Starting phenix.real_space_refine on Sun Dec 29 02:51:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hj5_34833/12_2024/8hj5_34833.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hj5_34833/12_2024/8hj5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hj5_34833/12_2024/8hj5_34833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hj5_34833/12_2024/8hj5_34833.map" model { file = "/net/cci-nas-00/data/ceres_data/8hj5_34833/12_2024/8hj5_34833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hj5_34833/12_2024/8hj5_34833.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 6.20, per 1000 atoms: 0.64 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: 2.90 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.09 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: 2.91 Time building geometry restraints manager: 3.27 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: 1.110 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.040 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.290 ------------------------------------------------------------------------------- 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 9887 Z= 0.243 Angle : 0.689 16.268 13402 Z= 0.368 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 : 8.22 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 (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: -0.98 (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 TRP 0.012 0.001 TRP B 103 HIS 0.005 0.001 HIS A 325 PHE 0.015 0.001 PHE F 104 TYR 0.014 0.001 TYR A 31 ARG 0.007 0.000 ARG B 240 *********************** 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 : 1.048 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: 1.3503 time to fit residues: 172.4976 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 : 1.288 ------------------------------------------------------------------------------- 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 102 optimal weight: 0.0670 chunk 91 optimal weight: 6.9990 chunk 50 optimal weight: 0.0770 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 overall best weight: 0.9678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN D 59 ASN F 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9887 Z= 0.193 Angle : 0.580 8.558 13402 Z= 0.302 Chirality : 0.042 0.140 1512 Planarity : 0.004 0.040 1691 Dihedral : 5.393 56.315 1359 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.40 % Allowed : 16.60 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.58 (0.24), residues: 1214 helix: 1.75 (0.27), residues: 364 sheet: -0.99 (0.28), residues: 348 loop : -1.52 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 103 HIS 0.005 0.001 HIS A 325 PHE 0.017 0.001 PHE F 104 TYR 0.015 0.001 TYR C 191 ARG 0.005 0.000 ARG B 240 *********************** 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 159 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 324 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7285 (mtm180) REVERT: B 151 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: D 46 LYS cc_start: 0.7819 (tttm) cc_final: 0.7454 (pptt) REVERT: F 56 MET cc_start: 0.5356 (ppp) cc_final: 0.5153 (ppp) outliers start: 36 outliers final: 17 residues processed: 143 average time/residue: 1.1212 time to fit residues: 173.6022 Evaluate side-chains 135 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 324 ARG 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 61 optimal weight: 0.7980 chunk 34 optimal weight: 0.2980 chunk 91 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9887 Z= 0.279 Angle : 0.618 7.440 13402 Z= 0.321 Chirality : 0.044 0.149 1512 Planarity : 0.004 0.037 1691 Dihedral : 5.058 54.934 1357 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.06 % Allowed : 17.17 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.58 (0.24), residues: 1214 helix: 1.68 (0.27), residues: 370 sheet: -0.92 (0.28), residues: 348 loop : -1.54 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 147 HIS 0.006 0.001 HIS A 325 PHE 0.019 0.002 PHE F 104 TYR 0.016 0.002 TYR C 191 ARG 0.005 0.000 ARG B 155 *********************** 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 157 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 324 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7252 (mtm180) REVERT: B 151 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8139 (mp0) REVERT: D 46 LYS cc_start: 0.7841 (tttm) cc_final: 0.7427 (pptt) REVERT: C 235 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8405 (pt0) REVERT: F 56 MET cc_start: 0.5432 (ppp) cc_final: 0.5103 (ppp) REVERT: F 159 MET cc_start: 0.5564 (tmm) cc_final: 0.5356 (tmm) outliers start: 43 outliers final: 22 residues processed: 138 average time/residue: 1.2208 time to fit residues: 181.2320 Evaluate side-chains 134 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 324 ARG 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 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 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 181 VAL 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 13 GLN 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 108 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9887 Z= 0.201 Angle : 0.571 10.749 13402 Z= 0.296 Chirality : 0.042 0.143 1512 Planarity : 0.003 0.035 1691 Dihedral : 4.859 53.530 1357 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.49 % Allowed : 18.58 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.42 (0.24), residues: 1214 helix: 1.84 (0.27), residues: 370 sheet: -0.79 (0.28), residues: 341 loop : -1.51 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 103 HIS 0.005 0.001 HIS A 325 PHE 0.020 0.001 PHE F 104 TYR 0.014 0.001 TYR C 191 ARG 0.006 0.000 ARG B 155 *********************** 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 153 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: A 285 ARG cc_start: 0.7428 (ptt90) cc_final: 0.7184 (ptt-90) REVERT: A 338 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7803 (pt0) REVERT: D 46 LYS cc_start: 0.7774 (tttm) cc_final: 0.7312 (pptt) REVERT: F 56 MET cc_start: 0.5437 (OUTLIER) cc_final: 0.5164 (ppp) REVERT: F 159 MET cc_start: 0.5485 (tmm) cc_final: 0.5255 (tmm) outliers start: 37 outliers final: 20 residues processed: 136 average time/residue: 1.1396 time to fit residues: 167.5912 Evaluate side-chains 132 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 255 PHE Chi-restraints excluded: chain B residue 288 ASP 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 F residue 56 MET 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 71 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9887 Z= 0.185 Angle : 0.574 11.720 13402 Z= 0.293 Chirality : 0.042 0.142 1512 Planarity : 0.003 0.035 1691 Dihedral : 4.760 52.646 1357 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.49 % Allowed : 18.87 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.31 (0.24), residues: 1214 helix: 1.93 (0.27), residues: 370 sheet: -0.82 (0.28), residues: 347 loop : -1.37 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 103 HIS 0.004 0.001 HIS A 325 PHE 0.019 0.001 PHE F 104 TYR 0.014 0.001 TYR C 191 ARG 0.006 0.000 ARG B 155 *********************** 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 150 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: A 285 ARG cc_start: 0.7434 (ptt90) cc_final: 0.7185 (ptt-90) REVERT: B 240 ARG cc_start: 0.7778 (ttm-80) cc_final: 0.7575 (ttm-80) REVERT: D 46 LYS cc_start: 0.7800 (tttm) cc_final: 0.7309 (pptt) REVERT: C 235 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8423 (pt0) REVERT: F 56 MET cc_start: 0.5400 (OUTLIER) cc_final: 0.5159 (ppp) REVERT: F 159 MET cc_start: 0.5389 (tmm) cc_final: 0.5162 (tmm) outliers start: 37 outliers final: 20 residues processed: 133 average time/residue: 1.2010 time to fit residues: 172.6683 Evaluate side-chains 133 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER 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 255 PHE Chi-restraints excluded: chain B residue 288 ASP 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 235 GLU Chi-restraints excluded: chain F residue 56 MET 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 71 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9887 Z= 0.225 Angle : 0.600 11.819 13402 Z= 0.306 Chirality : 0.042 0.144 1512 Planarity : 0.003 0.033 1691 Dihedral : 4.845 52.483 1357 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.49 % Allowed : 19.43 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1214 helix: 1.85 (0.27), residues: 369 sheet: -0.78 (0.28), residues: 340 loop : -1.38 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 212 HIS 0.005 0.001 HIS A 325 PHE 0.020 0.001 PHE F 104 TYR 0.016 0.001 TYR C 191 ARG 0.006 0.000 ARG B 155 *********************** 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 146 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: A 285 ARG cc_start: 0.7404 (ptt90) cc_final: 0.7191 (ptt-90) REVERT: B 238 MET cc_start: 0.6913 (ttp) cc_final: 0.6694 (ttm) REVERT: D 46 LYS cc_start: 0.7847 (tttm) cc_final: 0.7333 (pptt) REVERT: C 235 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8421 (pt0) REVERT: F 56 MET cc_start: 0.5356 (OUTLIER) cc_final: 0.5156 (ppp) outliers start: 37 outliers final: 22 residues processed: 131 average time/residue: 1.2048 time to fit residues: 170.1645 Evaluate side-chains 129 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER 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 255 PHE Chi-restraints excluded: chain B residue 288 ASP 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 56 MET 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 4 LEU Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9887 Z= 0.179 Angle : 0.573 11.883 13402 Z= 0.292 Chirality : 0.041 0.143 1512 Planarity : 0.003 0.033 1691 Dihedral : 4.709 51.816 1357 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.92 % Allowed : 20.09 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.22 (0.24), residues: 1214 helix: 2.01 (0.27), residues: 370 sheet: -0.79 (0.28), residues: 347 loop : -1.30 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 103 HIS 0.004 0.001 HIS A 325 PHE 0.019 0.001 PHE F 104 TYR 0.014 0.001 TYR F 106 ARG 0.007 0.000 ARG B 155 *********************** 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: 31 poor density : 113 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 285 ARG cc_start: 0.7338 (ptt90) cc_final: 0.7106 (ptt-90) REVERT: B 238 MET cc_start: 0.6701 (ttp) cc_final: 0.6332 (ttm) REVERT: D 46 LYS cc_start: 0.7805 (tttm) cc_final: 0.7311 (pptt) REVERT: F 56 MET cc_start: 0.5386 (OUTLIER) cc_final: 0.5133 (ppp) REVERT: F 159 MET cc_start: 0.5338 (tmm) cc_final: 0.5101 (tmm) outliers start: 31 outliers final: 24 residues processed: 132 average time/residue: 1.1557 time to fit residues: 165.2135 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 : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 302 VAL 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 346 MET Chi-restraints excluded: chain C residue 71 SER 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 F residue 56 MET 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 71 SER Chi-restraints excluded: chain E residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 101 optimal weight: 0.3980 chunk 108 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9887 Z= 0.202 Angle : 0.578 12.495 13402 Z= 0.297 Chirality : 