Starting phenix.real_space_refine
on Fri Aug 22 19:39:17 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8uqi_42469/08_2025/8uqi_42469.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uqi_42469/08_2025/8uqi_42469.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uqi_42469/08_2025/8uqi_42469.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uqi_42469/08_2025/8uqi_42469.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uqi_42469/08_2025/8uqi_42469.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uqi_42469/08_2025/8uqi_42469.cif"
  }
  resolution = 4.5
  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=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    4630      2.51       5
     N    1332      2.21       5
     O    1338      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7318
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 481, 3659
          Classifications: {'peptide': 481}
          Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 445}
    Chain: "B"
      Number of atoms: 3659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 481, 3659
          Classifications: {'peptide': 481}
          Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 445}
  Time building chain proxies: 2.17, per 1000 atoms: 0.30
  Number of scatterers: 7318
  At special positions: 0
  Unit cell: (72.584, 109.72, 114.784, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      18     16.00
     O    1338      8.00
     N    1332      7.00
     C    4630      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: 0.57
  Conformation dependent library (CDL) restraints added in 339.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1776

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 10 sheets defined
      42.6% alpha, 13.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 16
      removed outlier: 3.867A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 17 through 21
    Processing helix  chain 'A' and resid 47 through 52
    Processing helix  chain 'A' and resid 54 through 59
    Processing helix  chain 'A' and resid 62 through 67
      removed outlier: 3.577A  pdb=" N   VAL A  66 " --> pdb=" O   THR A  62 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU A  67 " --> pdb=" O   ALA A  63 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 62 through 67'
    Processing helix  chain 'A' and resid 68 through 82
      removed outlier: 4.364A  pdb=" N   GLU A  76 " --> pdb=" O   TRP A  72 " (cutoff:3.500A)
      removed outlier: 5.752A  pdb=" N   LEU A  77 " --> pdb=" O   ALA A  73 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ALA A  80 " --> pdb=" O   GLU A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 129
      removed outlier: 4.050A  pdb=" N   THR A 120 " --> pdb=" O   ASP A 116 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLU A 123 " --> pdb=" O   GLU A 119 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL A 129 " --> pdb=" O   VAL A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 154
      removed outlier: 3.618A  pdb=" N   LEU A 141 " --> pdb=" O   GLY A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 193
    Processing helix  chain 'A' and resid 194 through 204
      removed outlier: 3.694A  pdb=" N   ARG A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 252
      removed outlier: 4.267A  pdb=" N   MET A 252 " --> pdb=" O   TYR A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 330
      removed outlier: 4.095A  pdb=" N   VAL A 292 " --> pdb=" O   ARG A 288 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   LEU A 293 " --> pdb=" O   ALA A 289 " (cutoff:3.500A)
      Proline residue:  A 322  - end of helix
      removed outlier: 3.834A  pdb=" N   GLY A 328 " --> pdb=" O   ALA A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 340
    Processing helix  chain 'A' and resid 341 through 345
    Processing helix  chain 'A' and resid 369 through 379
    Processing helix  chain 'A' and resid 398 through 404
      removed outlier: 3.709A  pdb=" N   ALA A 402 " --> pdb=" O   TYR A 398 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ARG A 404 " --> pdb=" O   PRO A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 408
    Processing helix  chain 'A' and resid 448 through 452
      removed outlier: 4.419A  pdb=" N   ALA A 452 " --> pdb=" O   PRO A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 487
    Processing helix  chain 'B' and resid 17 through 21
    Processing helix  chain 'B' and resid 45 through 52
      removed outlier: 3.994A  pdb=" N   ALA B  49 " --> pdb=" O   ALA B  45 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   LEU B  50 " --> pdb=" O   ASN B  46 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LEU B  51 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 59
    Processing helix  chain 'B' and resid 62 through 67
    Processing helix  chain 'B' and resid 68 through 73
    Processing helix  chain 'B' and resid 74 through 82
      removed outlier: 4.782A  pdb=" N   ALA B  80 " --> pdb=" O   GLU B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 130
