Starting phenix.real_space_refine on Wed Feb 4 08:10:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hj5_34833/02_2026/8hj5_34833.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hj5_34833/02_2026/8hj5_34833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hj5_34833/02_2026/8hj5_34833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hj5_34833/02_2026/8hj5_34833.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hj5_34833/02_2026/8hj5_34833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hj5_34833/02_2026/8hj5_34833.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.049 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 66 5.16 5 C 6157 2.51 5 N 1658 2.21 5 O 1797 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9678 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1913 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2591 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "D" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 394 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "C" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "F" Number of atoms: 2001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2001 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 7, 'TRANS': 244} Chain breaks: 1 Chain: "E" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'U2U': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.28, per 1000 atoms: 0.24 Number of scatterers: 9678 At special positions: 0 Unit cell: (87.55, 133.45, 125.8, 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 66 16.00 O 1797 8.00 N 1658 7.00 C 6157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 230 " distance=2.04 Simple disulfide: pdb=" SG CYS F 161 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " 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=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 420.3 milliseconds 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2294 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 15 sheets defined 32.3% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 9 through 34 removed outlier: 3.864A pdb=" N THR A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.550A pdb=" N ILE A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 246 Processing helix chain 'A' and resid 261 through 271 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.956A pdb=" N ALA A 284 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG A 285 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 286 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 320 removed outlier: 3.705A pdb=" N THR A 303 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 304 " --> pdb=" O PRO A 300 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 359 removed outlier: 4.115A pdb=" N ARG A 342 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 46 removed outlier: 3.539A pdb=" N CYS B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.805A pdb=" N GLY B 152 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASN B 153 " --> pdb=" O ARG B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 153' Processing helix chain 'D' and resid 13 through 24 removed outlier: 4.079A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.759A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.651A pdb=" N PHE C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 52 Processing helix chain 'F' and resid 59 through 88 removed outlier: 3.666A pdb=" N PHE F 87 " --> pdb=" O SER F 83 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 126 Proline residue: F 100 - end of helix removed outlier: 3.937A pdb=" N PHE F 107 " --> pdb=" O MET F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 132 removed outlier: 3.549A pdb=" N TYR F 130 " --> pdb=" O TRP F 126 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG F 131 " --> pdb=" O PRO F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 160 Processing helix chain 'F' and resid 171 through 205 removed outlier: 4.050A pdb=" N THR F 175 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 240 Proline residue: F 231 - end of helix Processing helix chain 'F' and resid 251 through 277 removed outlier: 3.765A pdb=" N LEU F 255 " --> pdb=" O CYS F 251 " (cutoff:3.500A) Proline residue: F 269 - end of helix removed outlier: 3.890A pdb=" N TYR F 272 " --> pdb=" O ASN F 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.845A pdb=" N ASN E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 192 removed outlier: 5.081A pdb=" N VAL A 202 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 