Starting phenix.real_space_refine on Sun Jun 8 14:07:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hj5_34833/06_2025/8hj5_34833.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hj5_34833/06_2025/8hj5_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_34833/06_2025/8hj5_34833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hj5_34833/06_2025/8hj5_34833.map" model { file = "/net/cci-nas-00/data/ceres_data/8hj5_34833/06_2025/8hj5_34833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hj5_34833/06_2025/8hj5_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 5.93, per 1000 atoms: 0.61 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: 2.41 Conformation dependent library (CDL) restraints added in 1.1 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: 1.00 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: 2.77 Time building geometry restraints manager: 2.85 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: 1.780 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.110 Process input model: 24.430 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.040 ------------------------------------------------------------------------------- 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 : 8.22 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 Details of bonding type rmsd hydrogen bonds : bond 0.12866 ( 438) hydrogen bonds : angle 5.90942 ( 1230) SS BOND : bond 0.00393 ( 4) SS BOND : angle 2.86278 ( 8) covalent geometry : bond 0.00368 ( 9887) covalent geometry : angle 0.68899 (13402) *********************** 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 : 0.999 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: 1.3172 time to fit residues: 167.8921 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 : 1.039 ------------------------------------------------------------------------------- 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: 0.4980 overall best weight: 0.4676 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.173476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.120766 restraints weight = 9994.858| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.38 r_work: 0.3344 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9891 Z= 0.106 Angle : 0.552 8.514 13410 Z= 0.286 Chirality : 0.041 0.136 1512 Planarity : 0.003 0.039 1691 Dihedral : 5.359 56.373 1359 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.11 % Allowed : 16.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.24), residues: 1214 helix: 1.96 (0.27), residues: 362 sheet: -0.86 (0.29), residues: 328 loop : -1.55 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 103 HIS 0.003 0.001 HIS A 325 PHE 0.015 0.001 PHE F 104 TYR 0.014 0.001 TYR F 106 ARG 0.004 0.000 ARG B 240 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 438) hydrogen bonds : angle 4.46999 ( 1230) SS BOND : bond 0.00346 ( 4) SS BOND : angle 2.18871 ( 8) covalent geometry : bond 0.00216 ( 9887) covalent geometry : angle 0.54923 (13402) *********************** 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 168 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6575 (mt0) cc_final: 0.5804 (mp10) REVERT: A 338 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7994 (pt0) REVERT: B 151 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: B 193 GLU cc_start: 0.8106 (tp30) cc_final: 0.7900 (tp30) REVERT: D 46 LYS cc_start: 0.7960 (tttm) cc_final: 0.7409 (pptt) REVERT: D 59 ASN cc_start: 0.7478 (OUTLIER) cc_final: 0.6972 (t0) outliers start: 33 outliers final: 12 residues processed: 156 average time/residue: 1.0192 time to fit residues: 172.5442 Evaluate side-chains 131 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 80 TYR 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 D residue 59 ASN 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 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 116 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 ASN D 59 ASN C 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.174154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.121930 restraints weight = 10069.117| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.38 r_work: 0.3338 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9891 Z= 0.104 Angle : 0.533 7.580 13410 Z= 0.276 Chirality : 0.041 0.141 1512 Planarity : 0.003 0.037 1691 Dihedral : 4.804 54.681 1359 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.83 % Allowed : 17.64 % Favored : 79.53 % 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: -0.25 (0.25), residues: 1214 helix: 2.18 (0.28), residues: 364 sheet: -0.87 (0.28), residues: 341 loop : -1.39 (0.27), residues: 509 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 0.015 0.001 PHE F 104 TYR 0.012 0.001 TYR C 191 ARG 0.006 0.000 ARG B 240 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 438) hydrogen bonds : angle 4.23889 ( 1230) SS BOND : bond 0.00321 ( 4) SS BOND : angle 1.90881 ( 8) covalent geometry : bond 0.00221 ( 9887) covalent geometry : angle 0.53104 (13402) *********************** 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 151 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6584 (mt0) cc_final: 0.5829 (mp10) REVERT: A 338 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8019 (pt0) REVERT: B 193 GLU cc_start: 0.8084 (tp30) cc_final: 0.7828 (tp30) REVERT: D 46 LYS cc_start: 0.7849 (tttm) cc_final: 0.7259 (pptt) REVERT: C 62 ASP cc_start: 0.8592 (m-30) cc_final: 0.8048 (m-30) REVERT: