) REVERT: A 198 MET cc_start: 0.8558 (ttp) cc_final: 0.8291 (ttp) REVERT: A 309 ARG cc_start: 0.4794 (mtp-110) cc_final: 0.4367 (tmm-80) REVERT: A 311 GLU cc_start: 0.4685 (mm-30) cc_final: 0.3827 (mp0) REVERT: A 323 ARG cc_start: 0.6423 (mtt-85) cc_final: 0.6102 (mtm180) REVERT: A 336 THR cc_start: 0.6778 (OUTLIER) cc_final: 0.6532 (t) REVERT: B 64 TYR cc_start: 0.7851 (m-80) cc_final: 0.7583 (m-80) REVERT: B 103 SER cc_start: 0.7384 (m) cc_final: 0.6961 (p) REVERT: B 142 ARG cc_start: 0.7234 (tpp-160) cc_final: 0.6681 (tpp80) REVERT: B 154 CYS cc_start: 0.7557 (m) cc_final: 0.6914 (p) REVERT: B 180 GLN cc_start: 0.7451 (pp30) cc_final: 0.6736 (pp30) REVERT: B 219 ARG cc_start: 0.6226 (mtm110) cc_final: 0.5888 (mpp-170) REVERT: B 260 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7631 (mp) REVERT: B 264 GLN cc_start: 0.6513 (mt0) cc_final: 0.6310 (mt0) REVERT: B 265 GLU cc_start: 0.7129 (tt0) cc_final: 0.6729 (mm-30) REVERT: B 267 MET cc_start: 0.6698 (mmt) cc_final: 0.6225 (tpp) REVERT: B 272 ASP cc_start: 0.7029 (m-30) cc_final: 0.6625 (p0) REVERT: E 234 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6826 (mm-30) REVERT: G 22 GLU cc_start: 0.5404 (mt-10) cc_final: 0.5014 (mt-10) REVERT: R 59 LEU cc_start: 0.4447 (mt) cc_final: 0.3990 (pp) REVERT: R 247 ARG cc_start: 0.5604 (mmm-85) cc_final: 0.5274 (mtp180) REVERT: R 277 PHE cc_start: 0.5136 (m-10) cc_final: 0.4400 (t80) REVERT: R 322 TRP cc_start: 0.6074 (t60) cc_final: 0.5834 (t60) outliers start: 36 outliers final: 15 residues processed: 143 average time/residue: 1.0946 time to fit residues: 168.5889 Evaluate side-chains 120 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 319 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.0670 chunk 75 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 242 ASN R 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9036 Z= 0.192 Angle : 0.541 6.362 12267 Z= 0.280 Chirality : 0.041 0.198 1405 Planarity : 0.004 0.040 1548 Dihedral : 4.141 19.478 1241 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.15 % Allowed : 17.55 % Favored : 78.30 % 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: 1.14 (0.26), residues: 1111 helix: 2.37 (0.26), residues: 385 sheet: 1.04 (0.31), residues: 266 loop : -0.87 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 104 HIS 0.007 0.001 HIS B 59 PHE 0.010 0.001 PHE A 189 TYR 0.011 0.001 TYR B 64 ARG 0.004 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 1.077 Fit side-chains REVERT: A 20 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6245 (mm-30) REVERT: A 21 LYS cc_start: 0.6653 (mttt) cc_final: 0.6205 (mmtt) REVERT: A 309 ARG cc_start: 0.4607 (mtp-110) cc_final: 0.4360 (tmm-80) REVERT: A 323 ARG cc_start: 0.6488 (mtt-85) cc_final: 0.6100 (mtm180) REVERT: A 336 THR cc_start: 0.6782 (OUTLIER) cc_final: 0.6554 (t) REVERT: A 355 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6198 (mp) REVERT: B 64 TYR cc_start: 0.7880 (m-80) cc_final: 0.7519 (m-80) REVERT: B 103 SER cc_start: 0.7139 (m) cc_final: 0.6836 (p) REVERT: B 142 ARG cc_start: 0.7244 (tpp-160) cc_final: 0.6722 (tpp80) REVERT: B 154 CYS