221 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 222 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE A 258 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE A 224 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN A 260 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL A 226 " --> pdb=" O ASN A 260 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 70 through 72 removed outlier: 3.642A pdb=" N VAL B 348 " --> pdb=" O TRP B 360 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS B 338 " --> pdb=" O GLY B 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 79 through 84 removed outlier: 6.857A pdb=" N ALA B 94 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET B 82 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL B 92 " --> pdb=" O MET B 82 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N TRP B 84 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU B 90 " --> pdb=" O TRP B 84 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 91 " --> pdb=" O TRP B 103 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP B 104 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LYS B 110 " --> pdb=" O ASP B 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 121 through 126 removed outlier: 3.950A pdb=" N GLY B 137 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ILE B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS B 142 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU B 159 " --> pdb=" O CYS B 142 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 144 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B 155 " --> pdb=" O ASN B 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 167 through 174 removed outlier: 6.462A pdb=" N GLN B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 208 through 213 removed outlier: 6.959A pdb=" N GLY B 223 " --> pdb=" O MET B 209 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU B 211 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 221 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE B 220 " --> pdb=" O TRP B 232 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 250 through 255 removed outlier: 6.441A pdb=" N CYS B 271 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR B 284 " --> pdb=" O CYS B 271 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 273 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 294 through 299 removed outlier: 4.345A pdb=" N SER B 296 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.662A pdb=" N VAL C 5 " --> pdb=" O SER C 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.892A pdb=" N GLY C 10 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 147 through 149 removed outlier: 3.583A pdb=" N GLU C 247 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR C 228 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 175 " --> pdb=" O TYR C 191 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR C 191 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP C 177 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 156 through 161 Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.567A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.549A pdb=" N VAL E 12 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER E 59 " --> pdb=" O ASP E 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 17 through 20 438 hydrogen bonds defined for protein. 1230 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.44 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3122 1.34 - 1.46: 2473 1.46 - 1.58: 4200 1.58 - 1.70: 1 1.70 - 1.82: 91 Bond restraints: 9887 Sorted by residual: bond pdb=" C22 U2U F 501 " pdb=" N3 U2U F 501 " ideal model delta sigma weight residual 1.370 1.445 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" N1 U2U F 501 " pdb=" S1 U2U F 501 " ideal model delta sigma weight residual 1.643 1.700 -0.057 2.00e-02 2.50e+03 8.09e+00 bond pdb=" C18 U2U F 501 " pdb=" C20 U2U F 501 " ideal model delta sigma weight residual 1.419 1.365 0.054 2.00e-02 2.50e+03 7.23e+00 bond pdb=" C17 U2U F 501 " pdb=" C22 U2U F 501 " ideal model delta sigma weight residual 1.439 1.386 0.053 2.00e-02 2.50e+03 7.12e+00 bond pdb=" C17 U2U F 501 " pdb=" C18 U2U F 501 " ideal model delta sigma weight residual 1.421 1.374 0.047 2.00e-02 2.50e+03 5.45e+00 ... (remaining 9882 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 13318 3.25 - 6.51: 75 6.51 - 9.76: 8 9.76 - 13.01: 0 13.01 - 16.27: 1 Bond angle restraints: 13402 Sorted by residual: angle pdb=" O2 U2U F 501 " pdb=" S1 U2U F 501 " pdb=" O3 