F 159 MET cc_start: 0.5532 (tmm) cc_final: 0.5326 (tmm) outliers start: 30 outliers final: 20 residues processed: 138 average time/residue: 1.0815 time to fit residues: 161.8171 Evaluate side-chains 133 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 297 VAL 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 F residue 74 LEU Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 156 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 27 optimal weight: 3.9990 chunk 114 optimal weight: 0.4980 chunk 74 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 6 optimal weight: 0.0370 chunk 76 optimal weight: 0.9980 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.175285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.123608 restraints weight = 9960.137| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.32 r_work: 0.3311 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9891 Z= 0.102 Angle : 0.534 10.871 13410 Z= 0.274 Chirality : 0.041 0.172 1512 Planarity : 0.003 0.040 1691 Dihedral : 4.548 53.257 1357 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.68 % Allowed : 17.55 % 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: -0.13 (0.25), residues: 1214 helix: 2.17 (0.27), residues: 371 sheet: -0.74 (0.28), residues: 331 loop : -1.32 (0.26), residues: 512 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 0.015 0.001 PHE F 104 TYR 0.013 0.001 TYR C 191 ARG 0.006 0.000 ARG B 240 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 438) hydrogen bonds : angle 4.18219 ( 1230) SS BOND : bond 0.00317 ( 4) SS BOND : angle 1.71400 ( 8) covalent geometry : bond 0.00217 ( 9887) covalent geometry : angle 0.53270 (13402) *********************** 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 152 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6520 (mt0) cc_final: 0.5731 (mp10) REVERT: A 285 ARG cc_start: 0.7452 (ptt90) cc_final: 0.7240 (ptt-90) REVERT: A 338 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7957 (pt0) REVERT: D 46 LYS cc_start: 0.7823 (tttm) cc_final: 0.7208 (pptt) REVERT: C 11 LEU cc_start: 0.8156 (mp) cc_final: 0.7944 (mt) REVERT: C 62 ASP cc_start: 0.8580 (m-30) cc_final: 0.8001 (m-30) REVERT: F 159 MET cc_start: 0.5419 (tmm) cc_final: 0.5184 (tmm) outliers start: 39 outliers final: 19 residues processed: 137 average time/residue: 1.0749 time to fit residues: 159.7227 Evaluate side-chains 126 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 297 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 26 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.170210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118124 restraints weight = 10049.426| |-----------------------------------------------------------------------------| 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: 4.45 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9891 Z= 0.158 Angle : 0.590 9.562 13410 Z= 0.304 Chirality : 0.043 0.146 1512 Planarity : 0.004 0.040 1691 Dihedral : 4.768 52.812 1357 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.58 % Allowed : 18.58 % 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 (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: -0.75 (0.28), residues: 337 loop : -1.34 (0.26), residues: 507 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 0.018 0.001 PHE F 104 TYR 0.018 0.001 TYR C 191 ARG 0.005 0.000 ARG B 155 Details of bonding type rmsd hydrogen bonds : bond 0.05014 ( 438) hydrogen bonds : angle 4.39638 ( 1230) SS BOND : bond 0.00466 ( 4) SS BOND : angle 1.96788 ( 8) covalent geometry : bond 0.00374 ( 9887) covalent geometry : angle 0.58774 (13402) *********************** 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 152 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 285 ARG cc_start: 0.7482 (ptt90) cc_final: 0.7242 (ptt-90) REVERT: B 235 ARG cc_start: 0.7395 (mpt-90) cc_final: 0.7112 (mmt90) REVERT: D 46 LYS cc_start: 0.7877 (tttm) cc_final: 0.7309 (pptt) REVERT: C 11 LEU cc_start: 0.8203 (mp) cc_final: 0.7991 (mt) REVERT: C 161 ARG cc_start: 0.7230 (ttm110) cc_final: 0.6503 (mtp85) REVERT: C 235 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8570 (pt0) outliers start: 38 outliers final: 20 residues processed: 133 average time/residue: 1.2011 time to fit residues: 171.7804 Evaluate side-chains 133 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 297 VAL 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 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 F residue 261 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 47 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 0.0980 chunk 19 optimal weight: 7.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- 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** B 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.167425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.111866 restraints weight = 10112.804| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.57 r_work: 0.3231 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9891 Z= 0.196 Angle : 0.634 10.489 13410 Z= 0.328 Chirality : 0.044 0.150 1512 Planarity : 0.004 0.041 1691 Dihedral : 4.997 52.233 1357 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.06 % Allowed : 19.06 % 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 (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: -0.35 (0.24), residues: 1214 helix: 1.80 (0.27), residues: 370 sheet: -0.73 (0.29), residues: 338 loop : -1.40 (0.26), residues: 