Starting phenix.real_space_refine on Tue Jan 13 14:00:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7quc_14147/01_2026/7quc_14147.cif Found real_map, /net/cci-nas-00/data/ceres_data/7quc_14147/01_2026/7quc_14147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7quc_14147/01_2026/7quc_14147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7quc_14147/01_2026/7quc_14147.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7quc_14147/01_2026/7quc_14147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7quc_14147/01_2026/7quc_14147.map" } resolution = 3.2 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= 0.000 sd= 0.011 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 47 5.16 5 C 4207 2.51 5 N 1135 2.21 5 O 1285 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6680 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3350 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Chain breaks: 1 Chain: "B" Number of atoms: 3269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3269 Classifications: {'peptide': 415} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 395} Chain breaks: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.52, per 1000 atoms: 0.23 Number of scatterers: 6680 At special positions: 0 Unit cell: (94.544, 75.262, 101.386, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 5 15.00 Mg 1 11.99 O 1285 8.00 N 1135 7.00 C 4207 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.75 Conformation dependent library (CDL) restraints added in 287.1 milliseconds 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 52.9% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.532A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 removed outlier: 4.062A pdb=" N ASN A 50 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.455A pdb=" N VAL A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 128 removed outlier: 3.990A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.501A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A 160 " --> pdb=" O ARG A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.726A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.799A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 287 through 296 removed outlier: 4.061A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 336 Processing helix chain 'A' and resid 384 through 400 removed outlier: 3.616A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 415 through 436 removed outlier: 4.062A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 removed outlier: 4.186A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.652A pdb=" N GLU B 45 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.608A pdb=" N VAL B 49 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 70 through 78 removed outlier: 4.109A pdb=" N ASP B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 125 removed outlier: 3.588A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.568A pdb=" N GLY B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 195 removed outlier: 3.511A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.563A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N CYS B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.771A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.604A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 373 through 390 removed outlier: 4.182A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.722A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.616A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N SER A 140 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N VAL A 9 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 6.726A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N CYS A 376 " --> pdb=" O MET A 317 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N MET A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.268A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N VAL B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N HIS B 6 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 163 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER B 364 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE B 317 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR B 366 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA B 315 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE B 368 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL B 313 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN B 370 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 52 Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 170 316 hydrogen bonds defined for protein. 