Starting phenix.real_space_refine on Tue Feb 11 19:09:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ge9_29961/02_2025/8ge9_29961.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ge9_29961/02_2025/8ge9_29961.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/8ge9_29961/02_2025/8ge9_29961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ge9_29961/02_2025/8ge9_29961.map" model { file = "/net/cci-nas-00/data/ceres_data/8ge9_29961/02_2025/8ge9_29961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ge9_29961/02_2025/8ge9_29961.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= 0.031 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 44 5.16 5 C 4201 2.51 5 N 1121 2.21 5 O 1153 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6519 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1705 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 1, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 174 Chain: "B" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2393 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 123 Chain: "G" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 335 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "R" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2070 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 109 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 4.86, per 1000 atoms: 0.75 Number of scatterers: 6519 At special positions: 0 Unit cell: (68.9, 96.46, 126.14, 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 44 16.00 O 1153 8.00 N 1121 7.00 C 4201 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: 1.65 Conformation dependent library (CDL) restraints added in 1.1 seconds 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 48.1% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.569A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.610A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.667A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.785A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 7 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.702A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.915A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 31 through 61 removed outlier: 3.611A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 3.757A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.245A 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 removed outlier: 3.560A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.420A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 5.055A 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 removed outlier: 3.867A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 236 Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.903A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.940A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 327 removed outlier: 3.875A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.661A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.727A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.453A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 71 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.428A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.508A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.162A 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: 6.812A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.531A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.160A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1137 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: 1.90 Time building geometry restraints manager: 1.93 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: 2101 1.34 - 1.46: 1560 1.46 - 1.58: 2937 1.58 - 1.70: 1 1.70 - 1.81: 60 Bond restraints: 6659 Sorted by residual: bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.594 -0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.451 -0.054 2.00e-02 2.50e+03 7.22e+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 5.33e+00 bond pdb=" CAF G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.81e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.558 -0.038 2.00e-02 2.50e+03 3.69e+00 ... (remaining 6654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 8756 1.25 - 2.49: 274 2.49 - 3.74: 63 3.74 - 4.99: 12 4.99 - 6.24: 6 Bond angle restraints: 9111 Sorted by residual: angle pdb=" N ILE A 257 " pdb=" CA ILE A 257 " pdb=" C ILE A 257 " ideal model delta sigma weight residual 106.21 110.10 -3.89 1.07e+00 8.73e-01 1.32e+01 angle pdb=" C GLY A 226 " pdb=" N GLN A 227 " pdb=" CA GLN A 227 " ideal model delta sigma weight residual 121.54 127.50 -5.96 1.91e+00 2.74e-01 9.75e+00 angle pdb=" C TYR B 59 " pdb=" N ALA B 60 " pdb=" CA ALA B 60 " ideal model delta sigma weight residual 122.37 118.41 3.96 1.72e+00 3.38e-01 5.29e+00 angle pdb=" CA GLY B 53 " pdb=" C GLY B 53 " pdb=" N HIS B 54 " ideal model delta sigma weight residual 116.69 121.22 -4.53 2.04e+00 2.40e-01 4.94e+00 angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 117.13 -6.24 3.00e+00 1.11e-01 4.32e+00 ... (remaining 9106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3565 17.97 - 35.94: 229 35.94 - 53.91: 39 53.91 - 71.87: 6 71.87 - 89.84: 5 Dihedral angle restraints: 3844 sinusoidal: 1220 harmonic: 2624 Sorted by residual: dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual -180.00 -161.33 -18.67 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PRO B 194 " pdb=" C PRO B 194 " pdb=" N ASP B 195 " pdb=" CA ASP B 195 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 3841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 