      removed outlier: 3.934A  pdb=" N   ARG B 126 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   SER B 130 " --> pdb=" O   ARG B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 154
      removed outlier: 3.853A  pdb=" N   LEU B 142 " --> pdb=" O   THR B 138 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ALA B 151 " --> pdb=" O   ASN B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 204
    Processing helix  chain 'B' and resid 242 through 253
    Processing helix  chain 'B' and resid 283 through 327
      removed outlier: 3.511A  pdb=" N   ARG B 287 " --> pdb=" O   SER B 283 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ARG B 288 " --> pdb=" O   TYR B 284 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ALA B 289 " --> pdb=" O   GLU B 285 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   CYS B 290 " --> pdb=" O   ARG B 286 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   GLU B 291 " --> pdb=" O   ARG B 287 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   VAL B 292 " --> pdb=" O   ARG B 288 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLY B 321 " --> pdb=" O   ALA B 317 " (cutoff:3.500A)
      Proline residue:  B 322  - end of helix
    Processing helix  chain 'B' and resid 332 through 340
      removed outlier: 3.782A  pdb=" N   ASP B 340 " --> pdb=" O   ALA B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 349
      removed outlier: 4.095A  pdb=" N   GLU B 346 " --> pdb=" O   ALA B 342 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   LEU B 347 " --> pdb=" O   ARG B 343 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   THR B 348 " --> pdb=" O   VAL B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 381
    Processing helix  chain 'B' and resid 393 through 398
    Processing helix  chain 'B' and resid 398 through 403
    Processing helix  chain 'B' and resid 436 through 440
      removed outlier: 3.631A  pdb=" N   GLY B 439 " --> pdb=" O   SER B 436 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ASN B 440 " --> pdb=" O   TRP B 437 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 436 through 440'
    Processing helix  chain 'B' and resid 460 through 468
    Processing helix  chain 'B' and resid 475 through 487
      removed outlier: 3.972A  pdb=" N   LEU B 479 " --> pdb=" O   LYS B 475 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   GLU B 483 " --> pdb=" O   LEU B 479 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   GLY B 484 " --> pdb=" O   ALA B 480 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 87
      removed outlier: 3.546A  pdb=" N   HIS A  98 " --> pdb=" O   VAL A 105 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 87
      removed outlier: 4.124A  pdb=" N   THR A 104 " --> pdb=" O   PHE A  33 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   PHE A  33 " --> pdb=" O   THR A 104 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   LEU A  30 " --> pdb=" O   VAL A  43 " (cutoff:3.500A)
      removed outlier: 5.548A  pdb=" N   VAL A  43 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ALA A  32 " --> pdb=" O   GLU A  41 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 176
      removed outlier: 3.974A  pdb=" N   CYS A 274 " --> pdb=" O   PHE A 258 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   PHE A 258 " --> pdb=" O   CYS A 274 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ARG A 207 " --> pdb=" O   SER A 259 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 187
    Processing sheet with id=AA5, first strand: chain 'A' and resid 353 through 356
      removed outlier: 3.588A  pdb=" N   ALA A 354 " --> pdb=" O   LEU A 425 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 43 through 44
    Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 87
    Processing sheet with id=AA8, first strand: chain 'B' and resid 96 through 100
    Processing sheet with id=AA9, first strand: chain 'B' and resid 170 through 174
      removed outlier: 5.931A  pdb=" N   VAL B 171 " --> pdb=" O   ARG B 162 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   ARG B 162 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   LEU B 262 " --> pdb=" O   TRP B 269 " (cutoff:3.500A)
      removed outlier: 4.893A  pdb=" N   LEU B 271 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   LEU B 260 " --> pdb=" O   LEU B 271 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   ALA B 273 " --> pdb=" O   PHE B 258 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   PHE B 258 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   HIS B 275 " --> pdb=" O   ALA B 256 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ALA B 256 " --> pdb=" O   HIS B 275 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ARG B 207 " --> pdb=" O   SER B 259 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 352 through 355
      removed outlier: 3.559A  pdb=" N   GLY B 352 " --> pdb=" O   PHE B 427 " (cutoff:3.500A)

    303 hydrogen bonds defined for protein.
