Starting phenix.real_space_refine on Sun Apr 27 15:47:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gec_29965/04_2025/8gec_29965.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gec_29965/04_2025/8gec_29965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gec_29965/04_2025/8gec_29965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gec_29965/04_2025/8gec_29965.map" model { file = "/net/cci-nas-00/data/ceres_data/8gec_29965/04_2025/8gec_29965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gec_29965/04_2025/8gec_29965.cif" } resolution = 3.5 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= 0.029 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 26 5.16 5 C 3961 2.51 5 N 1081 2.21 5 O 1057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6125 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1622 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 4 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 2, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 194 Chain: "B" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2236 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 5, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 6, 'ARG:plan': 10, 'ASN:plan1': 7, 'ASP:plan': 24} Unresolved non-hydrogen planarities: 195 Chain: "G" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 305 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "R" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1947 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 402 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 141 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.49, per 1000 atoms: 0.73 Number of scatterers: 6125 At special positions: 0 Unit cell: (67.84, 97.52, 127.2, 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 26 16.00 O 1057 8.00 N 1081 7.00 C 3961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " 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: 1.63 Conformation dependent library (CDL) restraints added in 933.5 milliseconds 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 8 sheets defined 49.3% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 4.461A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.555A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.907A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.122A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.622A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 8 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 14 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.536A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 3.933A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.384A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 238 Processing helix chain 'R' and resid 270 through 298 removed outlier: 4.127A pdb=" N CYS R 285 " --> pdb=" O THR R 281 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.206A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 322 removed outlier: 3.955A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 327 Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 9.709A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 50 removed outlier: 5.828A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 61 removed outlier: 7.005A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.665A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.591A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.576A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.897A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.917A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2008 1.34 - 1.46: 1459 1.46 - 1.58: 2758 1.58 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 6259 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.448 -0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.570 -0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.440 -0.046 2.00e-02 2.50e+03 5.40e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.563 -0.043 2.00e-02 2.50e+03 4.58e+00 bond pdb=" CAI G1I R 501 " pdb=" NAN G1I R 501 " ideal model delta sigma weight residual 1.451 1.481 -0.030 2.00e-02 2.50e+03 2.28e+00 ... (remaining 6254 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 8531 1.99 - 3.98: 51 3.98 - 5.96: 6 5.96 - 7.95: 3 7.95 - 9.94: 1 Bond angle restraints: 8592 Sorted by residual: angle pdb=" C THR B 223 " pdb=" CA THR B 223 " pdb=" CB THR B 223 " ideal model delta sigma weight residual 116.63 110.50 6.13 1.16e+00 7.43e-01 2.79e+01 angle pdb=" CA THR B 223 " pdb=" C THR B 223 " pdb=" N GLY B 224 " ideal model delta sigma weight residual 119.63 117.22 2.41 8.10e-01 1.52e+00 8.89e+00 angle pdb=" CA LEU A 282 " pdb=" CB LEU A 282 " pdb=" CG LEU A 282 " ideal model delta sigma weight residual 116.30 126.24 -9.94 3.50e+00 8.16e-02 8.06e+00 angle pdb=" N PHE B 235 " pdb=" CA PHE B 235 " pdb=" C PHE B 235 " ideal model delta sigma weight residual 109.64 106.67 2.97 1.27e+00 6.20e-01 5.45e+00 angle pdb=" C THR B 243 " pdb=" N GLY B 244 " pdb=" CA GLY B 244 " ideal model delta sigma weight residual 122.36 120.26 2.10 9.70e-01 1.06e+00 4.71e+00 ... (remaining 8587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.57: 3093 12.57 - 25.13: 312 25.13 - 37.70: 108 37.70 - 50.26: 47 50.26 - 62.83: 13 Dihedral angle restraints: 3573 sinusoidal: 972 harmonic: 2601 Sorted by residual: dihedral pdb=" CA ARG B 68 " pdb=" C ARG B 68 " pdb=" N LEU B 69 " pdb=" CA LEU B 69 " ideal model delta harmonic sigma weight