cc_start: 0.7474 (m) cc_final: 0.6975 (p) REVERT: B 168 ASP cc_start: 0.7058 (OUTLIER) cc_final: 0.6312 (p0) REVERT: B 180 GLN cc_start: 0.7375 (pp30) cc_final: 0.6683 (pp30) REVERT: B 244 ASN cc_start: 0.7568 (t0) cc_final: 0.7368 (m-40) REVERT: B 272 ASP cc_start: 0.7045 (m-30) cc_final: 0.6662 (p0) REVERT: B 285 LYS cc_start: 0.7380 (tttm) cc_final: 0.7054 (tttm) REVERT: E 234 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6741 (mm-30) REVERT: G 19 LEU cc_start: 0.6361 (OUTLIER) cc_final: 0.5765 (pt) REVERT: G 22 GLU cc_start: 0.5364 (mt-10) cc_final: 0.4936 (mt-10) REVERT: R 59 LEU cc_start: 0.4440 (mt) cc_final: 0.4068 (pp) REVERT: R 212 GLU cc_start: 0.5734 (OUTLIER) cc_final: 0.4446 (mp0) REVERT: R 247 ARG cc_start: 0.5602 (mmm-85) cc_final: 0.5031 (tpt170) REVERT: R 322 TRP cc_start: 0.6177 (t60) cc_final: 0.5953 (t60) outliers start: 39 outliers final: 20 residues processed: 140 average time/residue: 1.0987 time to fit residues: 165.4947 Evaluate side-chains 127 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 319 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 0.0270 chunk 43 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 73 optimal weight: 0.0270 chunk 0 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 ASN B 242 ASN R 92 HIS R 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9036 Z= 0.145 Angle : 0.503 6.105 12267 Z= 0.261 Chirality : 0.040 0.171 1405 Planarity : 0.003 0.040 1548 Dihedral : 3.886 18.017 1241 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.15 % Allowed : 19.57 % Favored : 76.28 % 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: 1.21 (0.26), residues: 1111 helix: 2.50 (0.26), residues: 386 sheet: 1.12 (0.32), residues: 262 loop : -0.91 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 216 HIS 0.004 0.001 HIS E 35 PHE 0.009 0.001 PHE A 189 TYR 0.013 0.001 TYR A 327 ARG 0.004 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.936 Fit side-chains REVERT: A 20 GLU cc_start: 0.6777 (mt-10) cc_final: 0.6229 (mm-30) REVERT: A 21 LYS cc_start: 0.6672 (mttt) cc_final: 0.6202 (mmtt) REVERT: A 309 ARG cc_start: 0.4559 (mtp-110) cc_final: 0.4300 (tmm-80) REVERT: A 323 ARG cc_start: 0.6493 (mtt-85) cc_final: 0.6080 (mtm180) REVERT: A 336 THR cc_start: 0.6790 (OUTLIER) cc_final: 0.6555 (t) REVERT: A 348 ASP cc_start: 0.7793 (t0) cc_final: 0.7558 (t0) REVERT: A 355 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.6230 (mp) REVERT: B 64 TYR cc_start: 0.7829 (m-80) cc_final: 0.7525 (m-80) REVERT: B 103 SER cc_start: 0.7081 (m) cc_final: 0.6762 (p) REVERT: B 142 ARG cc_start: 0.7020 (tpp-160) cc_final: 0.6545 (tpp80) REVERT: B 154 CYS cc_start: 0.7333 (m) cc_final: 0.6958 (p) REVERT: B 168 ASP cc_start: 0.7030 (OUTLIER) cc_final: 0.6346 (p0) REVERT: B 180 GLN cc_start: 0.7277 (pp30) cc_final: 0.6601 (pp30) REVERT: B 191 ASP cc_start: 0.6183 (t0) cc_final: 0.5803 (t0) REVERT: B 219 ARG cc_start: 0.6286 (mpt180) cc_final: 0.5890 (mtm180) REVERT: B 252 ASP cc_start: 0.7375 (t0) cc_final: 0.7032 (t0) REVERT: B 272 ASP cc_start: 0.7034 (m-30) cc_final: 0.6642 (p0) REVERT: B 285 LYS cc_start: 0.7352 (tttm) cc_final: 