U2U F 501 " ideal model delta sigma weight residual 119.29 103.02 16.27 3.00e+00 1.11e-01 2.94e+01 angle pdb=" C ARG F 55 " pdb=" N MET F 56 " pdb=" CA MET F 56 " ideal model delta sigma weight residual 121.54 129.98 -8.44 1.91e+00 2.74e-01 1.95e+01 angle pdb=" CA GLU D 58 " pdb=" CB GLU D 58 " pdb=" CG GLU D 58 " ideal model delta sigma weight residual 114.10 122.30 -8.20 2.00e+00 2.50e-01 1.68e+01 angle pdb=" CA CYS E 107 " pdb=" CB CYS E 107 " pdb=" SG CYS E 107 " ideal model delta sigma weight residual 114.40 123.13 -8.73 2.30e+00 1.89e-01 1.44e+01 angle pdb=" N ARG F 55 " pdb=" CA ARG F 55 " pdb=" C ARG F 55 " ideal model delta sigma weight residual 108.24 112.81 -4.57 1.32e+00 5.74e-01 1.20e+01 ... (remaining 13397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.88: 5037 15.88 - 31.77: 606 31.77 - 47.65: 165 47.65 - 63.54: 29 63.54 - 79.42: 9 Dihedral angle restraints: 5846 sinusoidal: 2285 harmonic: 3561 Sorted by residual: dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 107 " pdb=" CB CYS E 107 " ideal model delta sinusoidal sigma weight residual -86.00 -140.04 54.04 1 1.00e+01 1.00e-02 3.96e+01 dihedral pdb=" CA CYS E 107 " pdb=" C CYS E 107 " pdb=" N PHE E 108 " pdb=" CA PHE E 108 " ideal model delta harmonic sigma weight residual -180.00 -156.93 -23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLU A 208 " pdb=" C GLU A 208 " pdb=" N ARG A 209 " pdb=" CA ARG A 209 " ideal model delta harmonic sigma weight residual 180.00 159.18 20.82 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 5843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 822 0.028 - 0.056: 435 0.056 - 0.084: 143 0.084 - 0.112: 80 0.112 - 0.140: 32 Chirality restraints: 1512 Sorted by residual: chirality pdb=" CA ILE C 190 " pdb=" N ILE C 190 " pdb=" C ILE C 190 " pdb=" CB ILE C 190 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA LEU F 51 " pdb=" N LEU F 51 " pdb=" C LEU F 51 " pdb=" CB LEU F 51 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ASP B 333 " pdb=" N ASP B 333 " pdb=" C ASP B 333 " pdb=" CB ASP B 333 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 1509 not shown) Planarity restraints: 1691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 152 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C LEU F 152 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU F 152 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG F 153 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 271 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.48e+00 pdb=" C ILE F 271 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE F 271 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR F 272 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE F 209 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO F 210 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO F 210 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 210 " 0.025 5.00e-02 4.00e+02 ... (remaining 1688 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1980 2.78 - 3.31: 8664 3.31 - 3.84: 15282 3.84 - 4.37: 17885 4.37 - 4.90: 32660 Nonbonded interactions: 76471 Sorted by model distance: nonbonded pdb=" OH TYR F 99 " pdb=" OE2 GLU F 157 " model vdw 2.244 3.040 nonbonded pdb=" OD1 ASP C 224 " pdb=" OH TYR C 228 " model vdw 2.262 3.040 nonbonded pdb=" OE2 GLU A 298 " pdb=" OG1 THR A 303 " model vdw 2.265 3.040 nonbonded pdb=" O SER E 85 " pdb=" OG SER E 85 " model vdw 2.270 3.040 nonbonded pdb=" OD1 ASP B 184 " pdb=" OG1 THR B 186 " model vdw 2.277 3.040 ... (remaining 76466 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.410 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9891 Z= 0.176 Angle : 0.692 16.268 13410 Z= 0.370 Chirality : 0.043 0.140 1512 Planarity : 0.004 0.044 1691 Dihedral : 14.847 79.419 3540 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.19 % Allowed : 18.68 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.24), residues: 1214 helix: 1.26 (0.27), residues: 370 sheet: -1.21 (0.27), residues: 347 loop : -1.65 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 240 TYR 0.014 0.001 TYR A 31 PHE 0.015 0.001 PHE F 104 TRP 0.012 0.001 TRP B 103 HIS 0.005 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9887) covalent geometry : angle 0.68899 (13402) SS BOND : bond 0.00393 ( 4) SS BOND : angle 2.86278 ( 8) hydrogen bonds : bond 0.12866 ( 438) hydrogen bonds : angle 5.90942 ( 1230) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 0.254 Fit side-chains REVERT: B 283 MET cc_start: 0.7954 (ttm) cc_final: 0.7654 (ttm) REVERT: D 