    831 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: 0.94

  Time building geometry restraints manager: 0.77 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.23 -     1.34: 2514
        1.34 -     1.46: 1343
        1.46 -     1.58: 3595
        1.58 -     1.69: 0
        1.69 -     1.81: 30
  Bond restraints: 7482
  Sorted by residual:
  bond pdb=" CA  PRO B 384 "
       pdb=" C   PRO B 384 "
    ideal  model  delta    sigma   weight residual
    1.526  1.518  0.008 8.50e-03 1.38e+04 9.70e-01
  bond pdb=" CA  ASP B 116 "
       pdb=" CB  ASP B 116 "
    ideal  model  delta    sigma   weight residual
    1.527  1.544 -0.017 1.70e-02 3.46e+03 9.59e-01
  bond pdb=" C   LYS A 136 "
       pdb=" N   GLY A 137 "
    ideal  model  delta    sigma   weight residual
    1.319  1.332 -0.013 1.44e-02 4.82e+03 8.48e-01
  bond pdb=" C   THR A 351 "
       pdb=" O   THR A 351 "
    ideal  model  delta    sigma   weight residual
    1.235  1.245 -0.010 1.10e-02 8.26e+03 8.08e-01
  bond pdb=" N   PRO A 399 "
       pdb=" CA  PRO A 399 "
    ideal  model  delta    sigma   weight residual
    1.465  1.483 -0.018 2.03e-02 2.43e+03 7.89e-01
  ... (remaining 7477 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 9837
        2.05 -     4.09: 319
        4.09 -     6.14: 29
        6.14 -     8.19: 9
        8.19 -    10.23: 2
  Bond angle restraints: 10196
  Sorted by residual:
  angle pdb=" N   GLY A 137 "
        pdb=" CA  GLY A 137 "
        pdb=" C   GLY A 137 "
      ideal   model   delta    sigma   weight residual
     110.20  115.83   -5.63 1.32e+00 5.74e-01 1.82e+01
  angle pdb=" N   GLU B 123 "
        pdb=" CA  GLU B 123 "
        pdb=" C   GLU B 123 "
      ideal   model   delta    sigma   weight residual
     112.89  108.39    4.50 1.24e+00 6.50e-01 1.32e+01
  angle pdb=" N   ALA B  83 "
        pdb=" CA  ALA B  83 "
        pdb=" C   ALA B  83 "
      ideal   model   delta    sigma   weight residual
     108.46  113.62   -5.16 1.51e+00 4.39e-01 1.17e+01
  angle pdb=" N   VAL B 432 "
        pdb=" CA  VAL B 432 "
        pdb=" C   VAL B 432 "
      ideal   model   delta    sigma   weight residual
     111.62  108.95    2.67 7.90e-01 1.60e+00 1.14e+01
  angle pdb=" C   SER A 283 "
        pdb=" N   TYR A 284 "
        pdb=" CA  TYR A 284 "
      ideal   model   delta    sigma   weight residual
     120.44  124.74   -4.30 1.30e+00 5.92e-01 1.09e+01
  ... (remaining 10191 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 4101
       17.84 -    35.67: 380
       35.67 -    53.51: 45
       53.51 -    71.35: 12
       71.35 -    89.18: 4
  Dihedral angle restraints: 4542
    sinusoidal: 1792
      harmonic: 2750
  Sorted by residual:
  dihedral pdb=" CA  ASP B 156 "
           pdb=" C   ASP B 156 "
           pdb=" N   ARG B 157 "
           pdb=" CA  ARG B 157 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.84  -23.16     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  LYS B 176 "
           pdb=" C   LYS B 176 "
           pdb=" N   ARG B 177 "
           pdb=" CA  ARG B 177 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.14   21.86     0      5.00e+00 4.00e-02 1.91e+01
  dihedral pdb=" CA  ALA B  83 "
           pdb=" C   ALA B  83 "
           pdb=" N   LEU B  84 "
           pdb=" CA  LEU B  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.56   20.44     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 4539 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 880
       0.044 -    0.088: 217
       0.088 -    0.132: 56
       0.132 -    0.176: 4
       0.176 -    0.220: 1
  Chirality restraints: 1158
  Sorted by residual:
  chirality pdb=" CB  VAL A 373 "
            pdb=" CA  VAL A 373 "
            pdb=" CG1 VAL A 373 "
            pdb=" CG2 VAL A 373 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  ASP B 116 "
            pdb=" N   ASP B 116 "
            pdb=" C   ASP B 116 "
            pdb=" CB  ASP B 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.56e-01
  chirality pdb=" CB  VAL A 160 "
            pdb=" CA  VAL A 160 "
            pdb=" CG1 VAL A 160 "
            pdb=" CG2 VAL A 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.45e-01
  ... (remaining 1155 not shown)

  Planarity restraints: 1342
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 229 "    0.033 5.00e-02 4.00e+02   5.09e-02 4.15e+00
        pdb=" N   PRO B 230 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO B 230 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 230 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 399 "    0.032 5.00e-02 4.00e+02   4.80e-02 3.68e+00
