Starting phenix.real_space_refine on Fri Aug 22 17:08:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gee_29967/08_2025/8gee_29967.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gee_29967/08_2025/8gee_29967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gee_29967/08_2025/8gee_29967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gee_29967/08_2025/8gee_29967.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gee_29967/08_2025/8gee_29967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gee_29967/08_2025/8gee_29967.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.026 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 30 5.16 5 C 4073 2.51 5 N 1104 2.21 5 O 1097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6304 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1808 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 6, 'TRANS': 264} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 446 Unresolved non-hydrogen angles: 549 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 13, 'ASN:plan1': 7, 'GLU:plan': 21, 'ASP:plan': 14, 'TYR:plan': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 273 Chain: "B" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2216 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 5, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 400 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 13, 'GLN:plan1': 7, 'GLU:plan': 6, 'ASP:plan': 25, 'ASN:plan1': 8, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 227 Chain: "G" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 299 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "R" Number of atoms: 1965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 1965 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 391 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 5, 'GLU:plan': 8, 'ASP:plan': 5, 'GLN:plan1': 6, 'ARG:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 136 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: 1.82, per 1000 atoms: 0.29 Number of scatterers: 6304 At special positions: 0 Unit cell: (67.84, 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 30 16.00 O 1097 8.00 N 1104 7.00 C 4073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 402.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1774 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 8 sheets defined 49.7% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.614A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 113 Processing helix chain 'A' and resid 160 through 169 removed outlier: 3.921A pdb=" N GLU A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 238 removed outlier: 4.030A 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 removed outlier: 3.579A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.792A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 4.396A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.142A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' 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 removed outlier: 3.782A 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 32 through 61 removed outlier: 3.837A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 Processing helix chain 'R' and resid 66 through 97 removed outlier: 3.558A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.192A 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 136 Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.133A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 removed outlier: 4.034A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix removed outlier: 3.548A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 187 Processing helix chain 'R' and resid 198 through 208 removed outlier: 3.947A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.786A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.773A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 322 removed outlier: 3.812A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 3.922A 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 210 removed outlier: 6.488A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 7.035A 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 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.443A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.505A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.829A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.278A 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: 3.554A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.224A 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: 6.459A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 4.013A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1113 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: 1.03 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.49: 3836 1.49 - 1.76: 2564 1.76 - 2.03: 38 2.03 - 2.30: 0 2.30 - 2.57: 1 Bond restraints: 6439 Sorted by residual: bond pdb=" C PRO A 328 " pdb=" N GLU A 330 " ideal model delta sigma weight residual 1.332 2.568 -1.236 1.40e-02 5.10e+03 7.79e+03 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 7.30e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.443 -0.049 2.00e-02 2.50e+03 6.00e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.567 -0.047 2.00e-02 2.50e+03 5.43e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.568 -0.045 2.00e-02 2.50e+03 5.13e+00 ... (remaining 6434 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.35: 