Starting phenix.real_space_refine on Thu Feb 13 18:17:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vfx_31962/02_2025/7vfx_31962.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vfx_31962/02_2025/7vfx_31962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vfx_31962/02_2025/7vfx_31962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vfx_31962/02_2025/7vfx_31962.map" model { file = "/net/cci-nas-00/data/ceres_data/7vfx_31962/02_2025/7vfx_31962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vfx_31962/02_2025/7vfx_31962.cif" } resolution = 2.8 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= 0.004 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 64 5.16 5 C 5781 2.51 5 N 1512 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9004 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2323 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 12, 'TRANS': 282} Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 38 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 102 Unusual residues: {'CLR': 3, 'PLM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.38, per 1000 atoms: 0.60 Number of scatterers: 9004 At special positions: 0 Unit cell: (90.1, 124.95, 123.25, 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 64 16.00 O 1647 8.00 N 1512 7.00 C 5781 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.1 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 38.9% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'R' and resid 22 through 54 removed outlier: 3.610A pdb=" N ASP R 26 " --> pdb=" O TYR R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 76 Processing helix chain 'R' and resid 77 through 87 removed outlier: 3.853A pdb=" N PHE R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 Processing helix chain 'R' and resid 129 through 137 Processing helix chain 'R' and resid 138 through 146 Processing helix chain 'R' and resid 146 through 163 removed outlier: 4.459A pdb=" N TRP R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 186 through 209 removed outlier: 3.825A pdb=" N ARG R 190 " --> pdb=" O ASP R 186 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN R 192 " --> pdb=" O LYS R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 231 Processing helix chain 'R' and resid 236 through 267 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 267 through 273 removed outlier: 4.193A pdb=" N GLN R 273 " --> pdb=" O ARG R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 303 removed outlier: 4.218A pdb=" N ALA R 288 " --> pdb=" O ASP R 284 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU R 289 " --> pdb=" O VAL R 285 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N SER R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N CYS R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 305 through 315 Processing helix chain 'A' and resid 8 through 31 Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 202 through 205 removed outlier: 4.000A pdb=" N ARG A 205 " --> pdb=" O GLY A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.811A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.537A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.552A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.612A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 351 removed outlier: 4.181A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.693A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.890A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 164 through 169 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 5.990A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.179A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.906A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.894A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.738A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.956A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.499A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.727A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.126A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.126A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'S' and resid 194 through 195 removed outlier: 6.607A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1287 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: 2.80 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2864 1.34 - 1.46: 2238 1.46 - 1.58: 4003 1.58 - 1.70: 0 1.70 - 1.82: 95 Bond restraints: 9200 Sorted by residual: bond pdb=" SD FME C 1 " pdb=" CE FME C 1 " ideal model delta sigma weight residual 1.805 1.750 0.055 2.00e-02 2.50e+03 7.58e+00 bond pdb=" CG FME C 1 " pdb=" SD FME C 1 " ideal model delta sigma weight residual 1.817 1.771 0.046 2.00e-02 2.50e+03 5.35e+00 bond pdb=" N FME C 1 " pdb=" CN FME C 1 " ideal model delta sigma weight residual 1.335 1.374 -0.039 2.00e-02 2.50e+03 3.88e+00 bond pdb=" CA GLN B 75 " pdb=" C GLN B 75 " ideal model delta sigma weight