Starting phenix.real_space_refine on Fri Jul 25 03:23:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gqy_51514/07_2025/9gqy_51514.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gqy_51514/07_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_51514/07_2025/9gqy_51514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gqy_51514/07_2025/9gqy_51514.map" model { file = "/net/cci-nas-00/data/ceres_data/9gqy_51514/07_2025/9gqy_51514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gqy_51514/07_2025/9gqy_51514.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.42, per 1000 atoms: 0.91 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: 1.91 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.07 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: 2.25 Time building geometry restraints manager: 2.21 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: 5.320 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: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.170 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.650 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.002 TRP C 196 HIS 0.005 0.001 HIS B 455 PHE 0.019 0.002 PHE B 310 TYR 0.009 0.002 TYR B 347 ARG 0.004 0.001 ARG C 449 Details of bonding type rmsd hydrogen bonds : bond 0.18407 ( 262) hydrogen bonds : angle 7.33837 ( 756) covalent geometry : bond 0.00447 ( 7201) covalent geometry : angle 0.57211 ( 9767) *********************** 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 : 0.830 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: 1.6551 time to fit residues: 232.6287 Evaluate side-chains 74 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 74 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 41 optimal weight: 0.0070 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 overall best weight: 0.9802 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.098033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.071309 restraints weight = 14456.746| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.59 r_work: 0.2852 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7201 Z= 0.127 Angle : 0.567 9.769 9767 Z= 0.293 Chirality : 0.045 0.165 1075 Planarity : 0.004 0.037 1234 Dihedral : 6.778 53.279 1164 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.62 % Allowed : 19.72 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.29), residues: 877 helix: 1.89 (0.36), residues: 213 sheet: -0.14 (0.37), residues: 210 loop : -0.96 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 196 HIS 0.002 0.000 HIS C 457 PHE 0.011 0.001 PHE C 482 TYR 0.008 0.001 TYR B 347 ARG 0.007 0.001 ARG C 358 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 262) hydrogen bonds : angle 5.20196 ( 756) covalent geometry : bond 0.00289 ( 7201) covalent geometry : angle 0.56674 ( 9767) *********************** 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: 19 poor density : 94 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 195 GLN cc_start: 0.7997 (pt0) cc_final: 0.7787 (pm20) REVERT: B 199 LYS cc_start: 0.9452 (mmpt) cc_final: 0.9205 (mmpt) REVERT: B 299 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8320 (tm-30) REVERT: B 384 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8814 (pmtt) REVERT: B 499 ASP cc_start: 0.8476 (t0) cc_final: 0.8220 (t0) REVERT: C 216 ASP cc_start: 0.8814 (t0) cc_final: 0.8570 (t0) REVERT: C 250 GLN cc_start: 0.9097 (mt0) cc_final: 0.8683 (mt0) REVERT: C 336 GLU cc_start: 0.8021 (mp0) cc_final: 0.7661 (mp0) REVERT: C 390 GLU cc_start: 0.9341 (pt0) cc_final: 0.8798 (pp20) REVERT: C 560 TYR cc_start: 0.8829 (m-80) cc_final: 0.8504 (m-80) REVERT: C 597 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8561 (mm-40) REVERT: C 606 LYS cc_start: 0.8797 (pttm) cc_final: 0.8589 (pttt) outliers start: 19 outliers final: 3 residues processed: 107 average time/residue: 1.4666 time to fit residues: 166.7954 Evaluate side-chains 81 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 570 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 54 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.093566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.067416 restraints weight = 14917.829| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.55 r_work: 0.2744 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 7201 Z= 0.259 