21 MET cc_start: 0.7123 (ttp) cc_final: 0.6835 (ttp) REVERT: D 46 LYS cc_start: 0.7833 (tttm) cc_final: 0.7619 (pptt) REVERT: D 59 ASN cc_start: 0.7599 (OUTLIER) cc_final: 0.7200 (t0) outliers start: 2 outliers final: 1 residues processed: 119 average time/residue: 0.5866 time to fit residues: 74.4907 Evaluate side-chains 114 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain D residue 59 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.0670 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 131 ASN D 59 ASN F 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.172627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.120245 restraints weight = 10046.818| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.38 r_work: 0.3321 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9891 Z= 0.113 Angle : 0.562 8.545 13410 Z= 0.292 Chirality : 0.041 0.139 1512 Planarity : 0.003 0.040 1691 Dihedral : 5.311 56.458 1359 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.30 % Allowed : 15.85 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.24), residues: 1214 helix: 1.90 (0.27), residues: 363 sheet: -0.97 (0.28), residues: 345 loop : -1.50 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 240 TYR 0.014 0.001 TYR F 106 PHE 0.016 0.001 PHE F 104 TRP 0.012 0.001 TRP B 103 HIS 0.004 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9887) covalent geometry : angle 0.55952 (13402) SS BOND : bond 0.00359 ( 4) SS BOND : angle 2.28522 ( 8) hydrogen bonds : bond 0.04457 ( 438) hydrogen bonds : angle 4.50851 ( 1230) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 151 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: D 46 LYS cc_start: 0.7950 (tttm) cc_final: 0.7418 (pptt) outliers start: 35 outliers final: 16 residues processed: 151 average time/residue: 0.5283 time to fit residues: 86.0354 Evaluate side-chains 135 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 87 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 110 optimal weight: 0.0980 chunk 40 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.0364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 ASN C 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.169953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.117131 restraints weight = 10109.492| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.39 r_work: 0.3289 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9891 Z= 0.133 Angle : 0.572 7.857 13410 Z= 0.296 Chirality : 0.042 0.144 1512 Planarity : 0.004 0.038 1691 Dihedral : 4.850 55.089 1357 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.02 % Allowed : 18.68 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.24), residues: 1214 helix: 2.02 (0.27), residues: 363 sheet: -0.87 (0.28), residues: 348 loop : -1.47 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 155 TYR 0.015 0.001 TYR C 191 PHE 0.017 0.001 PHE F 104 TRP 0.011 0.001 TRP B 103 HIS 0.005 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9887) covalent geometry : angle 0.56944 (13402) SS BOND : bond 0.00389 ( 4) SS BOND : angle 2.18652 ( 8) hydrogen bonds : bond 0.04776 ( 438) hydrogen bonds : angle 4.42469 ( 1230) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7968 (pt0) REVERT: B 151 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8127 (mp0) REVERT: D 46 LYS cc_start: 0.7919 (tttm) cc_final: 0.7308 (pptt) REVERT: F 159 MET cc_start: 0.5691 (tmm) cc_final: 0.5479 (tmm) outliers start: 32 outliers final: 18 residues processed: 133 average time/residue: 0.5468 time to fit residues: 78.0949 Evaluate side-chains 133 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 65 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 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 = 0.4010 r_free = 0.4010 target = 0.170505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.118169 restraints weight = 10075.081| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.33 r_work: 0.3271 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9891 Z= 0.145 Angle : 0.579 10.352 13410 Z= 0.301 Chirality : 0.042 0.143 1512 Planarity : 0.004 0.038 1691 Dihedral : 4.844 53.732 1357 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.96 % Allowed : 18.21 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.24), residues: 1214 helix: 1.92 (0.27), residues: 370 sheet: -0.74 (0.28), residues: 341 loop : -1.44 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 155 TYR 0.016 0.001 TYR C 191 PHE 0.019 0.001 PHE F 104 TRP 0.010 0.001 TRP A 212 HIS 0.005 