0.042 0.143 1512 Planarity : 0.003 0.033 1691 Dihedral : 4.727 51.653 1357 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.92 % Allowed : 20.66 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.23 (0.24), residues: 1214 helix: 1.99 (0.27), residues: 370 sheet: -0.78 (0.28), residues: 343 loop : -1.31 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 212 HIS 0.005 0.001 HIS A 325 PHE 0.019 0.001 PHE F 104 TYR 0.015 0.001 TYR C 191 ARG 0.007 0.000 ARG B 155 *********************** 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 138 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: B 238 MET cc_start: 0.6748 (ttp) cc_final: 0.6456 (ttm) REVERT: B 268 ASP cc_start: 0.7191 (t0) cc_final: 0.6894 (t0) REVERT: D 46 LYS cc_start: 0.7823 (tttm) cc_final: 0.7321 (pptt) REVERT: C 235 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8448 (pt0) REVERT: F 56 MET cc_start: 0.5280 (OUTLIER) cc_final: 0.5075 (ppp) REVERT: F 159 MET cc_start: 0.5386 (tmm) cc_final: 0.5185 (tmm) outliers start: 31 outliers final: 24 residues processed: 126 average time/residue: 1.1791 time to fit residues: 160.9693 Evaluate side-chains 131 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 302 VAL 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 71 SER 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 56 MET 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 4 LEU 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 111 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 114 optimal weight: 0.0060 chunk 70 optimal weight: 2.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9887 Z= 0.328 Angle : 0.655 12.766 13402 Z= 0.337 Chirality : 0.044 0.146 1512 Planarity : 0.004 0.032 1691 Dihedral : 5.057 52.274 1357 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.30 % Allowed : 20.66 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.42 (0.24), residues: 1214 helix: 1.72 (0.27), residues: 370 sheet: -0.80 (0.28), residues: 341 loop : -1.40 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 147 HIS 0.007 0.001 HIS A 325 PHE 0.020 0.002 PHE F 104 TYR 0.021 0.002 TYR C 191 ARG 0.007 0.000 ARG B 155 *********************** 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 142 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 1.088 Fit side-chains REVERT: B 238 MET cc_start: 0.7190 (ttp) cc_final: 0.6972 (ttm) REVERT: D 46 LYS cc_start: 0.7892 (tttm) cc_final: 0.7405 (pptt) REVERT: C 235 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8385 (pt0) REVERT: F 56 MET cc_start: 0.5363 (OUTLIER) cc_final: 0.5099 (ppp) REVERT: F 159 MET cc_start: 0.5322 (tmm) cc_final: 0.5107 (tmm) outliers start: 35 outliers final: 23 residues processed: 130 average time/residue: 1.2252 time to fit residues: 172.0273 Evaluate side-chains 128 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 302 VAL 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 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 71 SER 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 56 MET 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 230 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 110 optimal weight: 0.0070 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 76 optimal weight: 0.3980 chunk 102 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9887 Z= 0.148 Angle : 0.571 12.714 13402 Z= 0.291 Chirality : 0.041 0.145 1512 Planarity : 0.003 0.033 1691 Dihedral : 4.656 51.052 1357 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.17 % Allowed : 21.79 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1214 helix: 2.09 (0.27), residues: 370 sheet: -0.68 (0.28), residues: 337 loop : -1.31 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 212 HIS 0.003 0.001 HIS F 252 PHE 0.018 0.001 PHE F 104 TYR 0.014 0.001 TYR F 106 ARG 0.007 0.000 ARG B 155 ********************** 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 137 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 1.130 Fit side-chains REVERT: A 29 GLN cc_start: 0.6619 (mt0) cc_final: 0.5810 (mp10) REVERT: A 285 ARG cc_start: 0.7360 (ptt90) cc_final: 0.7075 (ptt180) REVERT: A 338 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7887 (pt0) REVERT: B 80 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.8224 (t80) REVERT: B 238 MET cc_start: 0.6642 (ttp) cc_final: 0.6436 (ttm) REVERT: D 46 LYS cc_start: 0.7821 (tttm) cc_final: 0.7313 (pptt) REVERT: C 235 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8409 (pt0) REVERT: F 159 MET cc_start: 0.5259 (tmm) cc_final: 0.5052 (tmm) outliers start: 23 outliers final: 15 residues processed: 125 average time/residue: 1.1577 time to fit residues: 157.1085 Evaluate side-chains 127 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 230 LEU Chi-restraints excluded: chain F residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.172834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.118584 restraints weight = 9877.037| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.48 r_work: 0.3292 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9887 Z= 0.192 Angle : 0.591 13.009 13402 Z= 0.302 Chirality : 0.042 0.145 1512 Planarity : 0.003 0.034 1691 Dihedral : 4.672 51.072 1357 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.17 % Allowed : 22.26 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.12 (0.25), residues: 1214 helix: 2.07 (0.27), residues: 370 sheet: -0.72 (0.28), residues: 343 loop : -1.22 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 103 HIS 0.004 0.001 HIS A 325 PHE 0.020 0.001 PHE F 104 TYR 0.014 0.001 TYR C 191 ARG 0.007 0.000 ARG B 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3568.88 seconds wall clock time: 64 minutes 49.19 seconds (3889.19 seconds total)