        pdb=" N   PRO A 400 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A 400 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 400 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 204 "   -0.032 5.00e-02 4.00e+02   4.77e-02 3.64e+00
        pdb=" N   PRO A 205 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 205 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 205 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1339 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 252
        2.67 -     3.23: 7983
        3.23 -     3.79: 12850
        3.79 -     4.34: 16390
        4.34 -     4.90: 24082
  Nonbonded interactions: 61557
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 332 "
            pdb=" OE1 GLU A 335 "
     model   vdw
     2.118 3.040
  nonbonded pdb=" O   ASN A 204 "
            pdb=" NH1 ARG A 207 "
     model   vdw
     2.154 3.120
  nonbonded pdb=" O   GLN A 300 "
            pdb=" OG  SER A 303 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" O   ALA A 199 "
            pdb=" OG1 THR A 202 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" OG  SER B 369 "
            pdb=" OD1 ASP B 371 "
     model   vdw
     2.172 3.040
  ... (remaining 61552 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
Set refine NCS operators
  NCS operators will be refined.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.090
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.010
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7482  Z= 0.157
  Angle     :  0.836  10.233  10196  Z= 0.469
  Chirality :  0.041   0.220   1158
  Planarity :  0.006   0.051   1342
  Dihedral  : 13.618  89.182   2766
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 25.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.67 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.83 (0.26), residues: 958
  helix:  0.02 (0.30), residues: 301
  sheet: -2.52 (0.41), residues: 121
  loop : -1.64 (0.26), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  81 
 TYR   0.021   0.002   TYR A 398 
 PHE   0.009   0.001   PHE A 155 
 TRP   0.012   0.002   TRP A  72 
 HIS   0.003   0.001   HIS B 455 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7482)
  covalent geometry    : angle       0.83574 (10196)
  hydrogen bonds       : bond        0.19684 (  297)
  hydrogen bonds       : angle       8.53993 (  831)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A   31 LEU cc_start: 0.9709 (mp) cc_final: 0.9457 (mp)
REVERT: A  117 MET cc_start: 0.8760 (ppp) cc_final: 0.8353 (ppp)
REVERT: A  485 PHE cc_start: 0.9111 (m-10) cc_final: 0.8874 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.0534
  time to fit residues: 3.0613
Evaluate side-chains
  30 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    0.0570
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0070
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.0050
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    0.0670
   overall best weight:    0.1268
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  12 GLN
** A  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.058366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.045915 restraints weight = 41916.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.047214 restraints weight = 23287.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.048067 restraints weight = 15369.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.048626 restraints weight = 11336.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.049056 restraints weight = 9101.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6369
moved from start:          2.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.095   7482  Z= 0.317
  Angle     :  1.109  11.962  10196  Z= 0.635
  Chirality :  0.058   0.490   1158
  Planarity :  0.010   0.128   1342
  Dihedral  :  8.636  62.106   1058
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 25.55
  Ramachandran Plot:
    Outliers :  5.01 %
    Allowed  :  7.72 %
    Favored  : 87.27 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  :  9.70 %
    Favored  : 88.68 %
  Cbeta Deviations :  0.23 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.57 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.73 (0.25), residues: 958
  helix:  0.16 (0.27), residues: 330
  sheet: -1.04 (0.42), residues: 124
  loop : -2.15 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 457 
 TYR   0.028   0.004   TYR B 201 
 PHE   0.012   0.002   PHE A 460 
 TRP   0.027   0.003   TRP A 463 
 HIS   0.009   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00565 ( 7482)
  covalent geometry    : angle       1.10852 (10196)
  hydrogen bonds       : bond        0.22972 (  297)
  hydrogen bonds       : angle       8.62314 (  831)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.8440 (ppp) cc_final: 0.8052 (ppp)