909 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: 1.14 Time building geometry restraints manager: 0.89 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: 2206 1.34 - 1.46: 1104 1.46 - 1.57: 3438 1.57 - 1.69: 9 1.69 - 1.81: 74 Bond restraints: 6831 Sorted by residual: bond pdb=" CB PRO A 298 " pdb=" CG PRO A 298 " ideal model delta sigma weight residual 1.492 1.658 -0.166 5.00e-02 4.00e+02 1.10e+01 bond pdb=" CG PRO A 298 " pdb=" CD PRO A 298 " ideal model delta sigma weight residual 1.503 1.426 0.077 3.40e-02 8.65e+02 5.07e+00 bond pdb=" CA GLY B 98 " pdb=" C GLY B 98 " ideal model delta sigma weight residual 1.530 1.514 0.017 1.04e-02 9.25e+03 2.58e+00 bond pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta sigma weight residual 1.470 1.455 0.015 1.01e-02 9.80e+03 2.20e+00 bond pdb=" N GLY B 98 " pdb=" CA GLY B 98 " ideal model delta sigma weight residual 1.464 1.448 0.016 1.12e-02 7.97e+03 2.05e+00 ... (remaining 6826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 9200 2.60 - 5.20: 71 5.20 - 7.80: 4 7.80 - 10.41: 2 10.41 - 13.01: 1 Bond angle restraints: 9278 Sorted by residual: angle pdb=" CA PRO A 298 " pdb=" N PRO A 298 " pdb=" CD PRO A 298 " ideal model delta sigma weight residual 112.00 98.99 13.01 1.40e+00 5.10e-01 8.63e+01 angle pdb=" N PRO A 298 " pdb=" CD PRO A 298 " pdb=" CG PRO A 298 " ideal model delta sigma weight residual 103.20 95.09 8.11 1.50e+00 4.44e-01 2.92e+01 angle pdb=" CA PRO A 298 " pdb=" CB PRO A 298 " pdb=" CG PRO A 298 " ideal model delta sigma weight residual 104.50 98.89 5.61 1.90e+00 2.77e-01 8.71e+00 angle pdb=" C PRO A 298 " pdb=" CA PRO A 298 " pdb=" CB PRO A 298 " ideal model delta sigma weight residual 110.00 113.05 -3.05 1.12e+00 7.97e-01 7.42e+00 angle pdb=" N ILE B 16 " pdb=" CA ILE B 16 " pdb=" C ILE B 16 " ideal model delta sigma weight residual 111.81 109.59 2.22 8.60e-01 1.35e+00 6.69e+00 ... (remaining 9273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.07: 3941 32.07 - 64.14: 101 64.14 - 96.21: 12 96.21 - 128.29: 1 128.29 - 160.36: 2 Dihedral angle restraints: 4057 sinusoidal: 1626 harmonic: 2431 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -91.09 160.36 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -34.63 139.22 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" O5' GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PA GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sinusoidal sigma weight residual 274.12 174.74 99.39 1 2.00e+01 2.50e-03 2.79e+01 ... (remaining 4054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 643 0.034 - 0.069: 270 0.069 - 0.103: 72 0.103 - 0.138: 31 0.138 - 0.172: 2 Chirality restraints: 1018 Sorted by residual: chirality pdb=" CB VAL B 180 " pdb=" CA VAL B 180 " pdb=" CG1 VAL B 180 " pdb=" CG2 VAL B 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.42e-01 chirality pdb=" CA PRO A 298 " pdb=" N PRO A 298 " pdb=" C PRO A 298 " pdb=" CB PRO A 298 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE B 4 " pdb=" N ILE B 4 " pdb=" C ILE B 4 " pdb=" CB ILE B 4 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 1015 not shown) Planarity restraints: 1204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 267 " 0.061 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO B 268 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO B 268 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 268 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 297 " -0.060 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO A 298 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 298 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 298 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 358 " -0.051 5.00e-02 4.00e+02 7.83e-02 9.82e+00 pdb=" N PRO A 359 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 359 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 359 " -0.043 5.00e-02 4.00e+02 ... (remaining 1201 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 58 2.62 - 3.19: 5879 3.19 - 3.76: 10305 3.76 - 4.33: 14891 4.33 - 4.90: 24872 Nonbonded interactions: 56005 Sorted by model distance: nonbonded pdb=" O2B GTP A 501 " pdb="MG MG A 502 " model vdw 2.056 2.170 nonbonded pdb=" O TYR A 399 " pdb=" NH1 ARG A 402 " model vdw 2.188 3.120 nonbonded pdb=" OG SER A 48 " pdb=" O ARG A 243 " model vdw 2.235 3.040 nonbonded pdb=" O MET B 233 " pdb=" OG1 THR B 237 " model vdw 2.245 3.040 nonbonded pdb=" OG SER A 140 " pdb=" O1A GTP A 501 " model vdw 2.280 3.040 ... (remaining 56000 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.990 Find NCS groups from input model: 0.030 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 6831 Z= 0.148 Angle : 0.580 