8846 9.35 - 18.71: 0 18.71 - 28.06: 1 28.06 - 37.41: 1 37.41 - 46.77: 1 Bond angle restraints: 8849 Sorted by residual: angle pdb=" O PRO A 328 " pdb=" C PRO A 328 " pdb=" N GLU A 330 " ideal model delta sigma weight residual 122.64 86.96 35.68 1.35e+00 5.49e-01 6.98e+02 angle pdb=" C PRO A 328 " pdb=" N GLU A 330 " pdb=" CA GLU A 330 " ideal model delta sigma weight residual 121.54 168.31 -46.77 1.91e+00 2.74e-01 6.00e+02 angle pdb=" CA PRO A 328 " pdb=" C PRO A 328 " pdb=" N GLU A 330 " ideal model delta sigma weight residual 116.70 139.56 -22.86 2.07e+00 2.33e-01 1.22e+02 angle pdb=" C THR A 325 " pdb=" N PRO A 326 " pdb=" CA PRO A 326 " ideal model delta sigma weight residual 120.51 113.81 6.70 1.26e+00 6.30e-01 2.83e+01 angle pdb=" CA THR A 325 " pdb=" C THR A 325 " pdb=" N PRO A 326 " ideal model delta sigma weight residual 117.75 114.22 3.53 9.90e-01 1.02e+00 1.27e+01 ... (remaining 8844 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 3424 17.46 - 34.91: 213 34.91 - 52.37: 29 52.37 - 69.83: 3 69.83 - 87.29: 3 Dihedral angle restraints: 3672 sinusoidal: 948 harmonic: 2724 Sorted by residual: dihedral pdb=" CA PRO A 328 " pdb=" C PRO A 328 " pdb=" N GLU A 330 " pdb=" CA GLU A 330 " ideal model delta harmonic sigma weight residual 180.00 -92.71 -87.29 0 5.00e+00 4.00e-02 3.05e+02 dihedral pdb=" CA HIS B 54 " pdb=" C HIS B 54 " pdb=" N LEU B 55 " pdb=" CA LEU B 55 " ideal model delta harmonic sigma weight residual -180.00 -160.32 -19.68 0 5.00e+00 4.00e-02 1.55e+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 180.00 160.48 19.52 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 3669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 718 0.032 - 0.064: 242 0.064 - 0.096: 86 0.096 - 0.128: 32 0.128 - 0.160: 2 Chirality restraints: 1080 Sorted by residual: 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 2.56 -0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CA VAL A 214 " pdb=" N VAL A 214 " pdb=" C VAL A 214 " pdb=" CB VAL A 214 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA PRO A 326 " pdb=" N PRO A 326 " pdb=" C PRO A 326 " pdb=" CB PRO A 326 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1077 not shown) Planarity restraints: 1127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 328 " -0.116 2.00e-02 2.50e+03 1.48e-01 2.19e+02 pdb=" C PRO A 328 " 0.254 2.00e-02 2.50e+03 pdb=" O PRO A 328 " -0.083 2.00e-02 2.50e+03 pdb=" N GLU A 330 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 325 " 0.041 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO A 326 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 325 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.92e+00 pdb=" C THR A 325 " 0.038 2.00e-02 2.50e+03 pdb=" O THR A 325 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO A 326 " -0.013 2.00e-02 2.50e+03 ... (remaining 1124 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 430 2.74 - 3.28: 6331 3.28 - 3.82: 10731 3.82 - 4.36: 10889 4.36 - 4.90: 20258 Nonbonded interactions: 48639 Sorted by model distance: nonbonded pdb=" OD1 ASN R 293 " pdb=" OH TYR R 308 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR R 185 " pdb=" O PHE R 194 " model vdw 2.241 3.040 nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.375 3.040 nonbonded pdb=" OD1 ASN B 295 " pdb=" NE ARG B 304 " model vdw 2.402 3.120 nonbonded pdb=" NH1 ARG B 49 " pdb=" O PHE G 61 " model vdw 2.420 3.120 ... (remaining 48634 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.240 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.016 1.236 6441 Z= 1.109 Angle : 0.817 46.766 8853 Z= 0.479 Chirality : 0.039 0.160 1080 Planarity : 0.005 0.148 1127 Dihedral : 12.170 87.287 1892 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.28), residues: 909 helix: 3.01 (0.25), residues: 407 sheet: -0.32 (0.41), residues: 163 loop : -0.48 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.011 0.001 TYR R 219 PHE 0.013 0.001 PHE B 234 TRP 0.037 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.01566 ( 6439) covalent geometry : angle 0.81739 ( 8849) SS BOND : bond 0.00387 ( 2) SS BOND : angle 0.39140 ( 4) hydrogen bonds : bond 0.16255 ( 385) hydrogen bonds : angle 5.62105 ( 1113) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.253 Fit side-chains REVERT: R 190 CYS cc_start: 0.7085 (t) cc_final: 0.6786 (t) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0781 time to fit residues: 9.6069 Evaluate side-chains 71 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** 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 = 0.3430 r_free = 0.3430 target = 0.109322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.092442 restraints weight = 12838.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094735 restraints weight = 7574.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.096184 restraints weight = 5216.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097371 restraints weight = 4021.