Starting phenix.real_space_refine on Wed Sep 17 08:10:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gqy_51514/09_2025/9gqy_51514.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gqy_51514/09_2025/9gqy_51514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gqy_51514/09_2025/9gqy_51514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gqy_51514/09_2025/9gqy_51514.map" model { file = "/net/cci-nas-00/data/ceres_data/9gqy_51514/09_2025/9gqy_51514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gqy_51514/09_2025/9gqy_51514.cif" } resolution = 2.8 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= 0.002 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 22 5.16 5 C 4452 2.51 5 N 1249 2.21 5 O 1325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7056 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3421 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 20, 'TRANS': 421} Chain breaks: 1 Chain: "C" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3431 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 20, 'TRANS': 422} Chain breaks: 1 Chain: "B" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'FAD': 1, 'NAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'FAD': 1, 'NAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 1.82, per 1000 atoms: 0.26 Number of scatterers: 7056 At special positions: 0 Unit cell: (84.18, 84.18, 115.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 8 15.00 O 1325 8.00 N 1249 7.00 C 4452 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: 0.60 Conformation dependent library (CDL) restraints added in 374.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 18 sheets defined 30.4% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'B' and resid 140 through 154 Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.594A pdb=" N PHE B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 182' Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 267 through 273 Processing helix chain 'B' and resid 274 through 280 Processing helix chain 'B' and resid 286 through 300 Processing helix chain 'B' and resid 309 through 327 removed outlier: 3.620A pdb=" N SER B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.601A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 469 Processing helix chain 'B' and resid 584 through 594 removed outlier: 3.593A pdb=" N ALA B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 154 Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 186 through 191 removed outlier: 3.589A pdb=" N THR C 190 " --> pdb=" O ASN C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 267 through 273 Processing helix chain 'C' and resid 274 through 280 Processing helix chain 'C' and resid 286 through 300 Processing helix chain 'C' and resid 309 through 327 removed outlier: 4.312A pdb=" N ALA C 325 " --> pdb=" O ARG C 321 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU C 326 " --> pdb=" O LYS C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 358 Processing helix chain 'C' and resid 404 through 411 removed outlier: 4.290A pdb=" N LYS C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 470 removed outlier: 3.570A pdb=" N THR C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 595 removed outlier: 3.951A pdb=" N ALA C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 606 removed outlier: 3.756A pdb=" N LYS C 606 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 224 through 229 removed outlier: 6.405A pdb=" N VAL B 159 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU B 228 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 161 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 132 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU B 160 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE B 134 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL B 162 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU B 136 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N HIS B 131 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYR B 253 " --> pdb=" O HIS B 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 224 through 229 removed outlier: 6.405A pdb=" N VAL B 159 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU B 228 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 161 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 132 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU B 160 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE B 134 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL B 162 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU B 136 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N HIS B 131 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYR B 253 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 