13.007 9278 Z= 0.312 Chirality : 0.043 0.172 1018 Planarity : 0.006 0.093 1204 Dihedral : 15.454 160.357 2497 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: 0.02 (0.29), residues: 832 helix: 0.26 (0.27), residues: 368 sheet: 0.50 (0.46), residues: 125 loop : -0.28 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 62 TYR 0.035 0.002 TYR A 24 PHE 0.010 0.001 PHE B 92 TRP 0.007 0.001 TRP B 101 HIS 0.009 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6831) covalent geometry : angle 0.57969 ( 9278) hydrogen bonds : bond 0.18451 ( 316) hydrogen bonds : angle 6.95718 ( 909) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.307 Fit side-chains REVERT: A 203 MET cc_start: 0.7108 (ttm) cc_final: 0.6863 (ttp) REVERT: A 433 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7206 (mt-10) REVERT: B 48 ASN cc_start: 0.6876 (p0) cc_final: 0.6655 (p0) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0751 time to fit residues: 13.2685 Evaluate side-chains 98 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 396 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.213735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.193118 restraints weight = 6800.743| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 1.47 r_work: 0.4186 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4056 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6831 Z= 0.150 Angle : 0.551 7.100 9278 Z= 0.284 Chirality : 0.043 0.210 1018 Planarity : 0.005 0.069 1204 Dihedral : 9.993 161.306 937 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.81 % Allowed : 5.58 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: 0.59 (0.29), residues: 832 helix: 1.00 (0.27), residues: 358 sheet: 0.73 (0.45), residues: 125 loop : -0.29 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 62 TYR 0.026 0.002 TYR A 24 PHE 0.010 0.001 PHE A 418 TRP 0.006 0.001 TRP B 344 HIS 0.008 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6831) covalent geometry : angle 0.55118 ( 9278) hydrogen bonds : bond 0.04796 ( 316) hydrogen bonds : angle 4.81711 ( 909) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.293 Fit side-chains REVERT: A 322 ASP cc_start: 0.6442 (t0) cc_final: 0.6239 (t0) REVERT: A 430 LYS cc_start: 0.6947 (tttm) cc_final: 0.6637 (ttpp) REVERT: A 433 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7287 (mt-10) REVERT: B 48 ASN cc_start: 0.7369 (p0) cc_final: 0.7145 (p0) REVERT: B 161 ASP cc_start: 0.6954 (m-30) cc_final: 0.6434 (p0) outliers start: 13 outliers final: 10 residues processed: 121 average time/residue: 0.0821 time to fit residues: 13.4997 Evaluate side-chains 122 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 414 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 64 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 0.1980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN B 6 HIS B 99 ASN B 134 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.213184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.192409 restraints weight = 6687.201| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 1.47 r_work: 0.4184 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4055 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6831 Z= 0.147 Angle : 0.542 7.363 9278 Z= 0.277 Chirality : 0.043 0.210 1018 Planarity : 0.004 0.057 1204 Dihedral : 10.091 161.064 937 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.09 % Allowed : 7.67 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: 0.59 (0.29), residues: 832 helix: 1.03 (0.27), residues: 359 sheet: 0.70 (0.44), residues: 128 loop : -0.31 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 62 TYR 0.025 0.002 TYR A 24 PHE 0.011 0.001 PHE A 138 TRP 0.006 0.001 TRP B 344 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6831) covalent geometry : angle 0.54211 ( 9278) hydrogen bonds : bond 0.04210 ( 316) hydrogen bonds : angle 4.48723 ( 909) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.281 Fit side-chains REVERT: A 18 ASN cc_start: 0.7003 (m-40) cc_final: 0.6199 (m-40) REVERT: A 90 GLU cc_start: 0.7946 (pt0) cc_final: 0.7490 (tt0) REVERT: A 322 ASP cc_start: 0.6564 (t0) cc_final: 0.6327 (t0) REVERT: A 425 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7865 (mp) REVERT: A 430 LYS cc_start: 0.7038 (tttm) cc_final: 0.6682 (ttpp) REVERT: A 433 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7254 (mt-10) REVERT: B 161 ASP cc_start: 0.7017 (m-30) cc_final: 0.6440 (p0) REVERT: B 246 LEU cc_start: 0.7926 (tp) cc_final: 0.7662 (tp) REVERT: B 408 PHE cc_start: 0.7461 (m-80) cc_final: 0.7151 (m-80) outliers start: 15 outliers final: 10 residues processed: 123 average time/residue: 