737 0.031 - 0.062: 235 0.062 - 0.093: 85 0.093 - 0.124: 37 0.124 - 0.155: 5 Chirality restraints: 1099 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CB ILE A 56 " pdb=" CA ILE A 56 " pdb=" CG1 ILE A 56 " pdb=" CG2 ILE A 56 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1096 not shown) Planarity restraints: 1145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C ILE R 205 " 0.024 2.00e-02 2.50e+03 pdb=" O ILE R 205 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL R 206 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO G 55 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 49 " -0.007 2.00e-02 2.50e+03 9.93e-03 1.73e+00 pdb=" CG PHE R 49 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE R 49 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE R 49 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE R 49 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 49 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE R 49 " -0.000 2.00e-02 2.50e+03 ... (remaining 1142 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 803 2.75 - 3.29: 6519 3.29 - 3.83: 11221 3.83 - 4.36: 12317 4.36 - 4.90: 22357 Nonbonded interactions: 53217 Sorted by model distance: nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.215 3.040 nonbonded pdb=" OG SER R 319 " pdb=" O HOH R 601 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR B 145 " pdb=" OD2 ASP B 186 " model vdw 2.260 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" NH1 ARG B 314 " model vdw 2.285 3.120 ... (remaining 53212 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=0.00 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.640 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 0.071 6659 Z= 0.209 Angle : 0.561 6.237 9111 Z= 0.317 Chirality : 0.038 0.155 1099 Planarity : 0.003 0.034 1145 Dihedral : 13.036 89.842 2137 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: 1.38 (0.28), residues: 884 helix: 2.34 (0.26), residues: 396 sheet: 0.88 (0.41), residues: 168 loop : -0.93 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 105 HIS 0.010 0.001 HIS B 54 PHE 0.023 0.001 PHE R 49 TYR 0.010 0.001 TYR R 199 ARG 0.002 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8277 (mtmt) cc_final: 0.8063 (mtpt) REVERT: B 243 THR cc_start: 0.8640 (p) cc_final: 0.8426 (p) REVERT: R 52 VAL cc_start: 0.9043 (t) cc_final: 0.8775 (m) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1645 time to fit residues: 24.9735 Evaluate side-chains 87 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.133307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113887 restraints weight = 10271.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.117145 restraints weight = 6106.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.119403 restraints weight = 4279.712| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6659 Z= 0.219 Angle : 0.507 7.809 9111 Z= 0.279 Chirality : 0.041 0.159 1099 Planarity : 0.003 0.034 1145 Dihedral : 4.898 62.416 968 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.17 % Allowed : 8.38 % Favored : 90.45 % 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: 1.48 (0.28), residues: 884 helix: 2.71 (0.26), residues: 382 sheet: 0.49 (0.39), residues: 179 loop : -0.91 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.003 0.001 HIS R 296 PHE 0.017 0.002 PHE R 49 TYR 0.021 0.002 TYR A 318 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8234 (tp40) cc_final: 0.7967 (tp-100) REVERT: A 309 GLU cc_start: 0.7796 (pm20) cc_final: 0.7558 (mp0) REVERT: B 147 SER cc_start: 0.8853 (m) cc_final: 0.8486 (t) outliers start: 7 outliers final: 5 residues processed: 98 average time/residue: 0.1643 time to fit residues: 22.5601 Evaluate side-chains 89 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain R residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 32 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.132221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.112782 restraints weight = 10299.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.116007 restraints weight = 6150.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.118225 restraints weight = 4327.256| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6659 Z= 0.208 Angle : 0.488 5.754 9111 Z= 0.269 Chirality : 0.040 0.155 1099 Planarity : 0.003 0.034 1145 Dihedral : 4.760 57.586 968 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.17 % Allowed : 12.56 % Favored : 86.26 % 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: 1.49 (0.28), residues: 884 helix: 2.79 (0.26), residues: 382 sheet: 0.32 (0.38), residues: 181 loop : -0.89 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS R 296 PHE 0.014 0.001 PHE B 241 TYR 0.014 0.001 TYR R 199 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8304 (tp40) cc_final: 0.8036 (tp-100) REVERT: A 309 GLU cc_start: 0.7744 (pm20) cc_final: 0.7485 (mp0) REVERT: B 147 SER cc_start: 0.8762 (m) cc_final: 0.8470 (t) outliers start: 7 outliers final: 5 residues processed: 92 average time/residue: 0.1411 time to fit residues: 18.8736 Evaluate side-chains 85 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 39 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 36 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.130865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.111372 restraints weight = 10493.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.114628 restraints weight = 6222.