Angle : 0.622 8.139 9767 Z= 0.321 Chirality : 0.047 0.171 1075 Planarity : 0.004 0.037 1234 Dihedral : 6.831 52.896 1161 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.00 % Allowed : 19.72 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.28), residues: 877 helix: 1.83 (0.36), residues: 213 sheet: -0.19 (0.36), residues: 210 loop : -1.01 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 196 HIS 0.004 0.001 HIS C 457 PHE 0.013 0.001 PHE C 310 TYR 0.014 0.001 TYR B 492 ARG 0.006 0.001 ARG B 358 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 262) hydrogen bonds : angle 5.15702 ( 756) covalent geometry : bond 0.00610 ( 7201) covalent geometry : angle 0.62247 ( 9767) *********************** 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 107 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 242 MET cc_start: 0.8436 (ttm) cc_final: 0.8231 (ttp) REVERT: B 250 GLN cc_start: 0.9220 (mt0) cc_final: 0.8914 (mt0) REVERT: B 299 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8360 (tm-30) REVERT: B 370 GLN cc_start: 0.8820 (mt0) cc_final: 0.8457 (mt0) REVERT: B 384 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8708 (pmtt) REVERT: B 499 ASP cc_start: 0.8445 (t0) cc_final: 0.8227 (t0) REVERT: C 195 GLN cc_start: 0.9073 (mt0) cc_final: 0.8623 (mp10) REVERT: C 216 ASP cc_start: 0.8978 (t0) cc_final: 0.8526 (t0) REVERT: C 336 GLU cc_start: 0.8056 (mp0) cc_final: 0.7807 (mp0) REVERT: C 493 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8415 (pt0) REVERT: C 499 ASP cc_start: 0.8264 (t0) cc_final: 0.8028 (t0) REVERT: C 560 TYR cc_start: 0.8865 (m-80) cc_final: 0.8542 (m-80) REVERT: C 597 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8346 (mm-40) REVERT: C 606 LYS cc_start: 0.8874 (pttm) cc_final: 0.8672 (pttt) outliers start: 29 outliers final: 11 residues processed: 100 average time/residue: 1.4316 time to fit residues: 150.2284 Evaluate side-chains 87 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 THR 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 188 THR 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 493 GLU Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 584 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 28 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.096077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.069662 restraints weight = 14677.556| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.57 r_work: 0.2792 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7201 Z= 0.131 Angle : 0.557 8.911 9767 Z= 0.287 Chirality : 0.045 0.154 1075 Planarity : 0.004 0.034 1234 Dihedral : 6.493 50.549 1161 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.34 % Allowed : 20.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.29), residues: 877 helix: 1.91 (0.36), residues: 213 sheet: -0.08 (0.37), residues: 210 loop : -0.87 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 196 HIS 0.003 0.001 HIS C 457 PHE 0.012 0.001 PHE C 482 TYR 0.014 0.001 TYR B 492 ARG 0.006 0.000 ARG B 358 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 262) hydrogen bonds : angle 4.89335 ( 756) covalent geometry : bond 0.00307 ( 7201) covalent geometry : angle 0.55662 ( 9767) *********************** 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 96 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 167 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8170 (mt-10) REVERT: B 242 MET cc_start: 0.8401 (ttm) cc_final: 0.8157 (ttp) REVERT: B 250 GLN cc_start: 0.9224 (mt0) cc_final: 0.8896 (mt0) REVERT: B 278 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8578 (mppt) REVERT: B 299 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8360 (tm-30) REVERT: B 370 GLN cc_start: 0.8852 (mt0) cc_final: 0.8517 (mt0) REVERT: B 384 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8787 (pmtt) REVERT: B 408 LYS cc_start: 0.9512 (tppp) cc_final: 0.9251 (tmtt) REVERT: B 499 ASP cc_start: 0.8435 (t0) cc_final: 0.8211 (t0) REVERT: C 216 ASP cc_start: 0.9012 (t0) cc_final: 0.8513 (t0) REVERT: C 336 GLU cc_start: 0.8016 (mp0) cc_final: 0.7756 (mp0) REVERT: C 499 ASP cc_start: 0.8195 (t0) cc_final: 0.7930 (t0) REVERT: C 560 TYR cc_start: 0.8833 (m-80) cc_final: 0.8526 (m-80) REVERT: C 596 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8788 (mm-30) REVERT: C 597 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8311 (mm-40) REVERT: C 606 LYS cc_start: 0.8898 (pttm) cc_final: 0.8688 (pttt) outliers start: 17 outliers final: 10 residues processed: 95 average time/residue: 1.2551 time to fit residues: 125.8131 Evaluate side-chains 85 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 THR 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 148 ARG Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 266 SER 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 24 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.093797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.067539 restraints weight = 14575.928| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.52 r_work: 0.2750 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7201 Z= 0.214 Angle : 0.588 8.311 9767 Z= 0.306 Chirality : 0.045 0.154 1075 Planarity : 0.004 0.033 1234 Dihedral : 6.650 51.025 1161 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.17 % Allowed : 19.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.29), residues: 877 helix: 1.82 (0.36), residues: 213 sheet: -0.06 (0.37), residues: 210 loop : -0.92 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 196 HIS 0.004 0.001 HIS C 457 PHE 0.013 0.001 PHE B 508 TYR 0.016 0.001 TYR B 492 ARG 0.006 0.000 ARG B 358 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 262) hydrogen bonds : angle 4.95680 ( 756) covalent geometry : bond 0.00506 ( 7201) covalent geometry : angle 0.58829 ( 9767) *********************** 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 99 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 167 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8154 (mt-10) REVERT: B 242 MET cc_start: 0.8440 (ttm) cc_final: 0.8074 (ttp) REVERT: B 250 GLN cc_start: 0.9233 (mt0) cc_final: 0.8850 (mt0) REVERT: B 278 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8635 (mppt) REVERT: B 299 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8394 (tm-30) REVERT: B 370 GLN cc_start: 0.8841 (mt0) cc_final: 0.8449 (mt0) REVERT: B 384 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8776 (pmtt) REVERT: B 401 GLU cc_start: 0.8268 (pt0) cc_final: 0.7381 (pp20) REVERT: B 408 LYS cc_start: 0.9542 (tppp) cc_final: 0.9264 (tmtt) REVERT: B 499 ASP cc_start: 0.8454 (t0) cc_final: 0.8247 (t0) REVERT: C 195 GLN cc_start: 0.9113 (mt0) cc_final: 0.8676 (mp10) REVERT: C 216 ASP cc_start: 0.9053 (t0) cc_final: 0.8500 (t0) REVERT: C 250 GLN cc_start: 0.9035 (mt0) cc_final: 0.8834 (mt0) REVERT: C 336 GLU cc_start: 0.8046 (mp0) cc_final: 0.7776 (mp0) REVERT: C 499 ASP cc_start: 0.8276 (t0) cc_final: 0.8003 (t0) REVERT: C 560 TYR cc_start: 0.8884 (m-80) cc_final: 0.8581 (m-80) REVERT: C 584 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7912 (mpp-170) REVERT: C 596 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8805 (mm-30) REVERT: C 597 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8377 (mm-40) REVERT: C 606 LYS cc_start: 0.8913 (pttm) cc_final: 0.8690 (pttt) outliers start: 23 outliers final: 13 residues processed: 94 average time/residue: 1.2835 time to fit residues: 127.2597 Evaluate side-chains 84 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 THR 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 188 THR 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 512 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.0060 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 8 optimal weight: 0.2980 chunk 71 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.097092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.070853 restraints weight = 14557.034| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.56 r_work: 0.2845 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7201 Z= 0.104 Angle : 0.534 9.125 9767 Z= 0.275 Chirality : 0.044 0.145 1075 Planarity : 0.004 0.037 1234 Dihedral : 6.299 51.076 1161 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.79 % Allowed : 20.41 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.29), residues: 877 helix: 2.00 (0.37), residues: 213 sheet: 0.08 (0.38), residues: 207 loop : -0.83 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 196 HIS 0.002 0.001 HIS C 457 PHE 0.016 0.001 PHE B 508 TYR 0.016 0.001 TYR B 492 ARG 0.007 0.000 ARG B 358 Details of bonding type rmsd hydrogen bonds : bond 0.02953 ( 262) hydrogen bonds : angle 