residual -180.00 -163.08 -16.92 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" N LYS B 78 " pdb=" CA LYS B 78 " pdb=" CB LYS B 78 " pdb=" CG LYS B 78 " ideal model delta sinusoidal sigma weight residual -180.00 -120.08 -59.92 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CG LYS A 293 " pdb=" CD LYS A 293 " pdb=" CE LYS A 293 " pdb=" NZ LYS A 293 " ideal model delta sinusoidal sigma weight residual 60.00 4.05 55.95 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 3570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 699 0.033 - 0.067: 242 0.067 - 0.100: 76 0.100 - 0.133: 21 0.133 - 0.167: 2 Chirality restraints: 1040 Sorted by residual: chirality pdb=" CA ARG B 52 " pdb=" N ARG B 52 " pdb=" C ARG B 52 " pdb=" CB ARG B 52 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.54 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ILE A 288 " pdb=" N ILE A 288 " pdb=" C ILE A 288 " pdb=" CB ILE A 288 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 1037 not shown) Planarity restraints: 1094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO B 236 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO G 49 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO B 194 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.016 5.00e-02 4.00e+02 ... (remaining 1091 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1341 2.78 - 3.31: 5831 3.31 - 3.84: 10167 3.84 - 4.37: 10628 4.37 - 4.90: 19785 Nonbonded interactions: 47752 Sorted by model distance: nonbonded pdb=" NE ARG B 251 " pdb=" OE2 GLU B 260 " model vdw 2.247 3.120 nonbonded pdb=" OD1 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR R 185 " pdb=" O PHE R 194 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLU R 107 " pdb=" OH TYR R 174 " model vdw 2.356 3.040 nonbonded pdb=" O TYR B 145 " pdb=" N GLY B 162 " model vdw 2.376 3.120 ... (remaining 47747 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 group one per residue 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.110 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6260 Z= 0.151 Angle : 0.474 9.938 8594 Z= 0.264 Chirality : 0.039 0.167 1040 Planarity : 0.003 0.040 1094 Dihedral : 13.971 62.827 1878 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.43 % Allowed : 21.38 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.29), residues: 871 helix: 2.62 (0.26), residues: 399 sheet: -0.36 (0.39), residues: 173 loop : -0.71 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.009 0.001 PHE B 235 TYR 0.014 0.001 TYR A 311 ARG 0.002 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.14679 ( 380) hydrogen bonds : angle 5.77129 ( 1107) SS BOND : bond 0.00211 ( 1) SS BOND : angle 0.43136 ( 2) covalent geometry : bond 0.00320 ( 6259) covalent geometry : angle 0.47419 ( 8592) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.604 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 71 average time/residue: 0.1394 time to fit residues: 14.5603 Evaluate side-chains 68 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 266 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 68 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 41 optimal weight: 0.0770 chunk 51 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.133460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115306 restraints weight = 10402.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.118278 restraints weight = 5964.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.120417 restraints weight = 4090.652| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6260 Z= 0.113 Angle : 0.439 8.102 8594 Z= 0.242 Chirality : 0.039 0.139 1040 Planarity : 0.003 0.035 1094 Dihedral : 4.581 40.474 957 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.32 % Allowed : 18.79 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.29), residues: 871 helix: 2.76 (0.26), residues: 402 sheet: 0.02 (0.40), residues: 165 loop : -0.84 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.003 0.001 HIS B 225 PHE 0.012 0.001 PHE B 222 TYR 0.012 0.001 TYR R 199 ARG 0.002 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 380) hydrogen bonds : angle 4.34835 ( 1107) SS BOND : bond 0.00166 ( 1) SS BOND : angle 0.33994 ( 2) covalent geometry : bond 0.00247 ( 6259) covalent geometry : angle 0.43860 ( 8592) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.685 Fit side-chains REVERT: B 54 HIS cc_start: 0.8357 (OUTLIER) cc_final: 0.7915 (m-70) outliers start: 20 outliers final: 10 residues processed: 80 average time/residue: 0.1177 time to fit residues: 14.6204 Evaluate side-chains 76 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 14 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 84 optimal weight: 0.0870 chunk 4 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.131514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.113140 restraints weight = 10166.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.116242 restraints weight = 5715.