0.6938 (ttmm) REVERT: E 155 VAL cc_start: 0.7474 (OUTLIER) cc_final: 0.7093 (m) REVERT: E 234 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6617 (mm-30) REVERT: G 19 LEU cc_start: 0.6318 (OUTLIER) cc_final: 0.5733 (pt) REVERT: G 22 GLU cc_start: 0.5072 (mt-10) cc_final: 0.4632 (mt-10) REVERT: R 59 LEU cc_start: 0.4520 (mt) cc_final: 0.4142 (pp) REVERT: R 92 HIS cc_start: 0.6243 (OUTLIER) cc_final: 0.5912 (m90) REVERT: R 212 GLU cc_start: 0.5641 (OUTLIER) cc_final: 0.4983 (mp0) REVERT: R 247 ARG cc_start: 0.5592 (mmm-85) cc_final: 0.5022 (tpt170) REVERT: R 322 TRP cc_start: 0.6210 (t60) cc_final: 0.5984 (t60) outliers start: 39 outliers final: 18 residues processed: 139 average time/residue: 1.1123 time to fit residues: 166.0576 Evaluate side-chains 125 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 92 HIS Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 319 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 0.0020 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN R 92 HIS R 96 ASN R 200 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9036 Z= 0.162 Angle : 0.513 6.114 12267 Z= 0.264 Chirality : 0.040 0.167 1405 Planarity : 0.004 0.044 1548 Dihedral : 3.899 18.500 1241 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.04 % Allowed : 20.53 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.26), residues: 1111 helix: 2.48 (0.26), residues: 387 sheet: 1.06 (0.32), residues: 262 loop : -0.89 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 216 HIS 0.007 0.001 HIS R 92 PHE 0.011 0.001 PHE A 189 TYR 0.012 0.001 TYR A 327 ARG 0.003 0.000 ARG R 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 1.018 Fit side-chains REVERT: A 20 GLU cc_start: 0.6789 (mt-10) cc_final: 0.6242 (mm-30) REVERT: A 21 LYS cc_start: 0.6700 (mttt) cc_final: 0.6224 (mmtt) REVERT: A 53 MET cc_start: 0.5098 (OUTLIER) cc_final: 0.4663 (mpt) REVERT: A 323 ARG cc_start: 0.6507 (mtt-85) cc_final: 0.6097 (mtm180) REVERT: A 336 THR cc_start: 0.6795 (OUTLIER) cc_final: 0.6555 (t) REVERT: A 348 ASP cc_start: 0.7790 (t0) cc_final: 0.7546 (t0) REVERT: A 355 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6232 (mp) REVERT: B 64 TYR cc_start: 0.7848 (m-80) cc_final: 0.7485 (m-80) REVERT: B 103 SER cc_start: 0.7122 (m) cc_final: 0.6819 (p) REVERT: B 142 ARG cc_start: 0.7044 (tpp-160) cc_final: 0.6560 (tpp80) REVERT: B 154 CYS cc_start: 0.7411 (m) cc_final: 0.6917 (p) REVERT: B 168 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6343 (p0) REVERT: B 180 GLN cc_start: 0.7286 (pp30) cc_final: 0.6605 (pp30) REVERT: B 191 ASP cc_start: 0.6143 (t0) cc_final: 0.5658 (t0) REVERT: B 219 ARG cc_start: 0.6379 (mpt180) cc_final: 0.5936 (mtm180) REVERT: B 252 ASP cc_start: 0.7306 (t0) cc_final: 0.6991 (t0) REVERT: B 260 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7624 (mp) REVERT: B 265 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6800 (tp30) REVERT: B 272 ASP cc_start: 0.7042 (m-30) cc_final: 0.6677 (p0) REVERT: B 285 LYS cc_start: 0.7365 (tttm) cc_final: 0.6951 (ttmm) REVERT: E 155 VAL cc_start: 0.7495 (OUTLIER) cc_final: 0.7103 (m) REVERT: E 189 