0.0702 time to fit residues: 12.0459 Evaluate side-chains 120 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 414 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 81 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 0.0570 chunk 3 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.214760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.193294 restraints weight = 6853.095| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 1.52 r_work: 0.4185 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4057 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6831 Z= 0.132 Angle : 0.517 7.172 9278 Z= 0.263 Chirality : 0.043 0.224 1018 Planarity : 0.004 0.051 1204 Dihedral : 10.109 160.229 937 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.37 % Allowed : 8.37 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: 0.66 (0.29), residues: 832 helix: 1.16 (0.28), residues: 358 sheet: 0.52 (0.44), residues: 131 loop : -0.27 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 229 TYR 0.022 0.001 TYR A 24 PHE 0.009 0.001 PHE A 138 TRP 0.006 0.001 TRP B 344 HIS 0.005 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6831) covalent geometry : angle 0.51715 ( 9278) hydrogen bonds : bond 0.03896 ( 316) hydrogen bonds : angle 4.32220 ( 909) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.264 Fit side-chains REVERT: A 18 ASN cc_start: 0.6991 (m-40) cc_final: 0.6305 (m-40) REVERT: A 90 GLU cc_start: 0.8009 (pt0) cc_final: 0.7564 (tt0) REVERT: A 322 ASP cc_start: 0.6505 (t0) cc_final: 0.6269 (t0) REVERT: A 425 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7900 (mp) REVERT: A 430 LYS cc_start: 0.7097 (tttm) cc_final: 0.6726 (ttpp) REVERT: B 408 PHE cc_start: 0.7402 (m-80) cc_final: 0.7103 (m-80) outliers start: 17 outliers final: 12 residues processed: 117 average time/residue: 0.0787 time to fit residues: 12.8851 Evaluate side-chains 120 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 414 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 40 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.214223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.192560 restraints weight = 6932.375| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 1.55 r_work: 0.4179 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4048 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 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 0.025 6831 Z= 0.132 Angle : 0.513 7.003 9278 Z= 0.262 Chirality : 0.043 0.225 1018 Planarity : 0.004 0.067 1204 Dihedral : 10.120 159.021 937 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.23 % Allowed : 10.46 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: 0.66 (0.29), residues: 832 helix: 1.20 (0.28), residues: 358 sheet: 0.50 (0.44), residues: 131 loop : -0.30 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 229 TYR 0.019 0.001 TYR A 24 PHE 0.008 0.001 PHE A 149 TRP 0.006 0.001 TRP B 344 HIS 0.004 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6831) covalent geometry : angle 0.51347 ( 9278) hydrogen bonds : bond 0.03847 ( 316) hydrogen bonds : angle 4.27968 ( 909) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.275 Fit side-chains REVERT: A 18 ASN cc_start: 0.6992 (m-40) cc_final: 0.6294 (m-40) REVERT: A 90 GLU cc_start: 0.8007 (pt0) cc_final: 0.7570 (tt0) REVERT: A 322 ASP cc_start: 0.6551 (t0) cc_final: 0.6293 (t0) REVERT: A 425 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7889 (mp) REVERT: A 430 LYS cc_start: 0.7096 (tttm) cc_final: 0.6718 (ttpp) REVERT: B 408 PHE cc_start: 0.7470 (m-80) cc_final: 0.7168 (m-80) REVERT: B 427 GLU cc_start: 0.5771 (mm-30) cc_final: 0.4735 (mm-30) outliers start: 16 outliers final: 12 residues processed: 115 average time/residue: 0.0782 time to fit residues: 12.4154 Evaluate side-chains 120 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 414 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 22 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 0.0040 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 48 optimal weight: 0.0060 chunk 58 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.1612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.216833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.195706 restraints weight = 6863.307| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 1.50 r_work: 0.4204 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4073 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6831 Z= 0.111 Angle : 0.488 6.377 9278 Z= 0.248 Chirality : 0.042 0.215 1018 Planarity : 0.004 0.065 1204 Dihedral : 10.009 159.301 937 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.23 % Allowed : 10.60 