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.118452 restraints weight = 3886.659| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6260 Z= 0.111 Angle : 0.425 6.439 8594 Z= 0.233 Chirality : 0.039 0.134 1040 Planarity : 0.003 0.033 1094 Dihedral : 4.056 24.092 955 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.40 % Allowed : 18.14 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.29), residues: 871 helix: 2.74 (0.25), residues: 402 sheet: 0.05 (0.40), residues: 165 loop : -0.82 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.003 0.001 HIS B 54 PHE 0.010 0.001 PHE B 222 TYR 0.012 0.001 TYR R 199 ARG 0.002 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 380) hydrogen bonds : angle 4.05960 ( 1107) SS BOND : bond 0.00182 ( 1) SS BOND : angle 0.30755 ( 2) covalent geometry : bond 0.00250 ( 6259) covalent geometry : angle 0.42531 ( 8592) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.633 Fit side-chains REVERT: B 54 HIS cc_start: 0.8498 (OUTLIER) cc_final: 0.8149 (m-70) REVERT: B 82 TRP cc_start: 0.7887 (OUTLIER) cc_final: 0.7595 (m-10) REVERT: B 234 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8295 (t80) REVERT: R 82 MET cc_start: 0.6674 (OUTLIER) cc_final: 0.6371 (ttm) REVERT: R 113 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7569 (t0) REVERT: R 300 ASP cc_start: 0.7253 (t70) cc_final: 0.6787 (t70) outliers start: 25 outliers final: 11 residues processed: 87 average time/residue: 0.1199 time to fit residues: 15.7232 Evaluate side-chains 82 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 84 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 26 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 16 optimal weight: 0.0670 chunk 21 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.133983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.115652 restraints weight = 10568.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.118715 restraints weight = 6018.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.120844 restraints weight = 4112.549| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6260 Z= 0.106 Angle : 0.417 6.192 8594 Z= 0.229 Chirality : 0.039 0.135 1040 Planarity : 0.003 0.031 1094 Dihedral : 3.928 24.824 955 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.32 % Allowed : 19.65 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.29), residues: 871 helix: 2.76 (0.25), residues: 403 sheet: 0.03 (0.40), residues: 165 loop : -0.83 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.011 0.001 PHE B 222 TYR 0.013 0.001 TYR R 185 ARG 0.001 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 380) hydrogen bonds : angle 3.94284 ( 1107) SS BOND : bond 0.00160 ( 1) SS BOND : angle 0.28925 ( 2) covalent geometry : bond 0.00236 ( 6259) covalent geometry : angle 0.41654 ( 8592) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.804 Fit side-chains REVERT: B 45 MET cc_start: 0.8146 (mmt) cc_final: 0.7540 (mtp) REVERT: B 54 HIS cc_start: 0.8408 (OUTLIER) cc_final: 0.8054 (m-70) REVERT: B 82 TRP cc_start: 0.7876 (OUTLIER) cc_final: 0.7572 (m-10) REVERT: B 234 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8314 (t80) REVERT: R 82 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6360 (ttm) REVERT: R 113 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7572 (t0) REVERT: R 300 ASP cc_start: 0.7288 (t70) cc_final: 0.6813 (t70) outliers start: 20 outliers final: 14 residues processed: 83 average time/residue: 0.1328 time to fit residues: 17.3434 Evaluate side-chains 83 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 71 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 74 optimal weight: 0.3980 chunk 8 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114092 restraints weight = 10106.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.117290 restraints weight = 5697.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.119440 restraints weight = 3846.582| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6260 Z= 0.100 Angle : 0.409 6.146 8594 Z= 0.224 Chirality : 0.038 0.133 1040 Planarity : 0.003 0.031 1094 Dihedral : 3.833 25.206 955 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 6.05 % Allowed : 18.79 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.29), residues: 871 helix: 2.79 (0.25), residues: 404 sheet: 0.02 (0.40), residues: 165 loop : -0.81 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.009 0.001 PHE B 222 TYR 0.011 0.001 TYR R 199 ARG 0.001 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 380) hydrogen bonds : angle 3.86581 ( 1107) SS BOND : bond 0.00141 ( 1) SS BOND : angle 0.23590 ( 2) covalent geometry : bond 0.00220 ( 6259) covalent geometry : angle 0.40945 ( 8592) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.606 Fit side-chains REVERT: B 45 MET cc_start: 0.8108 (mmt) cc_final: 0.7564 (mtp) REVERT: B 54 HIS cc_start: 0.8334 (OUTLIER) cc_final: 0.8008 (m-70) REVERT: B 82 TRP cc_start: 0.7870 (OUTLIER) cc_final: 0.7580 (m-10) REVERT: B 234 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8294 (t80) REVERT: R 82 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.6308 (ttm) REVERT: R 113 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7602 (t0) REVERT: R 300 ASP cc_start: 0.7242 (t70) cc_final: 0.6758 (t70) outliers start: 28 outliers final: 15 residues processed: 87 average time/residue: 0.1191 time to fit residues: 15.6743 Evaluate side-chains 83 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 6 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 40 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.114506 restraints weight = 10236.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.117572 restraints weight = 5823.