  outliers start: 6
  outliers final: 3
  residues processed: 56
  average time/residue: 0.0661
  time to fit residues: 4.7388
Evaluate side-chains
  40 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0980
   chunk 77 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 44 optimal weight:    8.9990
   chunk 74 optimal weight:    0.0270
   chunk 73 optimal weight:    0.0670
   chunk 54 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 94 optimal weight:    0.0770
   overall best weight:    0.1934
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  65 GLN
** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.061525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.048900 restraints weight = 40528.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.050196 restraints weight = 22602.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.051074 restraints weight = 14814.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.051653 restraints weight = 10821.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.052099 restraints weight = 8537.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6402
moved from start:          2.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   7482  Z= 0.244
  Angle     :  0.990  11.632  10196  Z= 0.563
  Chirality :  0.047   0.230   1158
  Planarity :  0.007   0.067   1342
  Dihedral  :  7.876  58.939   1058
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 21.07
  Ramachandran Plot:
    Outliers :  2.09 %
    Allowed  :  4.80 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 10.24 %
    Favored  : 89.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.90 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.50 (0.25), residues: 958
  helix:  0.23 (0.27), residues: 346
  sheet: -1.26 (0.36), residues: 152
  loop : -1.88 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 433 
 TYR   0.018   0.003   TYR A 398 
 PHE   0.012   0.002   PHE A 485 
 TRP   0.028   0.003   TRP A 437 
 HIS   0.010   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 7482)
  covalent geometry    : angle       0.98985 (10196)
  hydrogen bonds       : bond        0.18142 (  297)
  hydrogen bonds       : angle       8.22271 (  831)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.8787 (ppp) cc_final: 0.8156 (ppp)
REVERT: A  323 LEU cc_start: 0.8958 (pp) cc_final: 0.8543 (mm)
  outliers start: 2
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0600
  time to fit residues: 4.1788
Evaluate side-chains
  38 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    0.0040
   chunk 56 optimal weight:    2.9990
   chunk 92 optimal weight:    9.9990
   chunk 34 optimal weight:    5.9990
   chunk 25 optimal weight:    0.2980
   chunk 65 optimal weight:    3.9990
   chunk 69 optimal weight:   20.0000
   chunk 17 optimal weight:    0.1980
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.6794
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.061090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.048432 restraints weight = 40831.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.049708 restraints weight = 23080.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.050551 restraints weight = 15417.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.051179 restraints weight = 11460.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.051606 restraints weight = 9120.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6476
moved from start:          2.2833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7482  Z= 0.215
  Angle     :  0.895  10.255  10196  Z= 0.517
  Chirality :  0.046   0.220   1158
  Planarity :  0.007   0.059   1342
  Dihedral  :  7.380  64.104   1058
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 20.25
  Ramachandran Plot:
    Outliers :  1.25 %
    Allowed  :  6.47 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  5.39 %
    Favored  : 94.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.90 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.12 (0.26), residues: 958
  helix:  0.63 (0.28), residues: 336
  sheet: -1.07 (0.37), residues: 148
  loop : -1.66 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 198 
 TYR   0.036   0.004   TYR B 201 
 PHE   0.006   0.001   PHE A  33 
 TRP   0.014   0.002   TRP B  72 
 HIS   0.013   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 7482)
  covalent geometry    : angle       0.89549 (10196)
  hydrogen bonds       : bond        0.16569 (  297)
  hydrogen bonds       : angle       7.98218 (  831)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 LEU cc_start: 0.9676 (mp) cc_final: 0.9269 (tp)
REVERT: A  117 MET cc_start: 0.8819 (ppp) cc_final: 0.8350 (ppp)