192 through 193 Processing sheet with id=AA4, first strand: chain 'B' and resid 262 through 264 Processing sheet with id=AA5, first strand: chain 'B' and resid 281 through 283 removed outlier: 6.010A pdb=" N THR B 282 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL B 330 " --> pdb=" O LYS B 362 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N MET B 364 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLN B 332 " --> pdb=" O MET B 364 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 369 through 375 Processing sheet with id=AA7, first strand: chain 'B' and resid 421 through 422 removed outlier: 6.323A pdb=" N PHE B 421 " --> pdb=" O CYS B 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 443 through 444 Processing sheet with id=AA9, first strand: chain 'B' and resid 481 through 486 removed outlier: 3.706A pdb=" N VAL B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 224 through 229 removed outlier: 6.428A pdb=" N VAL C 159 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU C 228 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE C 161 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL C 132 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU C 160 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE C 134 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL C 162 " --> pdb=" O PHE C 134 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU C 136 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N HIS C 131 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYR C 253 " --> pdb=" O HIS C 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 224 through 229 removed outlier: 6.428A pdb=" N VAL C 159 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU C 228 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE C 161 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL C 132 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU C 160 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE C 134 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL C 162 " --> pdb=" O PHE C 134 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU C 136 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N HIS C 131 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYR C 253 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE C 433 " --> pdb=" O ALA C 429 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 192 through 193 Processing sheet with id=AB4, first strand: chain 'C' and resid 262 through 264 Processing sheet with id=AB5, first strand: chain 'C' and resid 281 through 283 removed outlier: 6.309A pdb=" N THR C 282 " --> pdb=" O ALA C 396 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N SER C 302 " --> pdb=" O HIS C 393 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL C 395 " --> pdb=" O SER C 302 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N THR C 304 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL C 330 " --> pdb=" O LYS C 362 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N MET C 364 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN C 332 " --> pdb=" O MET C 364 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 369 through 375 Processing sheet with id=AB7, first strand: chain 'C' and resid 421 through 422 removed outlier: 6.499A pdb=" N PHE C 421 " --> pdb=" O CYS C 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 443 through 444 Processing sheet with id=AB9, first strand: chain 'C' and resid 481 through 486 removed outlier: 4.132A pdb=" N VAL C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR C 567 " --> pdb=" O VAL C 574 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE C 576 " --> pdb=" O ILE C 565 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE C 565 " --> pdb=" O ILE C 576 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU C 578 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY C 563 " --> pdb=" O LEU C 578 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 504 " --> pdb=" O ASP C 515 " (cutoff:3.500A) 270 hydrogen bonds defined for protein. 