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.119714 restraints weight = 3980.516| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6260 Z= 0.110 Angle : 0.422 7.366 8594 Z= 0.228 Chirality : 0.039 0.133 1040 Planarity : 0.003 0.030 1094 Dihedral : 3.824 25.879 955 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 6.48 % Allowed : 18.79 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.29), residues: 871 helix: 2.75 (0.25), residues: 404 sheet: 0.05 (0.40), residues: 164 loop : -0.83 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.008 0.001 PHE B 222 TYR 0.011 0.001 TYR R 185 ARG 0.001 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03277 ( 380) hydrogen bonds : angle 3.85438 ( 1107) SS BOND : bond 0.00190 ( 1) SS BOND : angle 0.26006 ( 2) covalent geometry : bond 0.00249 ( 6259) covalent geometry : angle 0.42175 ( 8592) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 69 time to evaluate : 0.699 Fit side-chains REVERT: B 45 MET cc_start: 0.8131 (mmt) cc_final: 0.7630 (mtp) REVERT: B 54 HIS cc_start: 0.8320 (OUTLIER) cc_final: 0.8040 (m-70) REVERT: B 82 TRP cc_start: 0.7875 (OUTLIER) cc_final: 0.7551 (m-10) REVERT: B 234 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.8258 (t80) REVERT: B 286 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8115 (mt) REVERT: R 82 MET cc_start: 0.6676 (OUTLIER) cc_final: 0.6369 (ttm) REVERT: R 113 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7579 (t0) REVERT: R 300 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6800 (t70) outliers start: 30 outliers final: 17 residues processed: 89 average time/residue: 0.1186 time to fit residues: 16.1532 Evaluate side-chains 90 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 300 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 0.0980 chunk 63 optimal weight: 7.9990 chunk 65 optimal weight: 0.0170 chunk 3 optimal weight: 0.7980 chunk 74 optimal weight: 0.0000 chunk 85 optimal weight: 0.6980 overall best weight: 0.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.134270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.116266 restraints weight = 10267.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.119358 restraints weight = 5828.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.121522 restraints weight = 3971.354| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 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 0.025 6260 Z= 0.090 Angle : 0.406 6.792 8594 Z= 0.219 Chirality : 0.038 0.131 1040 Planarity : 0.003 0.028 1094 Dihedral : 3.721 24.318 955 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.40 % Allowed : 20.30 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.29), residues: 871 helix: 2.79 (0.25), residues: 404 sheet: 0.03 (0.40), residues: 164 loop : -0.81 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.007 0.001 PHE B 222 TYR 0.010 0.001 TYR R 199 ARG 0.001 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 380) hydrogen bonds : angle 3.75069 ( 1107) SS BOND : bond 0.00079 ( 1) SS BOND : angle 0.17292 ( 2) covalent geometry : bond 0.00194 ( 6259) covalent geometry : angle 0.40557 ( 8592) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.679 Fit side-chains REVERT: B 45 MET cc_start: 0.8073 (mmt) cc_final: 0.7613 (mtp) REVERT: B 82 TRP cc_start: 0.7693 (OUTLIER) cc_final: 0.7389 (m-10) REVERT: B 234 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.8258 (t80) REVERT: B 286 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8089 (mt) REVERT: R 113 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7596 (t0) REVERT: R 300 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6806 (t70) outliers start: 25 outliers final: 14 residues processed: 86 average time/residue: 0.1128 time to fit residues: 14.8591 Evaluate side-chains 83 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 300 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 34 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 29 optimal weight: 0.0970 chunk 74 optimal weight: 0.0020 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.133222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.115241 restraints weight = 10297.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.118324 restraints weight = 5839.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.120373 restraints weight = 3976.368| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6260 Z= 0.109 Angle : 0.437 9.615 8594 Z= 0.233 Chirality : 0.039 0.133 1040 Planarity : 0.003 0.028 1094 Dihedral : 3.746 25.487 955 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.40 % Allowed : 19.87 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.29), residues: 871 helix: 2.76 (0.25), residues: 405 sheet: 0.07 (0.40), residues: 162 loop : -0.81 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.007 0.001 HIS B 225 PHE 0.007 0.001 PHE B 235 TYR 0.011 0.001 TYR R 199 ARG 0.001 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03214 ( 380) hydrogen bonds : angle 3.78169 ( 1107) SS BOND : bond 0.00195 ( 1) SS BOND : angle 0.24204 ( 2) covalent geometry : bond 0.00244 ( 6259) covalent geometry : angle 0.43679 ( 8592) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.629 Fit side-chains REVERT: B 45 MET cc_start: 0.8105 (mmt) cc_final: 0.7879 (mtt) REVERT: B 82 TRP cc_start: 0.7777 (OUTLIER) cc_final: 0.7419 (m-10) REVERT: B 234 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8246 (t80) REVERT: B 286 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8110 (mt) REVERT: R 82 MET cc_start: 0.6654 (OUTLIER) cc_final: 0.6340 (ttm) REVERT: R 113 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7607 (t0) REVERT: R 300 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.6897 (t70) outliers start: 25 outliers final: 18 residues processed: 86 average time/residue: 0.1312 time to fit residues: 17.0766 Evaluate side-chains 89 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 300 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 35 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 10 optimal weight: 0.0980 chunk 61 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.133067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.114970 restraints weight = 10366.