506 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 0.021 0.002 PHE F 104 TYR 0.020 0.002 TYR C 191 ARG 0.006 0.000 ARG B 155 Details of bonding type rmsd hydrogen bonds : bond 0.05599 ( 438) hydrogen bonds : angle 4.59292 ( 1230) SS BOND : bond 0.00542 ( 4) SS BOND : angle 2.13760 ( 8) covalent geometry : bond 0.00473 ( 9887) covalent geometry : angle 0.63233 (13402) *********************** 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 156 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 113 time to evaluate : 0.999 Fit side-chains REVERT: A 285 ARG cc_start: 0.7450 (ptt90) cc_final: 0.7241 (ptt-90) REVERT: D 46 LYS cc_start: 0.7987 (tttm) cc_final: 0.7369 (pptt) REVERT: C 235 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8559 (pt0) outliers start: 43 outliers final: 21 residues processed: 139 average time/residue: 1.1160 time to fit residues: 167.9083 Evaluate side-chains 127 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER 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 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 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 181 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 116 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 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 = 0.4098 r_free = 0.4098 target = 0.173166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.118750 restraints weight = 10020.040| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.52 r_work: 0.3292 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9891 Z= 0.123 Angle : 0.578 11.677 13410 Z= 0.294 Chirality : 0.042 0.143 1512 Planarity : 0.003 0.039 1691 Dihedral : 4.712 51.235 1357 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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: -0.21 (0.24), residues: 1214 helix: 2.00 (0.27), residues: 370 sheet: -0.76 (0.28), residues: 337 loop : -1.30 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 0.006 0.000 ARG B 155 Details of bonding type rmsd hydrogen bonds : bond 0.04568 ( 438) hydrogen bonds : angle 4.38049 ( 1230) SS BOND : bond 0.00384 ( 4) SS BOND : angle 1.60730 ( 8) covalent geometry : bond 0.00277 ( 9887) covalent geometry : angle 0.57714 (13402) *********************** 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 147 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 ARG cc_start: 0.7419 (ptt90) cc_final: 0.7200 (ptt-90) REVERT: A 310 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6640 (ttm170) REVERT: B 238 MET cc_start: 0.7239 (ttm) cc_final: 0.6724 (ttt) REVERT: D 46 LYS cc_start: 0.7907 (tttm) cc_final: 0.7262 (pptt) REVERT: C 235 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8556 (pt0) outliers start: 31 outliers final: 21 residues processed: 137 average time/residue: 1.1054 time to fit residues: 163.6577 Evaluate side-chains 135 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 310 ARG 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 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 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 Chi-restraints excluded: chain E residue 83 MET 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 38 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 103 optimal weight: 0.0770 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.174480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120067 restraints weight = 10010.150| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.52 r_work: 0.3314 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9891 Z= 0.111 Angle : 0.559 11.959 13410 Z= 0.286 Chirality : 0.041 0.143 1512 Planarity : 0.003 0.038 1691 Dihedral : 4.558 50.133 1357 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.74 % Allowed : 20.66 % 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 (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: -0.08 (0.25), residues: 1214 helix: 2.16 (0.27), residues: 370 sheet: -0.74 (0.28), residues: 335 loop : -1.22 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 103 HIS 0.004 0.001 HIS A 325 PHE 0.018 0.001 PHE F 104 TYR 0.012 0.001 TYR F 106 ARG 0.007 0.000 ARG B 155 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 438) hydrogen bonds : angle 4.26513 ( 1230) SS BOND : bond 0.00343 ( 4) SS BOND : angle 1.40573 ( 8) covalent geometry : bond 0.00242 ( 9887) covalent geometry : angle 0.55835 (13402) *********************** 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: 29 poor density : 109 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6639 (mt0) cc_final: 0.5812 (mp10) REVERT: A 310 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6577 (ttm170) REVERT: B 238 MET cc_start: 0.7108 (ttm) cc_final: 0.6576 (ttt) REVERT: D 46 LYS cc_start: 0.7895 (tttm) cc_final: 0.7281 (pptt) REVERT: C 62 ASP cc_start: 0.8692 (m-30) cc_final: 0.8148 (m-30) REVERT: C 235 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8608 (pt0) outliers start: 29 outliers final: 18 residues processed: 127 average time/residue: 1.0705 time to fit residues: 147.3443 Evaluate side-chains 129 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 338 GLU 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 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 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 83 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 73 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 74 optimal weight: 0.0060 