REVERT: A  180 MET cc_start: 0.9553 (pmm) cc_final: 0.9288 (pmm)
REVERT: A  485 PHE cc_start: 0.8848 (m-80) cc_final: 0.8553 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 56
  average time/residue: 0.0719
  time to fit residues: 4.8576
Evaluate side-chains
  38 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0270
   chunk 68 optimal weight:    2.9990
   chunk 90 optimal weight:    0.0470
   chunk 24 optimal weight:    9.9990
   chunk 39 optimal weight:    4.9990
   chunk 42 optimal weight:    0.6980
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.9540
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  65 GLN
** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.061210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.048443 restraints weight = 40929.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.049692 restraints weight = 23879.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.050583 restraints weight = 16162.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.051176 restraints weight = 12000.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.051653 restraints weight = 9558.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6834
moved from start:          2.3026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7482  Z= 0.202
  Angle     :  0.866  10.697  10196  Z= 0.489
  Chirality :  0.044   0.181   1158
  Planarity :  0.007   0.054   1342
  Dihedral  :  7.095  62.960   1058
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 20.05
  Ramachandran Plot:
    Outliers :  1.25 %
    Allowed  :  5.64 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  3.77 %
    Favored  : 95.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.90 %

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: -0.80 (0.26), residues: 958
  helix:  0.95 (0.28), residues: 336
  sheet: -0.91 (0.37), residues: 156
  loop : -1.51 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 126 
 TYR   0.024   0.003   TYR B 398 
 PHE   0.017   0.002   PHE A 258 
 TRP   0.042   0.002   TRP B 437 
 HIS   0.003   0.001   HIS A 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 7482)
  covalent geometry    : angle       0.86585 (10196)
  hydrogen bonds       : bond        0.16140 (  297)
  hydrogen bonds       : angle       7.80265 (  831)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.9056 (ppp) cc_final: 0.8433 (ppp)
REVERT: A  180 MET cc_start: 0.8576 (pmm) cc_final: 0.8168 (pmm)
REVERT: A  186 MET cc_start: 0.7737 (tpp) cc_final: 0.6895 (tpp)
REVERT: A  206 LEU cc_start: 0.9559 (mm) cc_final: 0.9174 (tp)
REVERT: A  258 PHE cc_start: 0.9301 (t80) cc_final: 0.8979 (t80)
REVERT: A  370 MET cc_start: 0.9807 (pmm) cc_final: 0.9605 (pmm)
REVERT: A  485 PHE cc_start: 0.8776 (m-80) cc_final: 0.8549 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 52
  average time/residue: 0.0615
  time to fit residues: 3.9595
Evaluate side-chains
  34 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 42 optimal weight:    0.0870
   chunk 87 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 82 optimal weight:    0.0010
   chunk 58 optimal weight:    4.9990
   chunk 94 optimal weight:    0.8980
   chunk 41 optimal weight:    8.9990
   chunk 83 optimal weight:    0.8980
   chunk 91 optimal weight:    0.5980
   chunk 65 optimal weight:    0.0000
   chunk 1 optimal weight:    0.3980
   overall best weight:    0.2168
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.061890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.048965 restraints weight = 41031.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.050208 restraints weight = 23566.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.051053 restraints weight = 15985.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.051660 restraints weight = 12028.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.052082 restraints weight = 9664.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6421
moved from start:          2.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7482  Z= 0.204
  Angle     :  0.878  11.337  10196  Z= 0.498
  Chirality :  0.045   0.163   1158
  Planarity :  0.006   0.050   1342
  Dihedral  :  6.807  63.427   1058
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 19.85
  Ramachandran Plot:
    Outliers :  1.04 %
    Allowed  :  6.05 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  3.77 %
    Favored  : 95.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.67 %

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: -0.76 (0.27), residues: 958
  helix:  0.79 (0.28), residues: 338
  sheet: -0.73 (0.39), residues: 152
  loop : -1.40 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 203 
 TYR   0.026   0.002   TYR A 398 
 PHE   0.011   0.001   PHE A 258 