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8143 (mp) REVERT: E 234 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6620 (mm-30) REVERT: E 235 TYR cc_start: 0.4492 (OUTLIER) cc_final: 0.3990 (t80) REVERT: G 19 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.5641 (OUTLIER) REVERT: G 22 GLU cc_start: 0.5108 (mt-10) cc_final: 0.4722 (mt-10) REVERT: R 212 GLU cc_start: 0.5608 (OUTLIER) cc_final: 0.4956 (mp0) REVERT: R 247 ARG cc_start: 0.5573 (mmm-85) cc_final: 0.5004 (tpt170) REVERT: R 322 TRP cc_start: 0.6288 (t60) cc_final: 0.6069 (t60) outliers start: 38 outliers final: 21 residues processed: 128 average time/residue: 1.2096 time to fit residues: 165.7918 Evaluate side-chains 132 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 319 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.2980 chunk 60 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 0.0670 chunk 66 optimal weight: 0.0370 chunk 64 optimal weight: 0.0570 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.2314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN R 92 HIS R 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9036 Z= 0.122 Angle : 0.485 5.868 12267 Z= 0.249 Chirality : 0.039 0.150 1405 Planarity : 0.003 0.044 1548 Dihedral : 3.668 16.606 1241 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.55 % Allowed : 22.55 % Favored : 74.89 % 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: 1.33 (0.26), residues: 1111 helix: 2.64 (0.26), residues: 384 sheet: 1.16 (0.33), residues: 252 loop : -0.81 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 216 HIS 0.004 0.001 HIS E 35 PHE 0.010 0.001 PHE A 189 TYR 0.012 0.001 TYR A 327 ARG 0.007 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6287 (mm-30) REVERT: A 21 LYS cc_start: 0.6636 (mttt) cc_final: 0.6164 (mmtt) REVERT: A 53 MET cc_start: 0.4985 (OUTLIER) cc_final: 0.4596 (mpt) REVERT: A 323 ARG cc_start: 0.6500 (mtt-85) cc_final: 0.6095 (mtm180) REVERT: A 336 THR cc_start: 0.6798 (OUTLIER) cc_final: 0.6546 (t) REVERT: A 348 ASP cc_start: 0.7730 (t0) cc_final: 0.7490 (t0) REVERT: B 103 SER cc_start: 0.6938 (m) cc_final: 0.6699 (p) REVERT: B 154 CYS cc_start: 0.7216 (m) cc_final: 0.6997 (p) REVERT: B 168 ASP cc_start: 0.7050 (OUTLIER) cc_final: 0.6345 (p0) REVERT: B 180 GLN cc_start: 0.7230 (pp30) cc_final: 0.6520 (pp30) REVERT: B 191 ASP cc_start: 0.6122 (t0) cc_final: 0.5709 (t0) REVERT: B 252 ASP cc_start: 0.7230 (t0) cc_final: 0.6947 (t0) REVERT: B 272 ASP cc_start: 0.7082 (m-30) cc_final: 0.6706 (p0) REVERT: B 285 LYS cc_start: 0.7430 (tttm) cc_final: 0.7045 (ttmm) REVERT: B 309 ARG cc_start: 0.7357 (ttm170) cc_final: 0.6940 (ttm170) REVERT: E 155 VAL cc_start: 0.7464 (OUTLIER) cc_final: 0.7064 (m) REVERT: E 234 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6542 (mm-30) REVERT: E 235 TYR cc_start: 0.4230 (OUTLIER) cc_final: 0.3757 (t80) REVERT: G 19 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.5554 (pt) REVERT: G 22 GLU cc_start: 0.5141 (mt-10) cc_final: 0.4679 (mt-10) REVERT: R 59 LEU cc_start: 0.4239 (mt) cc_final: 0.3950 (pp) REVERT: R 247 ARG cc_start: 0.5604 (mmm-85) cc_final: 