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098160 restraints weight = 3283.306| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6441 Z= 0.175 Angle : 0.481 5.485 8853 Z= 0.270 Chirality : 0.041 0.152 1080 Planarity : 0.003 0.033 1127 Dihedral : 3.995 19.569 990 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 1.51 % Allowed : 12.07 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.29), residues: 911 helix: 2.89 (0.25), residues: 422 sheet: -0.36 (0.41), residues: 164 loop : -0.57 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 385 TYR 0.009 0.001 TYR R 308 PHE 0.022 0.001 PHE A 222 TRP 0.020 0.002 TRP R 173 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 6439) covalent geometry : angle 0.48053 ( 8849) SS BOND : bond 0.00510 ( 2) SS BOND : angle 0.57652 ( 4) hydrogen bonds : bond 0.04246 ( 385) hydrogen bonds : angle 4.44794 ( 1113) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.161 Fit side-chains REVERT: R 82 MET cc_start: 0.8012 (tmm) cc_final: 0.7140 (ttp) REVERT: R 190 CYS cc_start: 0.7108 (t) cc_final: 0.6836 (t) outliers start: 7 outliers final: 5 residues processed: 78 average time/residue: 0.0682 time to fit residues: 7.4218 Evaluate side-chains 72 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 73 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** 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 = 0.3447 r_free = 0.3447 target = 0.110363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.093468 restraints weight = 12582.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.095746 restraints weight = 7475.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.097220 restraints weight = 5153.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.098361 restraints weight = 3985.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.099170 restraints weight = 3263.811| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6441 Z= 0.125 Angle : 0.435 5.355 8853 Z= 0.244 Chirality : 0.040 0.150 1080 Planarity : 0.003 0.027 1127 Dihedral : 3.848 19.525 990 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.72 % Allowed : 15.73 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.28), residues: 911 helix: 3.04 (0.25), residues: 417 sheet: -0.29 (0.40), residues: 163 loop : -0.69 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 42 TYR 0.010 0.001 TYR B 59 PHE 0.011 0.001 PHE B 234 TRP 0.011 0.001 TRP R 173 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6439) covalent geometry : angle 0.43483 ( 8849) SS BOND : bond 0.00444 ( 2) SS BOND : angle 0.57447 ( 4) hydrogen bonds : bond 0.03760 ( 385) hydrogen bonds : angle 4.17172 ( 1113) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.191 Fit side-chains REVERT: R 82 MET cc_start: 0.7995 (tmm) cc_final: 0.7131 (ttp) REVERT: R 190 CYS cc_start: 0.7114 (t) cc_final: 0.6821 (t) outliers start: 8 outliers final: 7 residues processed: 77 average time/residue: 0.0662 time to fit residues: 7.2647 Evaluate side-chains 74 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 3 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 80 optimal weight: 0.0970 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN ** B 259 GLN ** 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 = 0.3433 r_free = 0.3433 target = 0.109172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.092211 restraints weight = 12632.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094466 restraints weight = 7516.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.095977 restraints weight = 5213.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.097111 restraints weight = 4019.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097986 restraints weight = 3296.194| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6441 Z= 0.142 Angle : 0.440 5.363 8853 Z= 0.246 Chirality : 0.040 0.130 1080 Planarity : 0.003 0.027 1127 Dihedral : 3.833 20.439 990 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 4.09 % Allowed : 17.67 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.28), residues: 911 helix: 2.98 (0.25), residues: 423 sheet: -0.36 (0.40), residues: 163 loop : -0.69 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 TYR 0.013 0.001 TYR R 174 PHE 0.010 0.001 PHE R 289 TRP 0.009 0.001 TRP R 313 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6439) covalent geometry : angle 0.43968 ( 8849) SS BOND : bond 0.00492 ( 2) SS BOND : angle 0.63135 ( 4) hydrogen bonds : bond 0.03725 ( 385) hydrogen bonds : angle 4.07637 ( 1113) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: B 254 ASP cc_start: 0.8363 (t0) cc_final: 0.8143 (t0) REVERT: R 82 MET cc_start: 0.7986 (tmm) cc_final: 0.7043 (ttp) outliers start: 19 outliers final: 13 residues processed: 84 average time/residue: 0.0562 time to fit residues: 6.7544 Evaluate side-chains 79 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 38 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 142 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.109173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.092200 restraints weight = 12908.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094446 restraints weight = 7568.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.095891 restraints weight = 5234.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097044 restraints weight = 4056.