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: 0.79 (0.29), residues: 832 helix: 1.32 (0.28), residues: 357 sheet: 0.53 (0.44), residues: 131 loop : -0.23 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 229 TYR 0.016 0.001 TYR A 24 PHE 0.008 0.001 PHE A 149 TRP 0.007 0.001 TRP B 344 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6831) covalent geometry : angle 0.48765 ( 9278) hydrogen bonds : bond 0.03540 ( 316) hydrogen bonds : angle 4.16702 ( 909) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.253 Fit side-chains REVERT: A 18 ASN cc_start: 0.6879 (m-40) cc_final: 0.6168 (m-40) REVERT: A 90 GLU cc_start: 0.7982 (pt0) cc_final: 0.7542 (tt0) REVERT: A 322 ASP cc_start: 0.6554 (t0) cc_final: 0.6315 (t0) REVERT: A 425 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7867 (mp) REVERT: A 430 LYS cc_start: 0.7097 (tttm) cc_final: 0.6649 (ttpp) REVERT: B 408 PHE cc_start: 0.7403 (m-80) cc_final: 0.7155 (m-80) outliers start: 16 outliers final: 13 residues processed: 119 average time/residue: 0.0741 time to fit residues: 12.3597 Evaluate side-chains 116 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 414 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 53 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.217108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.195875 restraints weight = 6819.952| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 1.51 r_work: 0.4212 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4079 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6831 Z= 0.100 Angle : 0.476 6.599 9278 Z= 0.242 Chirality : 0.041 0.195 1018 Planarity : 0.004 0.067 1204 Dihedral : 9.935 158.778 937 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.23 % Allowed : 11.58 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: 0.89 (0.29), residues: 832 helix: 1.45 (0.28), residues: 357 sheet: 0.59 (0.44), residues: 131 loop : -0.24 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 229 TYR 0.025 0.001 TYR A 24 PHE 0.008 0.001 PHE A 149 TRP 0.007 0.001 TRP B 344 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 6831) covalent geometry : angle 0.47586 ( 9278) hydrogen bonds : bond 0.03376 ( 316) hydrogen bonds : angle 4.08649 ( 909) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.295 Fit side-chains REVERT: A 18 ASN cc_start: 0.6802 (m-40) cc_final: 0.5990 (m-40) REVERT: A 90 GLU cc_start: 0.7990 (pt0) cc_final: 0.7544 (tt0) REVERT: A 322 ASP cc_start: 0.6573 (t0) cc_final: 0.6318 (t0) REVERT: A 425 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7852 (mp) REVERT: A 430 LYS cc_start: 0.7102 (tttm) cc_final: 0.6686 (ttpp) REVERT: A 433 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7055 (mp0) outliers start: 16 outliers final: 12 residues processed: 121 average time/residue: 0.0718 time to fit residues: 12.2458 Evaluate side-chains 118 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 414 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 29 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 11 optimal weight: 0.0370 chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 0.0060 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 overall best weight: 0.4674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.219818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.198672 restraints weight = 6870.168| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 1.51 r_work: 0.4246 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4111 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6831 Z= 0.089 Angle : 0.463 6.497 9278 Z= 0.235 Chirality : 0.040 0.188 1018 Planarity : 0.004 0.068 1204 Dihedral : 9.892 158.486 937 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.95 % Allowed : 12.69 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: 1.02 (0.29), residues: 832 helix: 1.62 (0.28), residues: 357 sheet: 0.40 (0.44), residues: 138 loop : -0.15 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 229 TYR 0.012 0.001 TYR A 24 PHE 0.010 0.001 PHE A 138 TRP 0.007 0.001 TRP B 344 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 6831) covalent geometry : angle 0.46324 ( 9278) hydrogen bonds : bond 0.03105 ( 316) hydrogen bonds : angle 4.01171 ( 909) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.233 Fit side-chains REVERT: A 18 ASN cc_start: 0.6674 (m-40) cc_final: 0.5837 (m-40) REVERT: A 90 GLU cc_start: 0.7980 (pt0) cc_final: 0.7545 (tt0) REVERT: A 425 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7803 (mp) REVERT: A 433 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7012 (mp0) outliers start: 14 outliers final: 9 residues processed: 118 average time/residue: 