756 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: 1.08 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: 1.20 - 1.32: 1284 1.32 - 1.44: 1781 1.44 - 1.56: 4082 1.56 - 1.68: 16 1.68 - 1.81: 38 Bond restraints: 7201 Sorted by residual: bond pdb=" CB PRO B 173 " pdb=" CG PRO B 173 " ideal model delta sigma weight residual 1.492 1.440 0.052 5.00e-02 4.00e+02 1.09e+00 bond pdb=" CB PRO C 173 " pdb=" CG PRO C 173 " ideal model delta sigma weight residual 1.492 1.440 0.052 5.00e-02 4.00e+02 1.09e+00 bond pdb=" CA GLU B 453 " pdb=" CB GLU B 453 " ideal model delta sigma weight residual 1.531 1.501 0.030 3.12e-02 1.03e+03 9.23e-01 bond pdb=" CA ARG B 172 " pdb=" C ARG B 172 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.26e-02 6.30e+03 8.17e-01 bond pdb=" CB GLU C 294 " pdb=" CG GLU C 294 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.09e-01 ... (remaining 7196 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 9491 1.40 - 2.81: 223 2.81 - 4.21: 39 4.21 - 5.62: 11 5.62 - 7.02: 3 Bond angle restraints: 9767 Sorted by residual: angle pdb=" N ARG B 172 " pdb=" CA ARG B 172 " pdb=" C ARG B 172 " ideal model delta sigma weight residual 109.81 116.83 -7.02 2.21e+00 2.05e-01 1.01e+01 angle pdb=" N PRO B 173 " pdb=" CA PRO B 173 " pdb=" C PRO B 173 " ideal model delta sigma weight residual 110.70 114.13 -3.43 1.22e+00 6.72e-01 7.89e+00 angle pdb=" N ARG C 172 " pdb=" CA ARG C 172 " pdb=" C ARG C 172 " ideal model delta sigma weight residual 109.81 115.67 -5.86 2.21e+00 2.05e-01 7.03e+00 angle pdb=" C GLU C 221 " pdb=" N ASN C 222 " pdb=" CA ASN C 222 " ideal model delta sigma weight residual 121.54 126.40 -4.86 1.91e+00 2.74e-01 6.47e+00 angle pdb=" N PRO C 173 " pdb=" CA PRO C 173 " pdb=" C PRO C 173 " ideal model delta sigma weight residual 110.70 113.77 -3.07 1.22e+00 6.72e-01 6.34e+00 ... (remaining 9762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 3945 17.07 - 34.15: 343 34.15 - 51.22: 84 51.22 - 68.29: 25 68.29 - 85.36: 4 Dihedral angle restraints: 4401 sinusoidal: 1902 harmonic: 2499 Sorted by residual: dihedral pdb=" CA LEU C 283 " pdb=" C LEU C 283 " pdb=" N PHE C 284 " pdb=" CA PHE C 284 " ideal model delta harmonic sigma weight residual -180.00 -162.86 -17.14 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA LYS C 177 " pdb=" C LYS C 177 " pdb=" N GLU C 178 " pdb=" CA GLU C 178 " ideal model delta harmonic sigma weight residual -180.00 -163.36 -16.64 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ARG B 450 " pdb=" C ARG B 450 " pdb=" N ARG B 451 " pdb=" CA ARG B 451 " ideal model delta harmonic sigma weight residual 180.00 163.60 16.40 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 4398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 537 0.027 - 0.053: 322 0.053 - 0.080: 89 0.080 - 0.106: 83 0.106 - 0.133: 44 Chirality restraints: 1075 Sorted by residual: chirality pdb=" CA ARG B 172 " pdb=" N ARG B 172 " pdb=" C ARG B 172 " pdb=" CB ARG B 172 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL C 564 " pdb=" N VAL C 564 " pdb=" C VAL C 564 " pdb=" CB VAL C 564 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE C 495 " pdb=" N ILE C 495 " pdb=" C ILE C 495 " pdb=" CB ILE C 495 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 1072 not shown) Planarity restraints: 1234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 173 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO C 174 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 174 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 174 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 334 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO B 335 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 335 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 335 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 172 " -0.023 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO C 173 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 173 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 173 " -0.019 5.00e-02 4.00e+02 ... (remaining 1231 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 52 2.62 - 3.19: 5829 3.19 - 3.76: 10433 3.76 - 4.33: 15393 4.33 - 4.90: 25531 Nonbonded interactions: 57238 Sorted by model distance: nonbonded pdb=" OE2 GLU B 336 " pdb=" O2B NAD B 702 " model vdw 2.053 3.040 nonbonded pdb=" O TYR B 170 " pdb=" O HOH B 801 " model vdw 2.098 3.040 nonbonded pdb=" O1A NAD B 702 " pdb=" O HOH B 802 " model vdw 2.177 3.040 nonbonded pdb=" O HOH B 801 " pdb=" O HOH B 805 " model vdw 2.220 3.040 nonbonded pdb=" O PRO C 345 " pdb=" OG SER C 349 " model vdw 2.240 3.040 ... (remaining 57233 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 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 128 through 610 or resid 701 through 702)) } 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: 7.250 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: 0.360 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.270 Find NCS groups from input model: 0.110 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:7.