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.116874 restraints weight = 4349.029| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6659 Z= 0.228 Angle : 0.484 5.717 9111 Z= 0.266 Chirality : 0.040 0.151 1099 Planarity : 0.003 0.033 1145 Dihedral : 4.678 52.676 968 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.01 % Allowed : 13.90 % Favored : 84.09 % 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: 1.45 (0.29), residues: 884 helix: 2.75 (0.26), residues: 386 sheet: 0.20 (0.38), residues: 186 loop : -0.89 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS R 296 PHE 0.018 0.001 PHE R 49 TYR 0.015 0.001 TYR R 199 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8321 (tp40) cc_final: 0.8034 (tp-100) REVERT: A 309 GLU cc_start: 0.7786 (pm20) cc_final: 0.7529 (mp0) REVERT: B 147 SER cc_start: 0.8802 (m) cc_final: 0.8537 (t) REVERT: R 173 TRP cc_start: 0.7722 (m-10) cc_final: 0.6478 (m100) outliers start: 12 outliers final: 9 residues processed: 90 average time/residue: 0.1440 time to fit residues: 18.8026 Evaluate side-chains 86 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 42 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.132767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.113432 restraints weight = 10330.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.116726 restraints weight = 6108.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.118961 restraints weight = 4261.089| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6659 Z= 0.156 Angle : 0.457 5.536 9111 Z= 0.252 Chirality : 0.039 0.154 1099 Planarity : 0.003 0.033 1145 Dihedral : 4.484 46.551 968 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.01 % Allowed : 15.08 % Favored : 82.91 % 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: 1.47 (0.28), residues: 884 helix: 2.78 (0.26), residues: 386 sheet: 0.17 (0.38), residues: 184 loop : -0.86 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS R 296 PHE 0.012 0.001 PHE R 289 TYR 0.024 0.001 TYR A 318 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8280 (tp40) cc_final: 0.7984 (tp-100) REVERT: A 309 GLU cc_start: 0.7761 (pm20) cc_final: 0.7526 (mp0) REVERT: B 164 THR cc_start: 0.7862 (p) cc_final: 0.7653 (p) REVERT: B 338 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8326 (mt) REVERT: R 86 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8579 (m) REVERT: R 173 TRP cc_start: 0.7445 (m-10) cc_final: 0.6366 (m100) outliers start: 12 outliers final: 7 residues processed: 101 average time/residue: 0.1441 time to fit residues: 20.9671 Evaluate side-chains 92 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 52 optimal weight: 0.0050 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 15 optimal weight: 0.0470 chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 88 optimal weight: 0.0000 chunk 5 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.1696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.135864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.116576 restraints weight = 10199.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.119883 restraints weight = 6029.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.122121 restraints weight = 4200.148| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6659 Z= 0.122 Angle : 0.447 5.511 9111 Z= 0.242 Chirality : 0.038 0.157 1099 Planarity : 0.003 0.034 1145 Dihedral : 4.241 38.160 968 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.01 % Allowed : 16.42 % Favored : 81.57 % 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 (0.28), residues: 884 helix: 2.83 (0.26), residues: 391 sheet: 0.25 (0.40), residues: 174 loop : -0.86 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.004 0.001 HIS R 296 PHE 0.023 0.001 PHE R 49 TYR 0.010 0.001 TYR R 199 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8245 (tp40) cc_final: 0.7921 (tp-100) REVERT: A 309 GLU cc_start: 0.7733 (pm20) cc_final: 0.7489 (mp0) REVERT: B 338 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8275 (mt) outliers start: 12 outliers final: 8 residues processed: 102 average time/residue: 0.1620 time to fit residues: 24.0502 Evaluate side-chains 95 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 83 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 85 optimal weight: 0.1980 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 77 optimal weight: 0.0970 chunk 72 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 82 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.134589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115362 restraints weight = 10276.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118618 restraints weight = 6066.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120895 restraints weight = 4245.324| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6659 Z= 0.158 Angle : 0.451 5.609 9111 Z= 0.244 Chirality : 0.039 0.155 1099 Planarity : 0.003 0.034 1145 Dihedral : 4.192 33.617 968 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.18 % Allowed : 16.92 % Favored : 80.90 % 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: 1.56 (0.29), residues: 884 helix: 2.89 (0.26), residues: 391 sheet: 0.10 (0.38), residues: 184 loop : -0.84 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 173 HIS 0.004 0.001 HIS R 296 PHE 0.011 0.001 PHE R 289 TYR 0.013 0.001 TYR R 199 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8279 (tp40) cc_final: 0.7957 (tp-100) REVERT: A 309 GLU cc_start: 0.7821 (pm20) cc_final: 0.7569 (mp0) REVERT: B 338 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8254 (mt) outliers start: 13 outliers final: 10 residues processed: 97 average time/residue: 0.1380 time to fit residues: 19.5978 Evaluate side-chains 93 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.0870 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.132021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112923 restraints weight = 10326.