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9887) covalent geometry : angle 0.57740 (13402) SS BOND : bond 0.00418 ( 4) SS BOND : angle 2.08278 ( 8) hydrogen bonds : bond 0.04927 ( 438) hydrogen bonds : angle 4.43539 ( 1230) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 114 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 ARG cc_start: 0.7483 (ptt90) cc_final: 0.7200 (ptt-90) REVERT: A 338 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7907 (pt0) REVERT: D 46 LYS cc_start: 0.7875 (tttm) cc_final: 0.7263 (pptt) REVERT: C 11 LEU cc_start: 0.8170 (mp) cc_final: 0.7960 (mt) REVERT: C 235 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8553 (pt0) REVERT: F 159 MET cc_start: 0.5630 (tmm) cc_final: 0.5421 (tmm) outliers start: 42 outliers final: 21 residues processed: 139 average time/residue: 0.5554 time to fit residues: 83.0427 Evaluate side-chains 132 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 28 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 120 optimal weight: 0.0470 chunk 95 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.175819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.121135 restraints weight = 9969.789| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.52 r_work: 0.3324 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9891 Z= 0.105 Angle : 0.545 7.977 13410 Z= 0.279 Chirality : 0.041 0.145 1512 Planarity : 0.003 0.039 1691 Dihedral : 4.616 52.418 1357 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.11 % Allowed : 19.43 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.25), residues: 1214 helix: 2.11 (0.27), residues: 370 sheet: -0.76 (0.28), residues: 332 loop : -1.35 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 155 TYR 0.012 0.001 TYR F 106 PHE 0.017 0.001 PHE F 104 TRP 0.012 0.001 TRP B 103 HIS 0.003 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 9887) covalent geometry : angle 0.54377 (13402) SS BOND : bond 0.00342 ( 4) SS BOND : angle 1.65454 ( 8) hydrogen bonds : bond 0.04195 ( 438) hydrogen bonds : angle 4.27803 ( 1230) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6577 (mt0) cc_final: 0.5781 (mp10) REVERT: A 285 ARG cc_start: 0.7451 (ptt90) cc_final: 0.7151 (ptt180) REVERT: A 338 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7951 (pt0) REVERT: D 46 LYS cc_start: 0.7910 (tttm) cc_final: 0.7279 (pptt) REVERT: C 11 LEU cc_start: 0.8174 (mp) cc_final: 0.7972 (mt) REVERT: C 62 ASP cc_start: 0.8686 (m-30) cc_final: 0.8156 (m-30) REVERT: F 159 MET cc_start: 0.5266 (tmm) cc_final: 0.5036 (tmm) outliers start: 33 outliers final: 19 residues processed: 142 average time/residue: 0.5021 time to fit residues: 77.2658 Evaluate side-chains 133 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 95 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 106 optimal weight: 0.0870 chunk 20 optimal weight: 0.0870 chunk 44 optimal weight: 0.3980 chunk 74 optimal weight: 0.7980 overall best weight: 0.3936 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.177617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.124010 restraints weight = 10038.480| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.42 r_work: 0.3374 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9891 Z= 0.095 Angle : 0.534 11.170 13410 Z= 0.270 Chirality : 0.041 0.140 1512 Planarity : 0.003 0.040 1691 Dihedral : 4.431 51.398 1357 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.02 % Allowed : 19.72 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.25), residues: 1214 helix: 2.28 (0.28), residues: 370 sheet: -0.67 (0.29), residues: 330 loop : -1.22 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 155 TYR 0.011 0.001 TYR A 31 PHE 0.015 0.001 PHE F 104 TRP 0.012 0.001 TRP B 103 HIS 0.003 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 9887) covalent geometry : angle 0.53342 (13402) SS BOND : bond 0.00293 ( 4) SS BOND : angle 1.38492 ( 8) hydrogen bonds : bond 0.03793 ( 438) hydrogen bonds : angle 4.13950 ( 1230) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6462 (mt0) cc_final: 0.5692 (mp10) REVERT: A 338 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7950 (pt0) REVERT: B 65 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: B 238 MET cc_start: 0.6505 (ttt) cc_final: 0.5937 (tpt) REVERT: D 46 LYS cc_start: 0.7879 (tttm) cc_final: 0.7261 (pptt) REVERT: C 11 LEU cc_start: 0.8201 (mp) cc_final: 0.7992 (mt) REVERT: C 62 ASP cc_start: 0.8582 (m-30) cc_final: 0.8077 (m-30) REVERT: C 235 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8600 (pt0) outliers start: 32 outliers