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.175178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.121401 restraints weight = 9914.568| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.40 r_work: 0.3329 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9891 Z= 0.112 Angle : 0.560 12.560 13410 Z= 0.286 Chirality : 0.041 0.143 1512 Planarity : 0.003 0.037 1691 Dihedral : 4.306 43.959 1355 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.64 % Allowed : 20.66 % Favored : 76.70 % 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: 0.01 (0.25), residues: 1214 helix: 2.23 (0.27), residues: 370 sheet: -0.68 (0.28), residues: 337 loop : -1.16 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 103 HIS 0.004 0.001 HIS A 325 PHE 0.018 0.001 PHE F 104 TYR 0.013 0.001 TYR A 31 ARG 0.007 0.000 ARG B 155 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 438) hydrogen bonds : angle 4.23209 ( 1230) SS BOND : bond 0.00352 ( 4) SS BOND : angle 1.35441 ( 8) covalent geometry : bond 0.00247 ( 9887) covalent geometry : angle 0.55951 (13402) *********************** 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 139 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6598 (mt0) cc_final: 0.5790 (mp10) REVERT: A 310 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6524 (ttm170) REVERT: B 238 MET cc_start: 0.7054 (ttm) cc_final: 0.6510 (ttt) REVERT: D 46 LYS cc_start: 0.7879 (tttm) cc_final: 0.7263 (pptt) REVERT: C 62 ASP cc_start: 0.8661 (m-30) cc_final: 0.8137 (m-30) REVERT: C 235 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8604 (pt0) outliers start: 28 outliers final: 21 residues processed: 126 average time/residue: 1.1232 time to fit residues: 152.9619 Evaluate side-chains 131 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 338 GLU 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 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 F residue 270 ILE 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 59 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 76 optimal weight: 0.3980 chunk 39 optimal weight: 0.0030 chunk 85 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 49 optimal weight: 0.0170 chunk 47 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 overall best weight: 0.3628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 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 = 0.4139 r_free = 0.4139 target = 0.178393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.124736 restraints weight = 10141.076| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.45 r_work: 0.3381 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9891 Z= 0.094 Angle : 0.533 12.448 13410 Z= 0.271 Chirality : 0.040 0.143 1512 Planarity : 0.003 0.037 1691 Dihedral : 4.110 44.084 1355 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.98 % Allowed : 21.32 % Favored : 76.70 % 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: 0.13 (0.25), residues: 1214 helix: 2.42 (0.27), residues: 369 sheet: -0.60 (0.29), residues: 325 loop : -1.18 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 103 HIS 0.003 0.001 HIS A 325 PHE 0.014 0.001 PHE F 104 TYR 0.011 0.001 TYR A 31 ARG 0.007 0.000 ARG B 155 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 438) hydrogen bonds : angle 4.08429 ( 1230) SS BOND : bond 0.00297 ( 4) SS BOND : angle 1.12864 ( 8) covalent geometry : bond 0.00193 ( 9887) covalent geometry : angle 0.53272 (13402) ********************** 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 134 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6462 (mt0) cc_final: 0.5711 (mp10) REVERT: B 238 MET cc_start: 0.6858 (ttm) cc_final: 0.6335 (ttt) REVERT: D 46 LYS cc_start: 0.7841 (tttm) cc_final: 0.7207 (pptt) REVERT: C 62 ASP cc_start: 0.8586 (m-30) cc_final: 0.8090 (m-30) outliers start: 21 outliers final: 16 residues processed: 124 average time/residue: 0.9751 time to fit residues: 132.1944 Evaluate side-chains 123 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU 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 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 173 CYS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 270 ILE 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 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.173095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.118605 restraints weight = 9970.081| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.52 r_work: 0.3288 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1597 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= 0.138 Angle : 0.587 12.701 13410 Z= 0.301 Chirality : 0.042 0.141 1512 Planarity : 0.003 0.038 1691 Dihedral : 4.371 44.448 1355 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.08 % Allowed : 21.79 % Favored : 76.13 % 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: 0.07 (0.25), residues: 1214 helix: 2.24 (0.27), residues: 370 sheet: -0.64 (0.28), residues: 338 loop : -1.10 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 103 HIS 0.005 0.001 HIS A 325 PHE 0.018 0.001 PHE F 104 TYR 0.016 0.001 TYR C 191 ARG 0.007 0.000 ARG B 155 Details of bonding type rmsd hydrogen bonds : bond 0.04654 ( 438) hydrogen bonds : angle 4.26690 ( 1230) SS BOND : bond 0.00426 ( 4) SS BOND : angle 1.43811 ( 8) covalent geometry : bond 0.00321 ( 9887) covalent geometry : angle 0.58604 (13402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7803.49 seconds wall clock time: 134 minutes 28.63 seconds (8068.63 seconds total)