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 0.052 7201 Z= 0.184 Angle : 0.572 7.022 9767 Z= 0.300 Chirality : 0.046 0.133 1075 Planarity : 0.005 0.043 1234 Dihedral : 14.181 85.362 2803 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.14 % Allowed : 17.10 % Favored : 82.76 % 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: -0.33 (0.28), residues: 877 helix: 1.43 (0.35), residues: 212 sheet: -0.30 (0.36), residues: 220 loop : -0.97 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 449 TYR 0.009 0.002 TYR B 347 PHE 0.019 0.002 PHE B 310 TRP 0.014 0.002 TRP C 196 HIS 0.005 0.001 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 7201) covalent geometry : angle 0.57211 ( 9767) hydrogen bonds : bond 0.18407 ( 262) hydrogen bonds : angle 7.33837 ( 756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 560 TYR cc_start: 0.8720 (m-80) cc_final: 0.8519 (m-80) outliers start: 1 outliers final: 1 residues processed: 134 average time/residue: 0.6462 time to fit residues: 90.5156 Evaluate side-chains 78 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 514 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 GLN B 366 ASN C 222 ASN C 366 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.096021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.069288 restraints weight = 14786.589| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.61 r_work: 0.2827 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7201 Z= 0.173 Angle : 0.592 9.159 9767 Z= 0.307 Chirality : 0.045 0.175 1075 Planarity : 0.004 0.038 1234 Dihedral : 6.912 53.141 1164 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.72 % Allowed : 19.31 % Favored : 76.97 % 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: -0.16 (0.29), residues: 877 helix: 1.86 (0.36), residues: 213 sheet: -0.20 (0.37), residues: 210 loop : -1.03 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 358 TYR 0.009 0.001 TYR B 347 PHE 0.011 0.001 PHE C 482 TRP 0.011 0.001 TRP C 196 HIS 0.003 0.001 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 7201) covalent geometry : angle 0.59243 ( 9767) hydrogen bonds : bond 0.04027 ( 262) hydrogen bonds : angle 5.28285 ( 756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 199 LYS cc_start: 0.9455 (mmpt) cc_final: 0.9159 (mmpt) REVERT: B 220 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8857 (mt) REVERT: B 299 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8343 (tm-30) REVERT: B 384 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8771 (pmtt) REVERT: B 499 ASP cc_start: 0.8450 (t0) cc_final: 0.8209 (t0) REVERT: C 195 GLN cc_start: 0.9043 (mt0) cc_final: 0.8666 (mp10) REVERT: C 216 ASP cc_start: 0.8867 (t0) cc_final: 0.8599 (t0) REVERT: C 250 GLN cc_start: 0.9096 (mt0) cc_final: 0.8677 (mt0) REVERT: C 336 GLU cc_start: 0.8019 (mp0) cc_final: 0.7666 (mp0) REVERT: C 370 GLN cc_start: 0.9100 (tm-30) cc_final: 0.8886 (tm-30) REVERT: C 384 LYS cc_start: 0.8732 (tppt) cc_final: 0.8278 (mppt) REVERT: C 390 GLU cc_start: 0.9348 (pt0) cc_final: 0.8806 (pp20) REVERT: C 408 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8752 (tmmm) REVERT: C 493 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8388 (pt0) REVERT: C 560 TYR cc_start: 0.8833 (m-80) cc_final: 0.8510 (m-80) REVERT: C 581 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8761 (pp) REVERT: C 597 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8521 (mm-40) REVERT: C 606 LYS cc_start: 0.8811 (pttm) cc_final: 0.8600 (pttt) outliers start: 27 outliers final: 6 residues processed: 108 average time/residue: 0.6501 time to fit residues: 73.5046 Evaluate side-chains 89 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain C residue 493 GLU Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 584 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 0.0670 chunk 36 optimal weight: 5.9990 chunk 85 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.097453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.071271 restraints weight = 14619.752| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.58 r_work: 0.2840 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7201 Z= 0.114 Angle : 0.546 8.974 9767 Z= 0.282 Chirality : 0.044 0.158 1075 Planarity : 0.004 0.036 1234 Dihedral : 6.391 50.962 1161 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.72 % Allowed : 19.45 % Favored : 76.83 % 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: 0.03 (0.29), residues: 877 helix: 2.11 (0.36), residues: 213 sheet: -0.08 (0.37), residues: 205 loop : -0.96 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 358 TYR 0.013 0.001 TYR B 492 PHE 0.011 0.001 PHE C 482 TRP 0.010 0.001 TRP C 196 HIS 0.003 0.001 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7201) covalent geometry : angle 0.54592 ( 9767) hydrogen bonds : bond 0.03317 ( 262) hydrogen bonds : angle 4.87539 ( 756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8800 (mt) REVERT: B 250 GLN cc_start: 0.9183 (mt0) cc_final: 0.8849 (mt0) REVERT: B 270 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8976 (pt) REVERT: B 278 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8578 (mppt) REVERT: B 299 