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.097629 restraints weight = 3353.359| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6441 Z= 0.140 Angle : 0.439 5.339 8853 Z= 0.244 Chirality : 0.040 0.131 1080 Planarity : 0.003 0.029 1127 Dihedral : 3.823 21.066 990 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.45 % Allowed : 19.61 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.29), residues: 911 helix: 3.01 (0.25), residues: 423 sheet: -0.55 (0.39), residues: 169 loop : -0.67 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.012 0.001 TYR B 59 PHE 0.014 0.001 PHE A 222 TRP 0.009 0.001 TRP R 313 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6439) covalent geometry : angle 0.43915 ( 8849) SS BOND : bond 0.00463 ( 2) SS BOND : angle 0.60972 ( 4) hydrogen bonds : bond 0.03676 ( 385) hydrogen bonds : angle 4.01124 ( 1113) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: B 111 TYR cc_start: 0.8195 (m-80) cc_final: 0.7945 (m-80) REVERT: R 82 MET cc_start: 0.7994 (tmm) cc_final: 0.7035 (ttp) outliers start: 16 outliers final: 13 residues processed: 84 average time/residue: 0.0563 time to fit residues: 6.9035 Evaluate side-chains 80 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN ** B 259 GLN ** 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 = 0.3440 r_free = 0.3440 target = 0.109709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.092833 restraints weight = 12682.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.095114 restraints weight = 7467.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.096520 restraints weight = 5158.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.097700 restraints weight = 4015.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.098516 restraints weight = 3306.935| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6441 Z= 0.117 Angle : 0.420 5.320 8853 Z= 0.234 Chirality : 0.039 0.131 1080 Planarity : 0.002 0.028 1127 Dihedral : 3.738 20.295 990 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.88 % Allowed : 19.40 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.29), residues: 911 helix: 3.07 (0.25), residues: 421 sheet: -0.37 (0.40), residues: 163 loop : -0.71 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.010 0.001 TYR B 59 PHE 0.010 0.001 PHE A 222 TRP 0.008 0.001 TRP R 313 HIS 0.002 0.000 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 6439) covalent geometry : angle 0.41992 ( 8849) SS BOND : bond 0.00392 ( 2) SS BOND : angle 0.51070 ( 4) hydrogen bonds : bond 0.03502 ( 385) hydrogen bonds : angle 3.91947 ( 1113) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.212 Fit side-chains REVERT: B 111 TYR cc_start: 0.8184 (m-80) cc_final: 0.7956 (m-80) REVERT: R 82 MET cc_start: 0.7962 (tmm) cc_final: 0.7027 (ttp) REVERT: R 190 CYS cc_start: 0.7101 (t) cc_final: 0.6810 (t) outliers start: 18 outliers final: 15 residues processed: 88 average time/residue: 0.0584 time to fit residues: 7.5826 Evaluate side-chains 82 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 72 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 47 optimal weight: 0.0670 chunk 5 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.109472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.092732 restraints weight = 12633.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.094985 restraints weight = 7455.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.096381 restraints weight = 5157.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.097589 restraints weight = 4005.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.098280 restraints weight = 3277.390| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6441 Z= 0.123 Angle : 0.439 6.948 8853 Z= 0.241 Chirality : 0.039 0.130 1080 Planarity : 0.003 0.027 1127 Dihedral : 3.748 19.872 990 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.88 % Allowed : 19.40 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.29), residues: 911 helix: 3.04 (0.25), residues: 423 sheet: -0.38 (0.40), residues: 164 loop : -0.66 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.017 0.001 TYR R 174 PHE 0.009 0.001 PHE R 289 TRP 0.008 0.001 TRP R 313 HIS 0.001 0.000 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6439) covalent geometry : angle 0.43930 ( 8849) SS BOND : bond 0.00398 ( 2) SS BOND : angle 0.51613 ( 4) hydrogen bonds : bond 0.03504 ( 385) hydrogen bonds : angle 3.88639 ( 1113) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: B 88 ASN cc_start: 0.7025 (t0) cc_final: 0.6661 (t0) REVERT: B 254 ASP cc_start: 0.8178 (t0) cc_final: 0.7958 (t0) REVERT: R 82 MET cc_start: 0.7987 (tmm) cc_final: 0.7056 (ttp) outliers start: 18 outliers final: 14 residues processed: 84 average time/residue: 0.0669 time to fit residues: 7.9470 Evaluate side-chains 79 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 31 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.092052 restraints weight = 12794.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.094272 restraints weight = 7593.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.095864 restraints weight = 5261.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.096920 restraints weight = 4015.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.097669 restraints weight = 3322.339| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6441 Z= 0.137 Angle : 0.450 6.740 8853 Z= 0.246 Chirality : 0.040 0.133 1080 Planarity : 0.003 0.028 1127 Dihedral : 3.791 20.381 990 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.45 % Allowed : 18.97 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.29), residues: 911 helix: 3.02 (0.25), residues: 423 sheet: -0.35 (0.40), residues: 162 loop : -0.65 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.011 0.001 TYR R 174 PHE 0.029 0.001 PHE A 222 TRP 0.008 0.001 TRP R 313 HIS 0.001 0.000 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6439) covalent geometry : angle 0.45004 ( 8849) SS BOND : bond 0.00431 ( 2) SS BOND : angle 0.58806 ( 4) hydrogen bonds : bond 0.03601 ( 385) hydrogen bonds : angle 3.92004 ( 1113) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: B 254 ASP cc_start: 0.8191 (t0) cc_final: 0.7972 (t0) REVERT: R 82 MET cc_start: 0.8046 (tmm) cc_final: 0.7090 (ttp) outliers start: 16 outliers final: 15 residues processed: 83 average time/residue: 0.0588 time to fit residues: 7.0806 Evaluate side-chains 81 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 82 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 11 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.093083 restraints weight = 12829.