0.5039 (tpt170) REVERT: R 322 TRP cc_start: 0.6295 (t60) cc_final: 0.6067 (t60) outliers start: 24 outliers final: 14 residues processed: 129 average time/residue: 1.3042 time to fit residues: 179.1720 Evaluate side-chains 123 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 319 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 92 optimal weight: 0.0870 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9036 Z= 0.149 Angle : 0.508 5.931 12267 Z= 0.260 Chirality : 0.040 0.153 1405 Planarity : 0.004 0.046 1548 Dihedral : 3.779 17.851 1241 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.51 % Allowed : 21.60 % Favored : 74.89 % 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: 1.31 (0.26), residues: 1111 helix: 2.64 (0.26), residues: 385 sheet: 1.12 (0.33), residues: 252 loop : -0.82 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 344 HIS 0.004 0.001 HIS E 35 PHE 0.012 0.001 PHE A 189 TYR 0.011 0.001 TYR A 327 ARG 0.011 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6223 (mm-30) REVERT: A 21 LYS cc_start: 0.6664 (mttt) cc_final: 0.6178 (mmtt) REVERT: A 53 MET cc_start: 0.5077 (OUTLIER) cc_final: 0.4728 (mpt) REVERT: A 198 MET cc_start: 0.8293 (ttp) cc_final: 0.7931 (tpp) REVERT: A 323 ARG cc_start: 0.6523 (mtt-85) cc_final: 0.6108 (mtm180) REVERT: A 336 THR cc_start: 0.6799 (OUTLIER) cc_final: 0.6544 (t) REVERT: A 348 ASP cc_start: 0.7751 (t0) cc_final: 0.7515 (t0) REVERT: B 103 SER cc_start: 0.6972 (m) cc_final: 0.6751 (p) REVERT: B 154 CYS cc_start: 0.7370 (m) cc_final: 0.6984 (p) REVERT: B 168 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6358 (p0) REVERT: B 180 GLN cc_start: 0.7250 (pp30) cc_final: 0.6574 (pp30) REVERT: B 191 ASP cc_start: 0.6046 (t0) cc_final: 0.5575 (t0) REVERT: B 219 ARG cc_start: 0.5623 (mmp80) cc_final: 0.5347 (mpt180) REVERT: B 252 ASP cc_start: 0.7230 (t0) cc_final: 0.6897 (t0) REVERT: B 272 ASP cc_start: 0.7158 (m-30) cc_final: 0.6760 (p0) REVERT: B 285 LYS cc_start: 0.7408 (tttm) cc_final: 0.7083 (tttm) REVERT: E 155 VAL cc_start: 0.7466 (OUTLIER) cc_final: 0.7052 (m) REVERT: E 189 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8256 (mp) REVERT: E 234 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6563 (mm-30) REVERT: G 19 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.5608 (pt) REVERT: G 22 GLU cc_start: 0.5079 (mt-10) cc_final: 0.4651 (mt-10) REVERT: R 59 LEU cc_start: 0.4377 (mt) cc_final: 0.4010 (pp) REVERT: R 212 GLU cc_start: 0.5480 (OUTLIER) cc_final: 0.4907 (mp0) REVERT: R 315 LEU cc_start: 0.5992 (mm) cc_final: 0.5764 (tp) REVERT: R 322 TRP cc_start: 0.6314 (t60) cc_final: 0.6085 (t60) outliers start: 33 outliers final: 18 residues processed: 125 average time/residue: 1.1795 time to fit residues: 157.9680 Evaluate side-chains 125 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 319 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 59 optimal weight: 0.0050 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 0.2980 chunk 89 optimal weight: 0.0970 chunk 93 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 63 optimal weight: 0.2980 overall best weight: 0.