final: 16 residues processed: 133 average time/residue: 0.4188 time to fit residues: 60.6191 Evaluate side-chains 128 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain E residue 25 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 116 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 50 optimal weight: 0.4980 chunk 98 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 ASN F 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.176137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.121806 restraints weight = 10000.582| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.52 r_work: 0.3331 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9891 Z= 0.110 Angle : 0.561 11.847 13410 Z= 0.284 Chirality : 0.041 0.140 1512 Planarity : 0.003 0.040 1691 Dihedral : 4.264 41.665 1355 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.21 % Allowed : 20.47 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.25), residues: 1214 helix: 2.25 (0.27), residues: 370 sheet: -0.70 (0.28), residues: 336 loop : -1.12 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 155 TYR 0.014 0.001 TYR C 191 PHE 0.016 0.001 PHE F 104 TRP 0.013 0.001 TRP B 103 HIS 0.004 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9887) covalent geometry : angle 0.56047 (13402) SS BOND : bond 0.00345 ( 4) SS BOND : angle 1.40238 ( 8) hydrogen bonds : bond 0.04135 ( 438) hydrogen bonds : angle 4.15649 ( 1230) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6638 (mt0) cc_final: 0.5854 (mp10) REVERT: A 338 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7937 (pt0) REVERT: B 65 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7496 (tt0) REVERT: B 193 GLU cc_start: 0.8029 (tp30) cc_final: 0.7802 (tp30) REVERT: B 238 MET cc_start: 0.6485 (ttt) cc_final: 0.5844 (tpt) REVERT: D 46 LYS cc_start: 0.7915 (tttm) cc_final: 0.7277 (pptt) REVERT: C 11 LEU cc_start: 0.8234 (mp) cc_final: 0.8021 (mt) REVERT: C 62 ASP cc_start: 0.8627 (m-30) cc_final: 0.8127 (m-30) REVERT: C 235 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8653 (pt0) REVERT: F 159 MET cc_start: 0.5346 (tmm) cc_final: 0.5131 (tmm) outliers start: 34 outliers final: 20 residues processed: 129 average time/residue: 0.4683 time to fit residues: 65.6349 Evaluate side-chains 132 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 29 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.172787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.118132 restraints weight = 9989.121| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.52 r_work: 0.3283 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9891 Z= 0.143 Angle : 0.594 12.167 13410 Z= 0.304 Chirality : 0.042 0.142 1512 Planarity : 0.003 0.040 1691 Dihedral : 4.475 43.166 1355 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.02 % Allowed : 20.38 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.25), residues: 1214 helix: 2.16 (0.27), residues: 370 sheet: -0.65 (0.28), residues: 333 loop : -1.17 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 155 TYR 0.018 0.001 TYR C 191 PHE 0.018 0.001 PHE F 104 TRP 0.012 0.001 TRP B 103 HIS 0.005 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9887) covalent geometry : angle 0.59282 (13402) SS BOND : bond 0.00436 ( 4) SS BOND : angle 1.60133 ( 8) hydrogen bonds : bond 0.04802 ( 438) hydrogen bonds : angle 4.32937 ( 1230) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 285 ARG cc_start: 0.7442 (ptt90) cc_final: 0.7177 (ptt180) REVERT: B 238 MET cc_start: 0.6729 (ttt) cc_final: 0.6237 (mmm) REVERT: D 46 LYS cc_start: 0.7913 (tttm) cc_final: 0.7280 (pptt) REVERT: C 11 LEU cc_start: 0.8303 (mp) cc_final: 0.8071 (mt) REVERT: C 62 ASP cc_start: 0.8703 (m-30) cc_final: 0.8161 (m-30) REVERT: C 235 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8633 (pt0) outliers start: 32 outliers final: 17 residues processed: 127 average time/residue: 0.5371 time to fit residues: 73.5779 Evaluate side-chains 123 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 65 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 102 optimal weight: 0.0870 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN B 361 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.169390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114872 restraints weight = 10031.591| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.52 r_work: 0.3242 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9891 Z= 0.196 Angle : 0.658 12.767 13410 Z= 0.337 Chirality : 0.044 0.144 1512 Planarity : 0.004 0.040 1691 Dihedral : 4.773 