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.118021 restraints weight = 5907.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.120125 restraints weight = 4037.839| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6260 Z= 0.110 Angle : 0.433 8.387 8594 Z= 0.231 Chirality : 0.039 0.134 1040 Planarity : 0.003 0.028 1094 Dihedral : 3.763 25.608 955 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.83 % Allowed : 20.09 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.29), residues: 871 helix: 2.72 (0.25), residues: 405 sheet: 0.03 (0.40), residues: 162 loop : -0.79 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.007 0.001 HIS B 225 PHE 0.007 0.001 PHE B 222 TYR 0.011 0.001 TYR R 199 ARG 0.001 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 380) hydrogen bonds : angle 3.79791 ( 1107) SS BOND : bond 0.00183 ( 1) SS BOND : angle 0.26583 ( 2) covalent geometry : bond 0.00247 ( 6259) covalent geometry : angle 0.43255 ( 8592) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.638 Fit side-chains REVERT: A 372 ILE cc_start: 0.9162 (mm) cc_final: 0.8801 (mt) REVERT: B 45 MET cc_start: 0.8122 (mmt) cc_final: 0.7896 (mtt) REVERT: B 82 TRP cc_start: 0.7819 (OUTLIER) cc_final: 0.7451 (m-10) REVERT: B 234 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8241 (t80) REVERT: B 286 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8084 (mt) REVERT: R 82 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.6345 (ttm) REVERT: R 113 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7607 (t0) REVERT: R 300 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6924 (t70) outliers start: 27 outliers final: 18 residues processed: 86 average time/residue: 0.1131 time to fit residues: 14.9382 Evaluate side-chains 89 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 300 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 70 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.132672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.113897 restraints weight = 10647.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.117047 restraints weight = 5976.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.119223 restraints weight = 4045.278| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6260 Z= 0.131 Angle : 0.451 8.431 8594 Z= 0.242 Chirality : 0.039 0.136 1040 Planarity : 0.003 0.028 1094 Dihedral : 3.870 26.356 955 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 5.40 % Allowed : 21.17 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.29), residues: 871 helix: 2.66 (0.25), residues: 405 sheet: -0.02 (0.40), residues: 162 loop : -0.84 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.007 0.001 HIS B 225 PHE 0.008 0.001 PHE B 235 TYR 0.012 0.001 TYR R 199 ARG 0.002 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 380) hydrogen bonds : angle 3.87640 ( 1107) SS BOND : bond 0.00310 ( 1) SS BOND : angle 0.47324 ( 2) covalent geometry : bond 0.00302 ( 6259) covalent geometry : angle 0.45122 ( 8592) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 1.229 Fit side-chains REVERT: A 372 ILE cc_start: 0.9172 (mm) cc_final: 0.8816 (mt) REVERT: B 82 TRP cc_start: 0.7854 (OUTLIER) cc_final: 0.7525 (m-10) REVERT: B 234 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8309 (t80) REVERT: B 286 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8138 (mt) REVERT: R 82 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.6372 (ttm) REVERT: R 113 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7667 (t0) REVERT: R 300 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6941 (t70) outliers start: 25 outliers final: 16 residues processed: 87 average time/residue: 0.1558 time to fit residues: 20.5274 Evaluate side-chains 91 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 300 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 85 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.132954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.114410 restraints weight = 10706.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.117422 restraints weight = 6152.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.119541 restraints weight = 4231.254| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6260 Z= 0.119 Angle : 0.456 8.535 8594 Z= 0.240 Chirality : 0.039 0.135 1040 Planarity : 0.003 0.029 1094 Dihedral : 3.848 25.859 955 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.18 % Allowed : 21.60 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.29), residues: 871 helix: 2.66 (0.25), residues: 405 sheet: -0.07 (0.40), residues: 162 loop : -0.85 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.007 0.001 PHE B 235 TYR 0.012 0.001 TYR R 199 ARG 0.001 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 380) hydrogen bonds : angle 3.86006 ( 1107) SS BOND : bond 0.00206 ( 1) SS BOND : angle 0.36763 ( 2) covalent geometry : bond 0.00273 ( 6259) covalent geometry : angle 0.45623 ( 8592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2079.21 seconds wall clock time: 37 minutes 16.48 seconds (2236.48 seconds total)