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8347 (tm-30) REVERT: B 384 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8801 (pmtt) REVERT: B 499 ASP cc_start: 0.8414 (t0) cc_final: 0.8150 (t0) REVERT: C 195 GLN cc_start: 0.9075 (mt0) cc_final: 0.8704 (mp10) REVERT: C 216 ASP cc_start: 0.8906 (t0) cc_final: 0.8560 (t0) REVERT: C 336 GLU cc_start: 0.7951 (mp0) cc_final: 0.7565 (mp0) REVERT: C 390 GLU cc_start: 0.9328 (pt0) cc_final: 0.8804 (pp20) REVERT: C 499 ASP cc_start: 0.8062 (t0) cc_final: 0.7840 (t0) REVERT: C 560 TYR cc_start: 0.8774 (m-80) cc_final: 0.8469 (m-80) REVERT: C 597 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8353 (mm-40) REVERT: C 606 LYS cc_start: 0.8857 (pttm) cc_final: 0.8611 (pttt) outliers start: 27 outliers final: 7 residues processed: 106 average time/residue: 0.6498 time to fit residues: 72.3884 Evaluate side-chains 89 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 570 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 38 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.095466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.069257 restraints weight = 14938.156| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.59 r_work: 0.2784 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7201 Z= 0.159 Angle : 0.558 8.524 9767 Z= 0.288 Chirality : 0.045 0.155 1075 Planarity : 0.004 0.034 1234 Dihedral : 6.458 51.371 1161 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.62 % Allowed : 20.28 % Favored : 77.10 % 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: 0.08 (0.29), residues: 877 helix: 2.10 (0.36), residues: 213 sheet: -0.04 (0.37), residues: 205 loop : -0.90 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 358 TYR 0.009 0.001 TYR C 347 PHE 0.012 0.001 PHE C 310 TRP 0.010 0.001 TRP C 196 HIS 0.003 0.001 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 7201) covalent geometry : angle 0.55820 ( 9767) hydrogen bonds : bond 0.03570 ( 262) hydrogen bonds : angle 4.79301 ( 756) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8832 (mt) REVERT: B 250 GLN cc_start: 0.9195 (mt0) cc_final: 0.8890 (mt0) REVERT: B 270 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.9000 (pt) REVERT: B 278 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8618 (mppt) REVERT: B 299 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8391 (tm-30) REVERT: B 370 GLN cc_start: 0.8851 (mt0) cc_final: 0.8428 (mt0) REVERT: B 384 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8794 (pmtt) REVERT: B 390 GLU cc_start: 0.8982 (pm20) cc_final: 0.8530 (tp30) REVERT: B 499 ASP cc_start: 0.8447 (t0) cc_final: 0.8215 (t0) REVERT: C 195 GLN cc_start: 0.9112 (mt0) cc_final: 0.8765 (mp10) REVERT: C 216 ASP cc_start: 0.8994 (t0) cc_final: 0.8507 (t0) REVERT: C 336 GLU cc_start: 0.8036 (mp0) cc_final: 0.7771 (mp0) REVERT: C 390 GLU cc_start: 0.9323 (pt0) cc_final: 0.9113 (pm20) REVERT: C 499 ASP cc_start: 0.8141 (t0) cc_final: 0.7906 (t0) REVERT: C 560 TYR cc_start: 0.8854 (m-80) cc_final: 0.8534 (m-80) REVERT: C 584 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7812 (mpp-170) REVERT: C 597 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8388 (mm-40) REVERT: C 606 LYS cc_start: 0.8889 (pttm) cc_final: 0.8675 (pttt) outliers start: 19 outliers final: 11 residues processed: 96 average time/residue: 0.6650 time to fit residues: 67.0448 Evaluate side-chains 92 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 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 = 0.3479 r_free = 0.3479 target = 0.096880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.070763 restraints weight = 14687.130| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.57 r_work: 0.2827 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7201 Z= 0.113 Angle : 0.547 8.936 9767 Z= 0.282 Chirality : 0.044 0.149 1075 Planarity : 0.004 0.036 1234 Dihedral : 6.297 50.368 1161 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.62 % Allowed : 19.86 % Favored : 77.52 % 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: 0.16 (0.29), residues: 877 helix: 2.16 (0.36), residues: 213 sheet: -0.00 (0.37), residues: 207 loop : -0.84 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 358 TYR 0.006 0.001 TYR C 347 PHE 0.012 0.001 PHE B 508 TRP 0.009 0.001 TRP C 196 HIS 0.003 0.001 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7201) covalent geometry : angle 0.54661 ( 9767) hydrogen bonds : bond 0.03031 ( 262) hydrogen bonds : angle 4.61659 ( 756) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 167 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8171 (mt-10) REVERT: B 220 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8825 (mt) REVERT: B 250 GLN cc_start: 0.9236 (mt0) cc_final: 0.8916 (mt0) REVERT: B 278 