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 96 ASN R 141 GLN R 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9036 Z= 0.124 Angle : 0.492 6.974 12267 Z= 0.252 Chirality : 0.040 0.152 1405 Planarity : 0.003 0.044 1548 Dihedral : 3.645 16.178 1241 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.45 % Allowed : 23.19 % Favored : 74.36 % 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: 1.37 (0.26), residues: 1111 helix: 2.68 (0.26), residues: 386 sheet: 1.11 (0.33), residues: 258 loop : -0.78 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 344 HIS 0.004 0.001 HIS E 35 PHE 0.011 0.001 PHE A 189 TYR 0.011 0.001 TYR A 327 ARG 0.010 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 1.071 Fit side-chains REVERT: A 20 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6253 (mm-30) REVERT: A 21 LYS cc_start: 0.6612 (mttt) cc_final: 0.6158 (mmtt) REVERT: A 198 MET cc_start: 0.8311 (ttp) cc_final: 0.7892 (tpp) REVERT: A 323 ARG cc_start: 0.6523 (mtt-85) cc_final: 0.6107 (mtm180) REVERT: A 336 THR cc_start: 0.6861 (OUTLIER) cc_final: 0.6610 (t) REVERT: A 348 ASP cc_start: 0.7759 (t0) cc_final: 0.7512 (t0) REVERT: B 103 SER cc_start: 0.6874 (m) cc_final: 0.6672 (p) REVERT: B 116 TYR cc_start: 0.7749 (m-80) cc_final: 0.7471 (m-80) REVERT: B 142 ARG cc_start: 0.6879 (tpp-160) cc_final: 0.6414 (tpp80) REVERT: B 154 CYS cc_start: 0.7215 (m) cc_final: 0.7008 (p) REVERT: B 168 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6391 (p0) REVERT: B 180 GLN cc_start: 0.7245 (pp30) cc_final: 0.6635 (pp30) REVERT: B 191 ASP cc_start: 0.6066 (t0) cc_final: 0.5655 (t0) REVERT: B 224 ARG cc_start: 0.6101 (pmm-80) cc_final: 0.5895 (pmm-80) REVERT: B 252 ASP cc_start: 0.7258 (t0) cc_final: 0.6908 (t0) REVERT: B 272 ASP cc_start: 0.7143 (m-30) cc_final: 0.6736 (p0) REVERT: B 285 LYS cc_start: 0.7464 (tttm) cc_final: 0.7094 (ttmm) REVERT: E 155 VAL cc_start: 0.7504 (OUTLIER) cc_final: 0.7055 (m) REVERT: E 189 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8251 (mp) REVERT: E 234 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6528 (mm-30) REVERT: G 22 GLU cc_start: 0.5114 (mt-10) cc_final: 0.4551 (mt-10) REVERT: R 59 LEU cc_start: 0.4465 (mt) cc_final: 0.4111 (pp) REVERT: R 212 GLU cc_start: 0.5359 (OUTLIER) cc_final: 0.4827 (mp0) REVERT: R 315 LEU cc_start: 0.5993 (mm) cc_final: 0.5758 (tp) REVERT: R 318 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6910 (tm) outliers start: 23 outliers final: 12 residues processed: 123 average time/residue: 1.2414 time to fit residues: 163.0570 Evaluate side-chains 122 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 319 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 0.3980 chunk 87 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 67 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN B 235 ASN R 96 ASN R 331 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9036 Z= 0.181 Angle : 0.555 7.851 12267 Z= 0.283 Chirality : 0.041 0.171 1405 Planarity : 0.004 0.044 1548 Dihedral : 3.927 19.094 1241 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.34 % Allowed : 23.72 % Favored : 73.94 % 