4.64721 ( 756) covalent geometry : bond 0.00235 ( 7201) covalent geometry : angle 0.53432 ( 9767) *********************** 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 95 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 167 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8168 (mt-10) REVERT: B 242 MET cc_start: 0.8374 (ttm) cc_final: 0.7962 (ttp) REVERT: B 250 GLN cc_start: 0.9248 (mt0) cc_final: 0.8838 (mt0) REVERT: B 278 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8719 (mppt) REVERT: B 299 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8348 (tm-30) REVERT: B 370 GLN cc_start: 0.8877 (mt0) cc_final: 0.8542 (mt0) REVERT: B 499 ASP cc_start: 0.8483 (t0) cc_final: 0.8243 (t0) REVERT: C 216 ASP cc_start: 0.9041 (t0) cc_final: 0.8439 (t0) REVERT: C 336 GLU cc_start: 0.7967 (mp0) cc_final: 0.7692 (mp0) REVERT: C 499 ASP cc_start: 0.8185 (t0) cc_final: 0.7890 (t0) REVERT: C 560 TYR cc_start: 0.8851 (m-80) cc_final: 0.8512 (m-80) REVERT: C 596 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8790 (mm-30) REVERT: C 597 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8278 (mm-40) REVERT: C 606 LYS cc_start: 0.8941 (pttm) cc_final: 0.8722 (pttt) outliers start: 13 outliers final: 8 residues processed: 94 average time/residue: 1.3105 time to fit residues: 129.6665 Evaluate side-chains 86 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 187 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 570 ASP 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 26 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN C 611 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.094496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.068188 restraints weight = 14736.040| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.55 r_work: 0.2766 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7201 Z= 0.201 Angle : 0.582 8.408 9767 Z= 0.301 Chirality : 0.045 0.149 1075 Planarity : 0.004 0.040 1234 Dihedral : 6.559 50.278 1161 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.34 % Allowed : 20.41 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.29), residues: 877 helix: 2.00 (0.36), residues: 212 sheet: -0.01 (0.37), residues: 210 loop : -0.86 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 196 HIS 0.003 0.001 HIS C 457 PHE 0.018 0.001 PHE B 508 TYR 0.010 0.001 TYR C 347 ARG 0.009 0.000 ARG B 358 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 262) hydrogen bonds : angle 4.82158 ( 756) covalent geometry : bond 0.00478 ( 7201) covalent geometry : angle 0.58231 ( 9767) *********************** 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 90 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 242 MET cc_start: 0.8409 (ttm) cc_final: 0.8045 (ttp) REVERT: B 250 GLN cc_start: 0.9244 (mt0) cc_final: 0.8864 (mt0) REVERT: B 278 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8737 (mppt) REVERT: B 370 GLN cc_start: 0.8841 (mt0) cc_final: 0.8464 (mt0) REVERT: B 384 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8827 (pmtt) REVERT: B 408 LYS cc_start: 0.9529 (tppp) cc_final: 0.9277 (tmtt) REVERT: B 499 ASP cc_start: 0.8494 (t0) cc_final: 0.8275 (t0) REVERT: C 194 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8682 (mmmm) REVERT: C 336 GLU cc_start: 0.8053 (mp0) cc_final: 0.7770 (mp0) REVERT: C 499 ASP cc_start: 0.8292 (t0) cc_final: 0.7974 (t0) REVERT: C 560 TYR cc_start: 0.8888 (m-80) cc_final: 0.8547 (m-80) REVERT: C 584 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7843 (mpp-170) REVERT: C 596 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8631 (mp0) REVERT: C 597 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8333 (mm-40) REVERT: C 606 LYS cc_start: 0.8937 (pttm) cc_final: 0.8687 (pttt) outliers start: 17 outliers final: 9 residues processed: 87 average time/residue: 1.4016 time to fit residues: 128.5452 Evaluate side-chains 84 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 187 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 512 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 39 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 68 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.094079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.067934 restraints weight = 14696.538| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.51 r_work: 0.2768 