 TRP   0.026   0.002   TRP B 426 
 HIS   0.003   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7482)
  covalent geometry    : angle       0.87795 (10196)
  hydrogen bonds       : bond        0.15787 (  297)
  hydrogen bonds       : angle       7.87041 (  831)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.8912 (ppp) cc_final: 0.8359 (ppp)
REVERT: A  180 MET cc_start: 0.9543 (pmm) cc_final: 0.9196 (pmm)
REVERT: A  206 LEU cc_start: 0.9136 (mm) cc_final: 0.8815 (tp)
REVERT: A  460 PHE cc_start: 0.4337 (OUTLIER) cc_final: 0.3869 (m-80)
REVERT: A  485 PHE cc_start: 0.8871 (m-80) cc_final: 0.8576 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0435
  time to fit residues: 2.7406
Evaluate side-chains
  35 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 34
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 60 optimal weight:    0.0020
   chunk 41 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 21 optimal weight:   20.0000
   chunk 91 optimal weight:    0.0870
   chunk 78 optimal weight:    0.9980
   chunk 27 optimal weight:    9.9990
   chunk 85 optimal weight:    0.0010
   chunk 8 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.3772
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  65 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.062059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.049322 restraints weight = 41420.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.050600 restraints weight = 23969.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.051490 restraints weight = 16271.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.052100 restraints weight = 12167.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.052563 restraints weight = 9766.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6374
moved from start:          2.3362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7482  Z= 0.195
  Angle     :  0.869  11.300  10196  Z= 0.488
  Chirality :  0.045   0.182   1158
  Planarity :  0.006   0.059   1342
  Dihedral  :  6.677  64.548   1058
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 19.91
  Ramachandran Plot:
    Outliers :  1.04 %
    Allowed  :  6.26 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  2.96 %
    Favored  : 96.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.45 %

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: -0.62 (0.27), residues: 958
  helix:  0.91 (0.28), residues: 338
  sheet: -0.52 (0.41), residues: 152
  loop : -1.37 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 203 
 TYR   0.026   0.002   TYR A 398 
 PHE   0.009   0.002   PHE A 460 
 TRP   0.023   0.002   TRP A 426 
 HIS   0.005   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7482)
  covalent geometry    : angle       0.86870 (10196)
  hydrogen bonds       : bond        0.15528 (  297)
  hydrogen bonds       : angle       7.77284 (  831)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.8946 (ppp) cc_final: 0.8479 (ppp)
REVERT: A  485 PHE cc_start: 0.8829 (m-80) cc_final: 0.8549 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0496
  time to fit residues: 3.1251
Evaluate side-chains
  33 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 39 optimal weight:    0.0770
   chunk 95 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 4 optimal weight:   10.0000
   chunk 64 optimal weight:   10.0000
   chunk 65 optimal weight:    8.9990
   chunk 18 optimal weight:    0.0970
   chunk 1 optimal weight:    0.0470
   overall best weight:    0.4034
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.062510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.049623 restraints weight = 40745.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.050915 restraints weight = 23710.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.051784 restraints weight = 16106.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.052425 restraints weight = 12075.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.052876 restraints weight = 9685.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6813
moved from start:          2.3460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7482  Z= 0.198
  Angle     :  0.884  11.201  10196  Z= 0.496
  Chirality :  0.045   0.186   1158
  Planarity :  0.006   0.053   1342
  Dihedral  :  6.535  64.304   1058
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 19.30
  Ramachandran Plot:
    Outliers :  1.04 %
    Allowed  :  6.05 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.45 %

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: -0.50 (0.27), residues: 958
  helix:  1.07 (0.28), residues: 332
  sheet: -0.53 (0.41), residues: 152
  loop : -1.29 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 207 