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: 1.24 (0.26), residues: 1111 helix: 2.57 (0.26), residues: 386 sheet: 0.89 (0.32), residues: 270 loop : -0.81 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 216 HIS 0.006 0.001 HIS B 59 PHE 0.012 0.001 PHE A 189 TYR 0.014 0.001 TYR B 269 ARG 0.013 0.001 ARG A 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6296 (mm-30) REVERT: A 21 LYS cc_start: 0.6731 (mttt) cc_final: 0.6246 (mmtt) REVERT: A 53 MET cc_start: 0.4625 (mpt) cc_final: 0.4336 (mpt) REVERT: A 198 MET cc_start: 0.8361 (ttp) cc_final: 0.7915 (tpp) REVERT: A 323 ARG cc_start: 0.6570 (mtt-85) cc_final: 0.6154 (mtm180) REVERT: A 336 THR cc_start: 0.6793 (OUTLIER) cc_final: 0.6504 (t) REVERT: A 348 ASP cc_start: 0.7748 (t0) cc_final: 0.7497 (t0) REVERT: B 64 TYR cc_start: 0.7723 (m-80) cc_final: 0.7438 (m-80) REVERT: B 103 SER cc_start: 0.7032 (m) cc_final: 0.6788 (p) REVERT: B 154 CYS cc_start: 0.7514 (m) cc_final: 0.7047 (p) REVERT: B 168 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6361 (p0) REVERT: B 191 ASP cc_start: 0.6061 (t0) cc_final: 0.5544 (t0) REVERT: B 219 ARG cc_start: 0.5877 (mmp-170) cc_final: 0.5503 (mpt180) REVERT: B 252 ASP cc_start: 0.7254 (t0) cc_final: 0.6916 (t0) REVERT: B 267 MET cc_start: 0.7047 (tpp) cc_final: 0.6648 (mmt) REVERT: B 272 ASP cc_start: 0.7135 (m-30) cc_final: 0.6741 (p0) REVERT: B 285 LYS cc_start: 0.7424 (tttm) cc_final: 0.7100 (tttm) REVERT: E 150 THR cc_start: 0.6146 (p) cc_final: 0.5861 (t) REVERT: E 155 VAL cc_start: 0.7557 (OUTLIER) cc_final: 0.7135 (m) REVERT: E 234 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6611 (mm-30) REVERT: G 22 GLU cc_start: 0.5191 (mt-10) cc_final: 0.4640 (mt-10) REVERT: R 59 LEU cc_start: 0.4404 (mt) cc_final: 0.4146 (pp) REVERT: R 212 GLU cc_start: 0.5446 (OUTLIER) cc_final: 0.4898 (mp0) outliers start: 22 outliers final: 13 residues processed: 125 average time/residue: 1.1440 time to fit residues: 153.6534 Evaluate side-chains 123 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 319 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 0.0010 chunk 4 optimal weight: 5.9990 chunk 63 optimal weight: 0.2980 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.199200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.163550 restraints weight = 9695.058| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.78 r_work: 0.3728 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9036 Z= 0.213 Angle : 0.580 8.148 12267 Z= 0.298 Chirality : 0.042 0.213 1405 Planarity : 0.004 0.039 1548 Dihedral : 4.172 19.878 1241 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.66 % Allowed : 23.51 % Favored : 73.83 % 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: 1.12 (0.26), residues: 1111 helix: 2.45 (0.26), residues: 388 sheet: 0.72 (0.31), residues: 275 loop : -0.80 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 216 HIS 0.008 0.001 HIS B 59 PHE 0.012 0.001 PHE A 189 TYR 0.013 0.001 TYR E 103 ARG 0.012 0.001 ARG A 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3490.67 seconds wall clock time: 64 minutes 40.47 seconds (3880.47 seconds total)