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7201 Z= 0.203 Angle : 0.597 8.492 9767 Z= 0.307 Chirality : 0.045 0.149 1075 Planarity : 0.004 0.044 1234 Dihedral : 6.624 50.641 1161 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.93 % Allowed : 21.38 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.29), residues: 877 helix: 1.95 (0.36), residues: 212 sheet: -0.04 (0.37), residues: 210 loop : -0.87 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 196 HIS 0.003 0.001 HIS C 457 PHE 0.020 0.001 PHE B 508 TYR 0.010 0.001 TYR C 347 ARG 0.009 0.000 ARG B 358 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 262) hydrogen bonds : angle 4.84266 ( 756) covalent geometry : bond 0.00480 ( 7201) covalent geometry : angle 0.59733 ( 9767) *********************** 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 87 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 167 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8174 (mt-10) REVERT: B 242 MET cc_start: 0.8402 (ttm) cc_final: 0.7994 (ttp) REVERT: B 250 GLN cc_start: 0.9250 (mt0) cc_final: 0.8851 (mt0) REVERT: B 278 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8737 (mppt) REVERT: B 299 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8374 (tm-30) REVERT: B 370 GLN cc_start: 0.8849 (mt0) cc_final: 0.8471 (mt0) REVERT: B 384 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8826 (pmtt) REVERT: B 401 GLU cc_start: 0.8310 (pt0) cc_final: 0.7400 (pp20) REVERT: B 499 ASP cc_start: 0.8499 (t0) cc_final: 0.8291 (t0) REVERT: C 336 GLU cc_start: 0.8043 (mp0) cc_final: 0.7763 (mp0) REVERT: C 499 ASP cc_start: 0.8316 (t0) cc_final: 0.7997 (t0) REVERT: C 560 TYR cc_start: 0.8900 (m-80) cc_final: 0.8567 (m-80) REVERT: C 584 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7825 (mpp-170) REVERT: C 596 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8650 (mp0) REVERT: C 597 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8380 (mm-40) REVERT: C 606 LYS cc_start: 0.8941 (pttm) cc_final: 0.8686 (pttt) outliers start: 14 outliers final: 9 residues processed: 84 average time/residue: 1.3302 time to fit residues: 117.5851 Evaluate side-chains 82 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 512 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 3 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.095969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.069936 restraints weight = 14644.255| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.52 r_work: 0.2819 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7201 Z= 0.116 Angle : 0.562 9.272 9767 Z= 0.289 Chirality : 0.044 0.146 1075 Planarity : 0.004 0.047 1234 Dihedral : 6.413 50.997 1161 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.07 % Allowed : 21.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.29), residues: 877 helix: 2.13 (0.37), residues: 212 sheet: 0.10 (0.37), residues: 210 loop : -0.80 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 196 HIS 0.003 0.001 HIS C 457 PHE 0.023 0.001 PHE B 508 TYR 0.007 0.001 TYR B 567 ARG 0.010 0.000 ARG B 358 Details of bonding type rmsd hydrogen bonds : bond 0.03071 ( 262) hydrogen bonds : angle 4.66286 ( 756) covalent geometry : bond 0.00270 ( 7201) covalent geometry : angle 0.56242 ( 9767) *********************** 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 92 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 167 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8172 (mt-10) REVERT: B 242 MET cc_start: 0.8365 (ttm) cc_final: 0.7958 (ttp) REVERT: B 250 GLN cc_start: 0.9249 (mt0) cc_final: 0.8849 (mt0) REVERT: B 278 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8764 (mppt) REVERT: B 299 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8390 (tm-30) REVERT: B 370 GLN cc_start: 0.8860 (mt0) cc_final: 0.8479 (mt0) REVERT: B 384 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8839 (pmtt) REVERT: B 401 GLU cc_start: 0.8321 (pt0) cc_final: 0.7416 (pp20) REVERT: B 499 ASP cc_start: 0.8513 (t0) cc_final: 0.8278 (t0) REVERT: C 196 TRP cc_start: 0.6716 (t-100) cc_final: 0.6506 (t60) REVERT: C 336 GLU cc_start: 0.7996 (mp0) cc_final: 0.7721 (mp0) REVERT: C 499 ASP cc_start: 0.8247 (t0) cc_final: 0.7945 (t0) REVERT: C 560 TYR cc_start: 0.8863 (m-80) cc_final: 0.8541 (m-80) REVERT: C 596 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8785 (mm-30) REVERT: C 597 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8323 (mm-40) REVERT: C 606 LYS cc_start: 0.8952 (pttm) cc_final: 0.8706 (pttt) outliers start: 15 outliers final: 8 residues processed: 88 average time/residue: 1.3161 time to fit residues: 122.1775 Evaluate side-chains 84 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 187 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 512 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 75 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 48 optimal weight: 0.0020 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.095160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.068834 restraints weight = 14942.917| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.60 r_work: 0.2783 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3401 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= 0.163 Angle : 0.587 8.919 9767 Z= 0.302 Chirality : 0.045 0.155 1075 Planarity : 0.004 0.048 1234 Dihedral : 6.505 50.236 1161 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.24 % Allowed : 22.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.29), residues: 877 helix: 2.09 (0.37), residues: 212 sheet: 0.05 (0.37), residues: 210 loop : -0.79 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 196 HIS 0.003 0.001 HIS C 457 PHE 0.022 0.001 PHE B 508 TYR 0.009 0.001 TYR C 347 ARG 0.011 0.000 ARG B 358 Details of bonding type rmsd hydrogen bonds : bond 0.03451 ( 262) hydrogen bonds : angle 4.69939 ( 756) covalent geometry : bond 0.00387 ( 7201) covalent geometry : angle 0.58706 ( 9767) ********************** 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 85 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 167 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8144 (mt-10) REVERT: B 242 MET cc_start: 0.8356 (ttm) cc_final: 0.7943 (ttp) REVERT: B 250 GLN cc_start: 0.9261 (mt0) cc_final: 0.8855 (mt0) REVERT: B 278 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8757 (mppt) REVERT: B 299 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8388 (tm-30) REVERT: B 370 GLN cc_start: 0.8816 (mt0) cc_final: 0.8487 (mt0) REVERT: B 384 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8844 (pmtt) REVERT: B 401 GLU cc_start: 0.8326 (pt0) cc_final: 0.7429 (pp20) REVERT: B 499 ASP cc_start: 0.8483 (t0) cc_final: 0.8276 (t0) REVERT: C 196 TRP cc_start: 0.6705 (t-100) cc_final: 0.6501 (t60) REVERT: C 336 GLU cc_start: 0.8008 (mp0) cc_final: 0.7728 (mp0) REVERT: C 499 ASP cc_start: 0.8187 (t0) cc_final: 0.7898 (t0) REVERT: C 560 TYR cc_start: 0.8861 (m-80) cc_final: 0.8544 (m-80) REVERT: C 596 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8781 (mm-30) REVERT: C 597 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8333 (mm-40) REVERT: C 606 LYS cc_start: 0.8950 (pttm) cc_final: 0.8692 (pttt) outliers start: 9 outliers final: 8 residues processed: 84 average time/residue: 1.3967 time to fit residues: 123.3116 Evaluate side-chains 84 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 187 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 512 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 85 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3462 r_free = 0.3462 target = 0.096014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.069781 restraints weight = 14607.316| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.57 r_work: 0.2806 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3478 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 : 0.571 9.251 9767 Z= 0.295 Chirality : 0.045 0.181 1075 Planarity : 0.004 0.050 1234 Dihedral : 6.396 50.693 1161 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.79 % Allowed : 22.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.29), residues: 877 helix: 2.16 (0.37), residues: 212 sheet: 0.08 (0.37), residues: 210 loop : -0.75 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 196 HIS 0.003 0.001 HIS C 457 PHE 0.026 0.001 PHE B 508 TYR 0.008 0.001 TYR B 567 ARG 0.011 0.000 ARG B 358 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 262) hydrogen bonds : angle 4.62197 ( 756) covalent geometry : bond 0.00290 ( 7201) covalent geometry : angle 0.57140 ( 9767) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5485.15 seconds wall clock time: 95 minutes 33.12 seconds (5733.12 seconds total)