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.116165 restraints weight = 6090.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.118419 restraints weight = 4241.990| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6659 Z= 0.196 Angle : 0.466 5.599 9111 Z= 0.253 Chirality : 0.039 0.152 1099 Planarity : 0.003 0.034 1145 Dihedral : 4.266 33.728 968 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.18 % Allowed : 17.25 % Favored : 80.57 % 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: 884 helix: 2.89 (0.26), residues: 391 sheet: -0.02 (0.38), residues: 184 loop : -0.81 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP R 173 HIS 0.004 0.001 HIS R 296 PHE 0.022 0.001 PHE R 49 TYR 0.014 0.001 TYR R 199 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8374 (tp40) cc_final: 0.8067 (tp-100) REVERT: A 309 GLU cc_start: 0.7822 (pm20) cc_final: 0.7564 (mp0) REVERT: B 59 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7338 (m-80) REVERT: B 338 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8269 (mt) outliers start: 13 outliers final: 9 residues processed: 96 average time/residue: 0.1395 time to fit residues: 19.4785 Evaluate side-chains 95 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 53 optimal weight: 3.9990 chunk 87 optimal weight: 0.0970 chunk 83 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.130173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.110562 restraints weight = 10495.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.113710 restraints weight = 6268.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.115861 restraints weight = 4420.174| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6659 Z= 0.204 Angle : 0.470 5.610 9111 Z= 0.256 Chirality : 0.039 0.152 1099 Planarity : 0.003 0.033 1145 Dihedral : 4.270 33.616 968 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.35 % Allowed : 17.42 % Favored : 80.23 % 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: 1.48 (0.28), residues: 884 helix: 2.85 (0.26), residues: 391 sheet: -0.09 (0.38), residues: 184 loop : -0.82 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS R 296 PHE 0.012 0.001 PHE R 289 TYR 0.014 0.001 TYR R 199 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8388 (tp40) cc_final: 0.8069 (tp-100) REVERT: A 309 GLU cc_start: 0.7753 (pm20) cc_final: 0.7510 (mp0) REVERT: B 59 TYR cc_start: 0.8352 (OUTLIER) cc_final: 0.7266 (m-80) REVERT: B 188 MET cc_start: 0.8226 (mmm) cc_final: 0.7785 (mtp) REVERT: B 338 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8249 (mt) outliers start: 14 outliers final: 10 residues processed: 96 average time/residue: 0.1420 time to fit residues: 19.9051 Evaluate side-chains 94 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 42 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.131035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.111855 restraints weight = 10451.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.115060 restraints weight = 6172.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.117338 restraints weight = 4321.762| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6659 Z= 0.200 Angle : 0.473 5.608 9111 Z= 0.257 Chirality : 0.039 0.151 1099 Planarity : 0.003 0.033 1145 Dihedral : 4.271 34.032 968 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.18 % Allowed : 17.42 % Favored : 80.40 % 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 (0.28), residues: 884 helix: 2.82 (0.26), residues: 391 sheet: -0.17 (0.37), residues: 185 loop : -0.79 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS R 296 PHE 0.021 0.001 PHE R 49 TYR 0.014 0.001 TYR R 199 ARG 0.002 0.000 ARG B 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8384 (tp40) cc_final: 0.8074 (tp-100) REVERT: A 309 GLU cc_start: 0.7797 (pm20) cc_final: 0.7567 (mp0) REVERT: B 59 TYR cc_start: 0.8366 (OUTLIER) cc_final: 0.7144 (m-80) REVERT: B 338 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8265 (mt) outliers start: 13 outliers final: 11 residues processed: 92 average time/residue: 0.1379 time to fit residues: 18.6632 Evaluate side-chains 94 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 5 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 35 optimal weight: 0.0770 chunk 37 optimal weight: 0.0770 chunk 76 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 0.0170 chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 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 = 0.3663 r_free = 0.3663 target = 0.134110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.114800 restraints weight = 10443.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118161 restraints weight = 6108.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120523 restraints weight = 4232.210| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6659 Z= 0.142 Angle : 0.453 5.522 9111 Z= 0.246 Chirality : 0.039 0.153 1099 Planarity : 0.003 0.033 1145 Dihedral : 4.193 34.551 968 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.68 % Allowed : 17.92 % Favored : 80.40 % 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: 1.50 (0.28), residues: 884 helix: 2.89 (0.26), residues: 391 sheet: -0.04 (0.39), residues: 169 loop : -0.84 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS R 296 PHE 0.011 0.001 PHE R 61 TYR 0.011 0.001 TYR R 199 ARG 0.002 0.000 ARG A 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2056.74 seconds wall clock time: 37 minutes 42.27 seconds (2262.27 seconds total)