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095317 restraints weight = 7553.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.096927 restraints weight = 5198.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.097920 restraints weight = 3966.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.098751 restraints weight = 3284.465| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6441 Z= 0.113 Angle : 0.439 6.492 8853 Z= 0.240 Chirality : 0.040 0.143 1080 Planarity : 0.003 0.027 1127 Dihedral : 3.733 19.602 990 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.02 % Allowed : 19.83 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.29), residues: 911 helix: 3.03 (0.25), residues: 423 sheet: -0.41 (0.40), residues: 164 loop : -0.61 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.009 0.001 TYR B 59 PHE 0.032 0.001 PHE A 222 TRP 0.009 0.001 TRP B 169 HIS 0.001 0.000 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6439) covalent geometry : angle 0.43861 ( 8849) SS BOND : bond 0.00373 ( 2) SS BOND : angle 0.47379 ( 4) hydrogen bonds : bond 0.03447 ( 385) hydrogen bonds : angle 3.85672 ( 1113) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.233 Fit side-chains REVERT: B 254 ASP cc_start: 0.8270 (t0) cc_final: 0.8053 (t0) REVERT: R 82 MET cc_start: 0.7992 (tmm) cc_final: 0.7069 (ttp) REVERT: R 190 CYS cc_start: 0.7123 (t) cc_final: 0.6849 (t) outliers start: 14 outliers final: 13 residues processed: 84 average time/residue: 0.0606 time to fit residues: 7.3799 Evaluate side-chains 80 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 80 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 79 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 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 292 ASN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.110051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.092722 restraints weight = 12722.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.094930 restraints weight = 7594.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.096539 restraints weight = 5321.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.097403 restraints weight = 4092.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.098345 restraints weight = 3455.323| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6441 Z= 0.115 Angle : 0.447 6.438 8853 Z= 0.243 Chirality : 0.040 0.155 1080 Planarity : 0.003 0.026 1127 Dihedral : 3.733 19.063 990 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.80 % Allowed : 20.04 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.29), residues: 911 helix: 3.03 (0.25), residues: 423 sheet: -0.41 (0.40), residues: 164 loop : -0.61 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.009 0.001 TYR R 308 PHE 0.011 0.001 PHE A 212 TRP 0.012 0.001 TRP B 99 HIS 0.001 0.000 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 6439) covalent geometry : angle 0.44721 ( 8849) SS BOND : bond 0.00381 ( 2) SS BOND : angle 0.46432 ( 4) hydrogen bonds : bond 0.03428 ( 385) hydrogen bonds : angle 3.87344 ( 1113) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.223 Fit side-chains REVERT: B 254 ASP cc_start: 0.8241 (t0) cc_final: 0.8036 (t0) REVERT: R 82 MET cc_start: 0.7977 (tmm) cc_final: 0.7060 (ttp) REVERT: R 190 CYS cc_start: 0.7131 (t) cc_final: 0.6861 (t) outliers start: 13 outliers final: 13 residues processed: 83 average time/residue: 0.0562 time to fit residues: 6.7944 Evaluate side-chains 83 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 6 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 12 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 58 optimal weight: 0.0670 chunk 49 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.111165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.093806 restraints weight = 12801.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.096153 restraints weight = 7581.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.097612 restraints weight = 5234.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.098741 restraints weight = 4056.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.099574 restraints weight = 3381.139| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6441 Z= 0.098 Angle : 0.432 6.264 8853 Z= 0.236 Chirality : 0.040 0.157 1080 Planarity : 0.003 0.026 1127 Dihedral : 3.677 17.447 990 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.37 % Allowed : 21.55 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.29), residues: 911 helix: 3.04 (0.25), residues: 423 sheet: -0.40 (0.40), residues: 158 loop : -0.62 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.010 0.001 TYR B 59 PHE 0.042 0.001 PHE A 222 TRP 0.021 0.001 TRP B 99 HIS 0.001 0.000 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 6439) covalent geometry : angle 0.43247 ( 8849) SS BOND : bond 0.00318 ( 2) SS BOND : angle 0.34935 ( 4) hydrogen bonds : bond 0.03272 ( 385) hydrogen bonds : angle 3.85644 ( 1113) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 987.07 seconds wall clock time: 17 minutes 39.74 seconds (1059.74 seconds total)