residual 1.522 1.490 0.032 1.72e-02 3.38e+03 3.45e+00 bond pdb=" C10 CLR R 402 " pdb=" C9 CLR R 402 " ideal model delta sigma weight residual 1.551 1.517 0.034 2.00e-02 2.50e+03 2.91e+00 ... (remaining 9195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 12159 1.70 - 3.39: 238 3.39 - 5.09: 60 5.09 - 6.78: 13 6.78 - 8.48: 1 Bond angle restraints: 12471 Sorted by residual: angle pdb=" N VAL S 64 " pdb=" CA VAL S 64 " pdb=" C VAL S 64 " ideal model delta sigma weight residual 113.20 109.73 3.47 9.60e-01 1.09e+00 1.30e+01 angle pdb=" CB MET R 197 " pdb=" CG MET R 197 " pdb=" SD MET R 197 " ideal model delta sigma weight residual 112.70 121.18 -8.48 3.00e+00 1.11e-01 7.98e+00 angle pdb=" CA VAL R 302 " pdb=" C VAL R 302 " pdb=" N PHE R 303 " ideal model delta sigma weight residual 116.60 120.42 -3.82 1.45e+00 4.76e-01 6.94e+00 angle pdb=" CA CYS S 96 " pdb=" CB CYS S 96 " pdb=" SG CYS S 96 " ideal model delta sigma weight residual 114.40 120.19 -5.79 2.30e+00 1.89e-01 6.33e+00 angle pdb=" C MET A 240 " pdb=" N ASN A 241 " pdb=" CA ASN A 241 " ideal model delta sigma weight residual 121.54 126.34 -4.80 1.91e+00 2.74e-01 6.32e+00 ... (remaining 12466 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 5263 24.42 - 48.83: 275 48.83 - 73.25: 34 73.25 - 97.67: 12 97.67 - 122.08: 1 Dihedral angle restraints: 5585 sinusoidal: 2300 harmonic: 3285 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 158.85 21.15 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLN S 142 " pdb=" C GLN S 142 " pdb=" N ALA S 143 " pdb=" CA ALA S 143 " ideal model delta harmonic sigma weight residual -180.00 -159.31 -20.69 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" C10 CLR R 403 " pdb=" C1 CLR R 403 " pdb=" C2 CLR R 403 " pdb=" C3 CLR R 403 " ideal model delta sinusoidal sigma weight residual -56.83 65.25 -122.08 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 5582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 992 0.042 - 0.084: 324 0.084 - 0.127: 94 0.127 - 0.169: 12 0.169 - 0.211: 7 Chirality restraints: 1429 Sorted by residual: chirality pdb=" C13 CLR R 403 " pdb=" C12 CLR R 403 " pdb=" C14 CLR R 403 " pdb=" C17 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.93 -2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C13 CLR R 402 " pdb=" C12 CLR R 402 " pdb=" C14 CLR R 402 " pdb=" C17 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.93 -2.74 -0.19 2.00e-01 2.50e+01 9.50e-01 chirality pdb=" C13 CLR R 401 " pdb=" C12 CLR R 401 " pdb=" C14 CLR R 401 " pdb=" C17 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.93 -2.75 -0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 1426 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL S 147 " 0.062 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO S 148 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO S 148 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO S 148 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B 194 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 158 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO R 159 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO R 159 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 159 " 0.024 5.00e-02 4.00e+02 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1355 2.76 - 3.29: 8272 3.29 - 3.83: 14381 3.83 - 4.36: 17237 4.36 - 4.90: 30477 Nonbonded interactions: 71722 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.225 3.040 nonbonded pdb=" OD2 ASP B 153 " pdb=" NE2 GLN B 156 " model vdw 2.292 3.120 nonbonded pdb=" ND2 ASN B 340 " pdb=" OD1 ASN G 59 " model vdw 2.300 3.120 nonbonded pdb=" O GLY S 112 " pdb=" OG SER S 184 " model vdw 2.333 3.040 nonbonded pdb=" NZ LYS S 163 " pdb=" OE2 GLU S 234 " model vdw 2.336 3.120 ... (remaining 71717 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.360 Find NCS groups from input model: 0.090 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:13.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9200 Z= 0.221 Angle : 0.654 8.477 12471 Z= 0.351 Chirality : 0.046 0.211 1429 Planarity : 0.004 0.094 1552 Dihedral : 15.033 122.082 3456 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.41 (0.25), residues: 1120 helix: 1.62 (0.27), residues: 400 sheet: 0.28 (0.30), residues: 287 loop : -0.99 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.019 0.001 PHE B 199 TYR 0.011 0.001 TYR S 190 ARG 0.005 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.040 Fit side-chains REVERT: R 44 ASN cc_start: 0.8230 (m110) cc_final: 0.7988 (m110) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 1.5032 time to fit residues: 190.8643 Evaluate side-chains 100 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN R 108 ASN S 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.133410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.090380 restraints weight = 12632.398| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.37 r_work: 0.2894 