44.373 1355 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.36 % Allowed : 21.13 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.24), residues: 1214 helix: 1.89 (0.27), residues: 370 sheet: -0.75 (0.28), residues: 346 loop : -1.20 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 155 TYR 0.022 0.002 TYR C 191 PHE 0.019 0.002 PHE F 104 TRP 0.013 0.002 TRP F 147 HIS 0.007 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 9887) covalent geometry : angle 0.65662 (13402) SS BOND : bond 0.00553 ( 4) SS BOND : angle 1.90871 ( 8) hydrogen bonds : bond 0.05549 ( 438) hydrogen bonds : angle 4.55741 ( 1230) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.430 Fit side-chains REVERT: A 285 ARG cc_start: 0.7309 (ptt90) cc_final: 0.7073 (ptt-90) REVERT: A 299 ASP cc_start: 0.7571 (t70) cc_final: 0.7234 (t0) REVERT: B 235 ARG cc_start: 0.7348 (mpt-90) cc_final: 0.7074 (mmt90) REVERT: B 238 MET cc_start: 0.7394 (ttt) cc_final: 0.7057 (ttm) REVERT: D 46 LYS cc_start: 0.7929 (tttm) cc_final: 0.7297 (pptt) REVERT: C 235 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8562 (pt0) outliers start: 25 outliers final: 18 residues processed: 126 average time/residue: 0.5514 time to fit residues: 74.4684 Evaluate side-chains 126 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 43 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 117 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.174611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120498 restraints weight = 9906.656| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.50 r_work: 0.3312 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9891 Z= 0.112 Angle : 0.579 12.992 13410 Z= 0.294 Chirality : 0.041 0.145 1512 Planarity : 0.003 0.039 1691 Dihedral : 4.407 44.354 1355 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.98 % Allowed : 21.13 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.25), residues: 1214 helix: 2.14 (0.27), residues: 370 sheet: -0.67 (0.28), residues: 336 loop : -1.13 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 155 TYR 0.013 0.001 TYR F 106 PHE 0.017 0.001 PHE F 104 TRP 0.011 0.001 TRP B 103 HIS 0.004 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9887) covalent geometry : angle 0.57791 (13402) SS BOND : bond 0.00363 ( 4) SS BOND : angle 1.39565 ( 8) hydrogen bonds : bond 0.04259 ( 438) hydrogen bonds : angle 4.29222 ( 1230) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.317 Fit side-chains REVERT: A 29 GLN cc_start: 0.6618 (mt0) cc_final: 0.5794 (mp10) REVERT: A 285 ARG cc_start: 0.7394 (ptt90) cc_final: 0.7119 (ptt180) REVERT: A 299 ASP cc_start: 0.7613 (t70) cc_final: 0.7285 (t0) REVERT: B 193 GLU cc_start: 0.7990 (tp30) cc_final: 0.7768 (tp30) REVERT: B 238 MET cc_start: 0.6716 (ttt) cc_final: 0.5907 (tpp) REVERT: D 46 LYS cc_start: 0.7900 (tttm) cc_final: 0.7245 (pptt) REVERT: C 62 ASP cc_start: 0.8706 (m-30) cc_final: 0.8139 (m-30) REVERT: C 235 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8638 (pt0) outliers start: 21 outliers final: 16 residues processed: 128 average time/residue: 0.4976 time to fit residues: 69.2057 Evaluate side-chains 128 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 119 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 8 optimal weight: 0.0980 chunk 17 optimal weight: 0.0870 chunk 61 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 ASN B 361 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.171971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116078 restraints weight = 10016.749| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.62 r_work: 0.3229 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9891 Z= 0.115 Angle : 0.581 12.914 13410 Z= 0.296 Chirality : 0.042 0.142 1512 Planarity : 0.003 0.039 1691 Dihedral : 4.358 44.140 1355 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.79 % Allowed : 21.89 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.25), residues: 1214 helix: 2.18 (0.27), residues: 370 sheet: -0.69 (0.28), residues: 337 loop : -1.06 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 155 TYR 0.013 0.001 TYR C 191 PHE 0.017 0.001 PHE F 104 TRP 0.012 0.001 TRP B 103 HIS 0.004 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9887) covalent geometry : angle 0.58035 (13402) SS BOND : bond 0.00361 ( 4) SS BOND : angle 1.31728 ( 8) hydrogen bonds : bond 0.04267 ( 438) hydrogen bonds : angle 4.24872 ( 1230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3563.93 seconds wall clock time: 61 minutes 30.16 seconds (3690.16 seconds total)