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8634 (mppt) REVERT: B 299 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8383 (tm-30) REVERT: B 370 GLN cc_start: 0.8854 (mt0) cc_final: 0.8464 (mt0) REVERT: B 384 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8832 (pmtt) REVERT: B 401 GLU cc_start: 0.8190 (pt0) cc_final: 0.7213 (pp20) REVERT: B 408 LYS cc_start: 0.9506 (tppp) cc_final: 0.9249 (tmtt) REVERT: B 499 ASP cc_start: 0.8440 (t0) cc_final: 0.8200 (t0) REVERT: C 195 GLN cc_start: 0.9109 (mt0) cc_final: 0.8770 (mp10) REVERT: C 216 ASP cc_start: 0.8990 (t0) cc_final: 0.8502 (t0) REVERT: C 336 GLU cc_start: 0.7988 (mp0) cc_final: 0.7704 (mp0) REVERT: C 390 GLU cc_start: 0.9322 (pt0) cc_final: 0.9120 (pm20) REVERT: C 499 ASP cc_start: 0.8037 (t0) cc_final: 0.7549 (t0) REVERT: C 560 TYR cc_start: 0.8827 (m-80) cc_final: 0.8516 (m-80) REVERT: C 597 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8377 (mm-40) REVERT: C 606 LYS cc_start: 0.8907 (pttm) cc_final: 0.8687 (pttt) outliers start: 19 outliers final: 7 residues processed: 96 average time/residue: 0.6399 time to fit residues: 64.7088 Evaluate side-chains 85 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 584 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.096681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.070431 restraints weight = 14736.840| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.57 r_work: 0.2824 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7201 Z= 0.123 Angle : 0.536 8.870 9767 Z= 0.277 Chirality : 0.044 0.148 1075 Planarity : 0.004 0.036 1234 Dihedral : 6.287 50.961 1161 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.21 % Allowed : 20.97 % Favored : 76.83 % 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: 0.16 (0.29), residues: 877 helix: 2.10 (0.36), residues: 213 sheet: 0.01 (0.37), residues: 207 loop : -0.81 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 358 TYR 0.015 0.001 TYR B 492 PHE 0.015 0.001 PHE B 508 TRP 0.009 0.001 TRP C 196 HIS 0.003 0.001 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7201) covalent geometry : angle 0.53607 ( 9767) hydrogen bonds : bond 0.03152 ( 262) hydrogen bonds : angle 4.66247 ( 756) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 167 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8170 (mt-10) REVERT: B 220 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8794 (mt) REVERT: B 250 GLN cc_start: 0.9265 (mt0) cc_final: 0.8944 (mt0) REVERT: B 278 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8666 (mppt) REVERT: B 299 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8392 (tm-30) REVERT: B 370 GLN cc_start: 0.8851 (mt0) cc_final: 0.8494 (mt0) REVERT: B 384 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8863 (pmtt) REVERT: B 401 GLU cc_start: 0.8239 (pt0) cc_final: 0.7294 (pp20) REVERT: B 408 LYS cc_start: 0.9528 (tppp) cc_final: 0.9262 (tmtt) REVERT: B 499 ASP cc_start: 0.8485 (t0) cc_final: 0.8242 (t0) REVERT: C 216 ASP cc_start: 0.9017 (t0) cc_final: 0.8455 (t0) REVERT: C 336 GLU cc_start: 0.8015 (mp0) cc_final: 0.7726 (mp0) REVERT: C 560 TYR cc_start: 0.8860 (m-80) cc_final: 0.8584 (m-80) REVERT: C 597 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8422 (mm-40) REVERT: C 606 LYS cc_start: 0.8924 (pttm) cc_final: 0.8699 (pttt) outliers start: 16 outliers final: 8 residues processed: 95 average time/residue: 0.6243 time to fit residues: 62.3749 Evaluate side-chains 86 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 584 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 8 optimal weight: 0.0070 chunk 68 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 ASN C 235 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.095129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.068886 restraints weight = 14771.560| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.54 r_work: 0.2787 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7201 Z= 0.178 Angle : 0.583 8.576 9767 Z= 0.301 Chirality : 0.045 0.149 1075 Planarity : 0.004 0.037 1234 Dihedral : 6.495 51.944 1161 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.34 % Allowed : 20.28 % Favored : 77.38 % 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: 0.07 (0.29), residues: 877 helix: 1.99 (0.36), residues: 212 sheet: -0.01 (0.37), residues: 205 loop : -0.86 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 358 TYR 0.010 0.001 TYR C 347 PHE 0.019 0.001 PHE B 508 TRP 0.015 0.001 TRP C 196 HIS 0.003 0.001 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 7201) covalent geometry : angle 0.58333 ( 9767) hydrogen bonds : bond 0.03597 ( 262) hydrogen bonds : angle 4.80076 ( 756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 165 ASP cc_start: 0.8437 (t70) cc_final: 0.8234 (t0) REVERT: B 167 