0.0734 time to fit residues: 12.0148 Evaluate side-chains 118 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 415 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 8.9990 chunk 7 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 16 optimal weight: 0.0030 chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.218093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.196693 restraints weight = 6827.826| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 1.52 r_work: 0.4219 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4085 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6831 Z= 0.107 Angle : 0.486 6.735 9278 Z= 0.246 Chirality : 0.041 0.188 1018 Planarity : 0.004 0.068 1204 Dihedral : 9.881 158.581 937 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.81 % Allowed : 13.39 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: 1.01 (0.29), residues: 832 helix: 1.60 (0.28), residues: 356 sheet: 0.69 (0.44), residues: 131 loop : -0.26 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 229 TYR 0.013 0.001 TYR A 210 PHE 0.009 0.001 PHE B 92 TRP 0.007 0.001 TRP B 344 HIS 0.003 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 6831) covalent geometry : angle 0.48562 ( 9278) hydrogen bonds : bond 0.03316 ( 316) hydrogen bonds : angle 4.04240 ( 909) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 18 ASN cc_start: 0.6755 (m-40) cc_final: 0.5924 (m-40) REVERT: A 90 GLU cc_start: 0.7987 (pt0) cc_final: 0.7551 (tt0) REVERT: A 425 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7843 (mp) REVERT: A 433 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: B 116 VAL cc_start: 0.6929 (t) cc_final: 0.6306 (m) outliers start: 13 outliers final: 10 residues processed: 115 average time/residue: 0.0763 time to fit residues: 12.1383 Evaluate side-chains 115 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 414 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.217357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.195891 restraints weight = 6891.591| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 1.52 r_work: 0.4219 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4086 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6831 Z= 0.113 Angle : 0.493 6.715 9278 Z= 0.250 Chirality : 0.042 0.183 1018 Planarity : 0.004 0.069 1204 Dihedral : 9.883 158.507 937 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.67 % Allowed : 13.53 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: 0.96 (0.29), residues: 832 helix: 1.56 (0.28), residues: 356 sheet: 0.62 (0.44), residues: 131 loop : -0.26 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 123 TYR 0.014 0.001 TYR A 210 PHE 0.009 0.001 PHE B 92 TRP 0.007 0.001 TRP B 344 HIS 0.003 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6831) covalent geometry : angle 0.49333 ( 9278) hydrogen bonds : bond 0.03393 ( 316) hydrogen bonds : angle 4.04431 ( 909) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 18 ASN cc_start: 0.6843 (m-40) cc_final: 0.6008 (m-40) REVERT: A 90 GLU cc_start: 0.7991 (pt0) cc_final: 0.7560 (tt0) REVERT: A 425 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7848 (mp) REVERT: A 433 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7012 (mp0) outliers start: 12 outliers final: 9 residues processed: 113 average time/residue: 0.0809 time to fit residues: 12.4916 Evaluate side-chains 116 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 414 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 0.0470 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.216539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.195720 restraints weight = 6752.748| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 1.47 r_work: 0.4218 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4088 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6831 Z= 0.106 Angle : 0.490 6.745 9278 Z= 0.247 Chirality : 0.041 0.183 1018 Planarity : 0.004 0.070 1204 Dihedral : 9.845 158.349 937 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.53 % Allowed : 13.67 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: 0.95 (0.29), residues: 832 helix: 1.58 (0.28), residues: 356 sheet: 0.59 (0.44), residues: 131 loop : -0.29 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 229 TYR 0.013 0.001 TYR A 210 PHE 0.009 0.001 PHE B 92 TRP 0.006 0.001 TRP B 344 HIS 0.003 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6831) covalent geometry : angle 0.49047 ( 9278) hydrogen bonds : bond 0.03324 ( 316) hydrogen bonds : angle 4.03865 ( 909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1877.26 seconds wall clock time: 32 minutes 55.90 seconds (1975.90 seconds total)