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9200 Z= 0.229 Angle : 0.596 7.092 12471 Z= 0.315 Chirality : 0.044 0.140 1429 Planarity : 0.004 0.040 1552 Dihedral : 7.563 58.535 1436 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.65 % Allowed : 6.91 % Favored : 91.44 % 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: 0.56 (0.25), residues: 1120 helix: 1.78 (0.26), residues: 402 sheet: 0.35 (0.30), residues: 286 loop : -0.94 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.016 0.001 PHE A 189 TYR 0.013 0.001 TYR S 190 ARG 0.003 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 1.022 Fit side-chains REVERT: A 242 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7076 (mtp180) REVERT: A 297 GLU cc_start: 0.7882 (mp0) cc_final: 0.7662 (mp0) REVERT: G 19 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5335 (mp) outliers start: 16 outliers final: 1 residues processed: 113 average time/residue: 1.4530 time to fit residues: 174.5025 Evaluate side-chains 109 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 19 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 20 optimal weight: 0.9980 chunk 63 optimal weight: 0.2980 chunk 67 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN R 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.133150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.089772 restraints weight = 12836.973| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.39 r_work: 0.2883 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 9200 Z= 0.226 Angle : 0.571 7.494 12471 Z= 0.305 Chirality : 0.044 0.139 1429 Planarity : 0.004 0.037 1552 Dihedral : 6.792 56.473 1436 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.24 % Allowed : 9.90 % Favored : 88.87 % 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: 0.56 (0.25), residues: 1120 helix: 1.74 (0.26), residues: 409 sheet: 0.36 (0.30), residues: 292 loop : -0.98 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.017 0.001 PHE A 189 TYR 0.014 0.001 TYR A 287 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 1.077 Fit side-chains REVERT: A 242 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7085 (mtp180) REVERT: A 287 TYR cc_start: 0.7648 (m-80) cc_final: 0.7418 (m-80) REVERT: G 19 LEU cc_start: 0.5692 (OUTLIER) cc_final: 0.5184 (mp) REVERT: S 234 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8193 (mt-10) outliers start: 12 outliers final: 2 residues processed: 108 average time/residue: 1.4289 time to fit residues: 163.8752 Evaluate side-chains 107 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 108 ASN ** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.090688 restraints weight = 12705.602| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.41 r_work: 0.2898 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9200 Z= 0.183 Angle : 0.536 6.345 12471 Z= 0.287 Chirality : 0.042 0.137 1429 Planarity : 0.003 0.035 1552 Dihedral : 6.517 57.869 1436 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.44 % Allowed : 11.44 % Favored : 87.11 % 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: 0.70 (0.25), residues: 1120 helix: 1.86 (0.26), residues: 409 sheet: 0.43 (0.30), residues: 291 loop : -0.89 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.015 0.001 PHE B 199 TYR 0.013 0.001 TYR A 287 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 1.127 Fit side-chains REVERT: A 242 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7102 (mtp180) REVERT: A 287 TYR cc_start: 0.7655 (m-80) cc_final: 0.7361 (m-80) REVERT: A 318 GLU cc_start: 0.8095 (tt0) cc_final: 0.7562 (mm-30) REVERT: B 217 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7042 (pp-130) REVERT: G 19 LEU cc_start: 0.5626 (OUTLIER) cc_final: 0.5124 (mp) REVERT: G 21 MET cc_start: 0.7314 (tpp) cc_final: 0.6912 (mmp) REVERT: S 43 LYS cc_start: 0.8425 (mptt) cc_final: 0.8143 (mppt) REVERT: S 234 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8184 (mt-10) REVERT: S 245 LEU cc_start: 0.8764 (tt) cc_final: 0.8501 (tp) outliers start: 14 outliers final: 4 residues processed: 110 average time/residue: 1.4179 time to fit residues: 165.7118 Evaluate side-chains 110 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 74 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 90 HIS R 108 ASN B 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.131292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.087099 restraints weight = 12748.024| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.13 r_work: 0.2875 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9200 Z= 0.332 Angle : 0.624 6.919 12471 Z= 0.334 Chirality : 0.046 0.143 1429 Planarity : 0.004 0.038 1552 Dihedral : 6.867 56.881 1436 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.65 % Allowed : 12.68 % Favored : 85.67 % 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: 0.54 (0.25), residues: 1120 helix: 1.68 (0.26), residues: 408 sheet: 0.36 (0.30), residues: 295 loop : -0.94 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS R 90 PHE 0.021 0.002 PHE B 199 TYR 0.013 0.002 TYR A 320 ARG 0.004 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 1.020 Fit side-chains REVERT: A 242 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7122 (mtp180) REVERT: G 19 LEU cc_start: 0.5689 (OUTLIER) cc_final: 0.5144 (mp) REVERT: S 234 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8155 (mt-10) outliers start: 16 outliers final: 6 residues processed: 108 average time/residue: 1.4808 time to fit residues: 170.0707 Evaluate side-chains 108 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.133134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.090241 restraints weight = 12614.345| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.28 r_work: 0.2896 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9200 Z= 0.203 Angle : 0.551 7.896 12471 Z= 0.295 Chirality : 0.043 0.137 1429 Planarity : 0.003 0.036 1552 Dihedral : 6.475 56.101 1436 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.55 % Allowed : 13.81 % Favored : 84.64 % 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: 0.71 (0.25), residues: 1120 helix: 1.85 (0.26), residues: 409 sheet: 0.50 (0.30), residues: 289 loop : -0.90 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.016 0.001 PHE A 189 TYR 0.012 0.001 TYR S 190 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 1.007 Fit side-chains REVERT: A 242 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7075 (mtp180) REVERT: A 287 TYR cc_start: 0.7601 (m-80) cc_final: 0.7337 (m-80) REVERT: A 311 ASN cc_start: 0.8581 (t0) cc_final: 0.8162 (t0) REVERT: A 318 GLU cc_start: 0.8032 (tt0) cc_final: 0.7499 (mm-30) REVERT: B 217 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.7136 (pp-130) REVERT: G 19 LEU cc_start: 0.5744 (OUTLIER) cc_final: 0.5221 (mp) REVERT: S 234 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: S 245 LEU cc_start: 0.8736 (tt) cc_final: 0.8523 (tp) outliers start: 15 outliers final: 6 residues processed: 112 average time/residue: 1.3651 time to fit residues: 162.7316 Evaluate side-chains 112 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 44 optimal weight: 0.0970 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.132901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.088928 restraints weight = 12907.637| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.16 r_work: 0.2909 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9200 Z= 0.223 Angle : 0.563 8.784 12471 Z= 0.300 Chirality : 0.043 0.140 1429 Planarity : 0.004 0.036 1552 Dihedral : 6.467 56.714 1436 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.06 % Allowed : 13.92 % Favored : 84.02 % 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: 0.73 (0.25), residues: 1120 helix: 1.86 (0.26), residues: 409 sheet: 0.50 (0.30), residues: 289 loop : -0.88 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.017 0.001 PHE A 189 TYR 0.012 0.001 TYR S 190 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 1.121 Fit side-chains REVERT: A 242 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7100 (mtp180) REVERT: A 287 TYR cc_start: 0.7629 (m-80) cc_final: 0.7337 (m-80) REVERT: A 311 ASN cc_start: 0.8607 (t0) cc_final: 0.8182 (t0) REVERT: A 318 GLU cc_start: 0.8106 (tt0) cc_final: 0.7858 (tt0) REVERT: B 217 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.7073 (pp-130) REVERT: G 19 LEU cc_start: 0.5769 (OUTLIER) cc_final: 0.5236 (mp) REVERT: S 234 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8087 (mt-10) REVERT: S 245 LEU cc_start: 0.8778 (tt) cc_final: 0.8518 (tp) outliers start: 20 outliers final: 10 residues processed: 116 average time/residue: 1.3409 time to fit residues: 165.6146 Evaluate side-chains 119 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 34 optimal weight: 0.0070 chunk 68 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 293 ASN ** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.136282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.093425 restraints weight = 12974.491| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.39 r_work: 0.2959 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9200 Z= 0.124 Angle : 0.498 9.189 12471 Z= 0.266 Chirality : 0.041 0.129 1429 Planarity : 0.003 0.035 1552 Dihedral : 5.984 57.676 1436 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.24 % Allowed : 15.15 % Favored : 83.61 % 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: 1.02 (0.25), residues: 1120 helix: 2.11 (0.26), residues: 409 sheet: 0.78 (0.31), residues: 270 loop : -0.77 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.002 0.000 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.012 0.001 TYR S 190 ARG 0.005 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 1.046 Fit side-chains REVERT: R 44 ASN cc_start: 0.8188 (m110) cc_final: 0.7918 (m110) REVERT: R 152 MET cc_start: 0.8491 (mtm) cc_final: 0.8187 (mtt) REVERT: A 287 TYR cc_start: 0.7566 (m-80) cc_final: 0.7245 (m-80) REVERT: A 311 ASN cc_start: 0.8560 (t0) cc_final: 0.8244 (t0) REVERT: A 318 GLU cc_start: 0.8105 (tt0) cc_final: 0.7651 (tt0) REVERT: B 38 ASP cc_start: 0.8170 (t0) cc_final: 0.7967 (m-30) REVERT: B 217 MET cc_start: 0.7392 (ptt) cc_final: 0.7178 (pp-130) REVERT: G 19 LEU cc_start: 0.5724 (OUTLIER) cc_final: 0.5210 (mp) REVERT: S 245 LEU cc_start: 0.8792 (tt) cc_final: 0.8565 (tp) outliers start: 12 outliers final: 7 residues processed: 114 average time/residue: 1.3096 time to fit residues: 159.3757 Evaluate side-chains 111 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 219 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 74 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 93 optimal weight: 0.0980 chunk 22 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.132543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.089278 restraints weight = 12795.917| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.35 r_work: 0.2874 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9200 Z= 0.264 Angle : 0.592 9.157 12471 Z= 0.316 Chirality : 0.044 0.141 1429 Planarity : 0.004 0.036 1552 Dihedral : 6.418 55.901 1436 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.13 % Allowed : 15.57 % Favored : 83.30 % 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: 0.86 (0.25), residues: 1120 helix: 1.92 (0.26), residues: 410 sheet: 0.62 (0.30), residues: 282 loop : -0.78 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.018 0.002 PHE B 199 TYR 0.012 0.001 TYR S 190 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 1.005 Fit side-chains REVERT: A 287 TYR cc_start: 0.7651 (m-80) cc_final: 0.7359 (m-80) REVERT: A 318 GLU cc_start: 0.8175 (tt0) cc_final: 0.7917 (tt0) REVERT: B 172 GLU cc_start: 0.7386 (mp0) cc_final: 0.7135 (mp0) REVERT: B 217 MET cc_start: 0.7339 (ptt) cc_final: 0.7044 (pp-130) REVERT: G 19 LEU cc_start: 0.5752 (OUTLIER) cc_final: 0.5207 (mp) REVERT: S 234 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8194 (mt-10) REVERT: S 245 LEU cc_start: 0.8797 (tt) cc_final: 0.8558 (tp) outliers start: 11 outliers final: 7 residues processed: 112 average time/residue: 1.3467 time to fit residues: 160.6696 Evaluate side-chains 112 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 66 optimal weight: 0.0570 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.137489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.094598 restraints weight = 12833.303| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.15 r_work: 0.2997 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9200 Z= 0.131 Angle : 0.508 9.733 12471 Z= 0.271 Chirality : 0.041 0.128 1429 Planarity : 0.003 0.034 1552 Dihedral : 5.887 58.249 1436 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.03 % Allowed : 15.77 % Favored : 83.20 % 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: 1.06 (0.25), residues: 1120 helix: 2.14 (0.26), residues: 409 sheet: 0.80 (0.31), residues: 267 loop : -0.73 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.002 0.001 HIS S 35 PHE 0.013 0.001 PHE B 199 TYR 0.012 0.001 TYR S 190 ARG 0.004 0.000 ARG G 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.983 Fit side-chains REVERT: R 44 ASN cc_start: 0.8197 (m110) cc_final: 0.7959 (m110) REVERT: A 287 TYR cc_start: 0.7562 (m-80) cc_final: 0.7235 (m-80) REVERT: A 311 ASN cc_start: 0.8552 (t0) cc_final: 0.8285 (t0) REVERT: A 318 GLU cc_start: 0.8059 (tt0) cc_final: 0.7825 (tt0) REVERT: B 217 MET cc_start: 0.7353 (ptt) cc_final: 0.7129 (pp-130) REVERT: G 19 LEU cc_start: 0.5729 (OUTLIER) cc_final: 0.5216 (mp) REVERT: S 234 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7886 (mt-10) outliers start: 10 outliers final: 5 residues processed: 115 average time/residue: 1.2874 time to fit residues: 157.9252 Evaluate side-chains 110 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 295 CYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 16 optimal weight: 0.0970 chunk 74 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.136915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.094289 restraints weight = 12743.625| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.42 r_work: 0.2949 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9200 Z= 0.142 Angle : 0.515 9.826 12471 Z= 0.274 Chirality : 0.041 0.135 1429 Planarity : 0.003 0.035 1552 Dihedral : 5.868 58.420 1436 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.93 % Allowed : 15.57 % Favored : 83.51 % 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: 1.15 (0.25), residues: 1120 helix: 2.20 (0.26), residues: 409 sheet: 0.78 (0.31), residues: 268 loop : -0.61 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.013 0.001 PHE A 189 TYR 0.012 0.001 TYR S 190 ARG 0.004 0.000 ARG G 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7635.41 seconds wall clock time: 135 minutes 16.39 seconds (8116.39 seconds total)