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8119 (mt-10) REVERT: B 220 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8766 (mt) REVERT: B 250 GLN cc_start: 0.9288 (mt0) cc_final: 0.8960 (mt0) REVERT: B 278 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8696 (mppt) REVERT: B 299 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8415 (tm-30) REVERT: B 370 GLN cc_start: 0.8843 (mt0) cc_final: 0.8510 (mt0) REVERT: B 384 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8847 (pmtt) REVERT: B 401 GLU cc_start: 0.8291 (pt0) cc_final: 0.7395 (pp20) REVERT: B 499 ASP cc_start: 0.8516 (t0) cc_final: 0.8287 (t0) REVERT: C 194 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8640 (mmmm) REVERT: C 216 ASP cc_start: 0.9038 (t0) cc_final: 0.8411 (t0) REVERT: C 560 TYR cc_start: 0.8880 (m-80) cc_final: 0.8592 (m-80) REVERT: C 597 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8479 (mm-40) REVERT: C 606 LYS cc_start: 0.8931 (pttm) cc_final: 0.8678 (pttt) outliers start: 17 outliers final: 9 residues processed: 92 average time/residue: 0.5850 time to fit residues: 56.6555 Evaluate side-chains 82 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 42 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 75 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 ASN B 332 GLN C 235 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.092510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.066243 restraints weight = 15001.194| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.52 r_work: 0.2740 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 7201 Z= 0.309 Angle : 0.675 7.867 9767 Z= 0.347 Chirality : 0.047 0.163 1075 Planarity : 0.005 0.043 1234 Dihedral : 7.186 59.948 1161 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.03 % Allowed : 20.83 % Favored : 76.14 % 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: -0.15 (0.29), residues: 877 helix: 1.69 (0.36), residues: 212 sheet: -0.24 (0.36), residues: 215 loop : -0.88 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 358 TYR 0.013 0.001 TYR C 347 PHE 0.021 0.002 PHE B 508 TRP 0.018 0.001 TRP C 196 HIS 0.003 0.001 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00727 ( 7201) covalent geometry : angle 0.67522 ( 9767) hydrogen bonds : bond 0.04403 ( 262) hydrogen bonds : angle 5.07130 ( 756) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 167 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8099 (mt-10) REVERT: B 220 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8695 (mt) REVERT: B 221 GLU cc_start: 0.9091 (tp30) cc_final: 0.8796 (tm-30) REVERT: B 250 GLN cc_start: 0.9302 (mt0) cc_final: 0.8986 (mt0) REVERT: B 370 GLN cc_start: 0.8850 (mt0) cc_final: 0.8529 (mt0) REVERT: B 401 GLU cc_start: 0.8366 (pt0) cc_final: 0.7485 (pp20) REVERT: B 499 ASP cc_start: 0.8516 (t0) cc_final: 0.8258 (t0) REVERT: B 571 LYS cc_start: 0.8503 (mmtm) cc_final: 0.7866 (mmmm) REVERT: C 221 GLU cc_start: 0.9211 (tp30) cc_final: 0.8915 (tp30) REVERT: C 336 GLU cc_start: 0.8012 (mp0) cc_final: 0.7763 (mp0) REVERT: C 493 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8387 (pt0) REVERT: C 560 TYR cc_start: 0.8964 (m-80) cc_final: 0.8599 (m-80) REVERT: C 597 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8548 (mm-40) REVERT: C 606 LYS cc_start: 0.8935 (pttm) cc_final: 0.8659 (pttt) outliers start: 22 outliers final: 10 residues processed: 91 average time/residue: 0.6188 time to fit residues: 59.0442 Evaluate side-chains 79 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 493 GLU Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 584 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 8 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.095945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.069583 restraints weight = 14714.035| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.57 r_work: 0.2800 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7201 Z= 0.130 Angle : 0.609 9.233 9767 Z= 0.311 Chirality : 0.045 0.156 1075 Planarity : 0.004 0.045 1234 Dihedral : 6.703 58.757 1161 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.52 % Allowed : 21.66 % Favored : 76.83 % 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: 0.05 (0.29), residues: 877 helix: 1.95 (0.36), residues: 212 sheet: -0.10 (0.36), residues: 215 loop : -0.83 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 358 TYR 0.008 0.001 TYR B 567 PHE 0.022 0.001 PHE B 508 TRP 0.011 0.001 TRP C 196 HIS 0.003 0.001 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7201) covalent geometry : angle 0.60917 ( 9767) hydrogen bonds : bond 0.03186 ( 262) hydrogen bonds : angle 4.73327 ( 756) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 167 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8170 (mt-10) REVERT: B 220 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8702 (mt) REVERT: B 221 GLU cc_start: 0.9060 (tp30) cc_final: 0.8762 (tm-30) REVERT: B 250 GLN cc_start: 0.9319 (mt0) cc_final: 0.8995 (mt0) REVERT: B 278 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8715 (mppt) REVERT: B 299 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8425 (tm-30) REVERT: B 370 GLN cc_start: 0.8857 (mt0) cc_final: 0.8545 (mt0) REVERT: B 401 GLU cc_start: 0.8323 (pt0) cc_final: 0.7451 (pp20) REVERT: B 499 ASP cc_start: 0.8515 (t0) cc_final: 0.8281 (t0) REVERT: C 221 GLU cc_start: 0.9201 (tp30) cc_final: 0.8874 (tp30) REVERT: C 336 GLU cc_start: 0.7962 (mp0) cc_final: 0.7624 (mp0) REVERT: C 337 LYS cc_start: 0.9164 (mmmm) cc_final: 0.8835 (mmmt) REVERT: C 560 TYR cc_start: 0.8894 (m-80) cc_final: 0.8550 (m-80) REVERT: C 597 GLN cc_start: 0.8993 (mm-40) cc_final: 0.8498 (mm-40) REVERT: C 606 LYS cc_start: 0.8958 (pttm) cc_final: 0.8720 (pttt) outliers start: 11 outliers final: 6 residues processed: 84 average time/residue: 0.6347 time to fit residues: 55.9576 Evaluate side-chains 82 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 584 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 24 optimal weight: 9.9990 chunk 65 optimal weight: 0.1980 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 235 GLN C 332 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.096181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.070048 restraints weight = 14715.499| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.57 r_work: 0.2825 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7201 Z= 0.124 Angle : 0.590 9.227 9767 Z= 0.303 Chirality : 0.044 0.180 1075 Planarity : 0.004 0.050 1234 Dihedral : 6.594 59.686 1161 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.10 % Allowed : 22.76 % Favored : 76.14 % 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: 0.14 (0.29), residues: 877 helix: 2.10 (0.36), residues: 212 sheet: 0.08 (0.37), residues: 205 loop : -0.87 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 358 TYR 0.007 0.001 TYR C 347 PHE 0.021 0.001 PHE B 508 TRP 0.008 0.001 TRP C 579 HIS 0.003 0.001 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7201) covalent geometry : angle 0.58974 ( 9767) hydrogen bonds : bond 0.03116 ( 262) hydrogen bonds : angle 4.59536 ( 756) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: B 167 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8137 (mt-10) REVERT: B 220 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8697 (mt) REVERT: B 221 GLU cc_start: 0.9046 (tp30) cc_final: 0.8756 (tm-30) REVERT: B 250 GLN cc_start: 0.9333 (mt0) cc_final: 0.9010 (mt0) REVERT: B 278 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8746 (mppt) REVERT: B 299 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8400 (tm-30) REVERT: B 370 GLN cc_start: 0.8832 (mt0) cc_final: 0.8512 (mt0) REVERT: B 401 GLU cc_start: 0.8300 (pt0) cc_final: 0.7536 (pp20) REVERT: B 499 ASP cc_start: 0.8515 (t0) cc_final: 0.8288 (t0) REVERT: C 221 GLU cc_start: 0.9211 (tp30) cc_final: 0.8891 (tp30) REVERT: C 336 GLU cc_start: 0.7943 (mp0) cc_final: 0.7625 (mp0) REVERT: C 337 LYS cc_start: 0.9160 (mmmm) cc_final: 0.8838 (mmmt) REVERT: C 560 TYR cc_start: 0.8855 (m-80) cc_final: 0.8530 (m-80) REVERT: C 597 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8499 (mm-40) REVERT: C 606 LYS cc_start: 0.8939 (pttm) cc_final: 0.8689 (pttt) outliers start: 8 outliers final: 7 residues processed: 86 average time/residue: 0.6313 time to fit residues: 57.0388 Evaluate side-chains 85 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 584 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.096344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.070200 restraints weight = 14601.906| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.57 r_work: 0.2817 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7201 Z= 0.123 Angle : 0.598 9.290 9767 Z= 0.307 Chirality : 0.044 0.195 1075 Planarity : 0.004 0.050 1234 Dihedral : 6.563 59.857 1161 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.10 % Allowed : 22.34 % Favored : 76.55 % 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: 0.17 (0.29), residues: 877 helix: 2.12 (0.37), residues: 212 sheet: 0.10 (0.37), residues: 205 loop : -0.85 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 358 TYR 0.008 0.001 TYR B 567 PHE 0.026 0.001 PHE B 508 TRP 0.008 0.001 TRP C 579 HIS 0.003 0.001 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7201) covalent geometry : angle 0.59846 ( 9767) hydrogen bonds : bond 0.03045 ( 262) hydrogen bonds : angle 4.56648 ( 756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2615.24 seconds wall clock time: 45 minutes 25.17 seconds (2725.17 seconds total)