 TYR   0.043   0.004   TYR B 201 
 PHE   0.008   0.001   PHE B 460 
 TRP   0.022   0.002   TRP B 426 
 HIS   0.004   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 7482)
  covalent geometry    : angle       0.88421 (10196)
  hydrogen bonds       : bond        0.15523 (  297)
  hydrogen bonds       : angle       7.81432 (  831)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.8884 (ppp) cc_final: 0.8231 (ppp)
REVERT: A  163 PHE cc_start: 0.9561 (m-10) cc_final: 0.9334 (m-10)
REVERT: A  180 MET cc_start: 0.8192 (pmm) cc_final: 0.7949 (pmm)
REVERT: A  201 TYR cc_start: 0.8628 (m-80) cc_final: 0.8371 (m-80)
REVERT: A  485 PHE cc_start: 0.8784 (m-80) cc_final: 0.8562 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0540
  time to fit residues: 3.3835
Evaluate side-chains
  36 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0570
   chunk 80 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 73 optimal weight:    0.0060
   chunk 93 optimal weight:    2.9990
   chunk 27 optimal weight:   10.0000
   chunk 84 optimal weight:    0.4980
   chunk 16 optimal weight:    0.0370
   chunk 68 optimal weight:    0.0470
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.1290
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.063220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.050476 restraints weight = 41176.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.051738 restraints weight = 23849.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.052642 restraints weight = 16290.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.053271 restraints weight = 12202.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.053697 restraints weight = 9806.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6790
moved from start:          2.3629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7482  Z= 0.197
  Angle     :  0.879  11.367  10196  Z= 0.491
  Chirality :  0.045   0.185   1158
  Planarity :  0.006   0.061   1342
  Dihedral  :  6.458  64.954   1058
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 21.00
  Ramachandran Plot:
    Outliers :  1.04 %
    Allowed  :  6.68 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.45 %

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: -0.42 (0.27), residues: 958
  helix:  1.04 (0.28), residues: 334
  sheet: -0.45 (0.42), residues: 152
  loop : -1.19 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 203 
 TYR   0.039   0.004   TYR A 201 
 PHE   0.022   0.002   PHE B 258 
 TRP   0.020   0.002   TRP A 426 
 HIS   0.004   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 7482)
  covalent geometry    : angle       0.87912 (10196)
  hydrogen bonds       : bond        0.15397 (  297)
  hydrogen bonds       : angle       7.64677 (  831)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.9040 (ppp) cc_final: 0.8483 (ppp)
REVERT: A  163 PHE cc_start: 0.9589 (m-10) cc_final: 0.9353 (m-10)
REVERT: A  180 MET cc_start: 0.8160 (pmm) cc_final: 0.7912 (pmm)
REVERT: A  201 TYR cc_start: 0.8589 (m-80) cc_final: 0.8364 (m-80)
REVERT: A  206 LEU cc_start: 0.9512 (mm) cc_final: 0.9170 (tp)
REVERT: A  476 ARG cc_start: 0.9723 (ppt170) cc_final: 0.9469 (tmm160)
REVERT: A  485 PHE cc_start: 0.8757 (m-80) cc_final: 0.8557 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0460
  time to fit residues: 2.8761
Evaluate side-chains
  39 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0970
   chunk 28 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 11 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0570
   chunk 46 optimal weight:    0.0030
   chunk 5 optimal weight:    0.9980
   chunk 80 optimal weight:   20.0000
   chunk 13 optimal weight:   10.0000
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.3706
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 114 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.063039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.050491 restraints weight = 41105.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.051764 restraints weight = 23859.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.052648 restraints weight = 16288.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.053276 restraints weight = 12276.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.053723 restraints weight = 9908.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6797
moved from start:          2.3740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7482  Z= 0.195
  Angle     :  0.864  11.106  10196  Z= 0.483
  Chirality :  0.045   0.185   1158
  Planarity :  0.007   0.061   1342
  Dihedral  :  6.329  65.148   1058
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 20.18
  Ramachandran Plot:
    Outliers :  1.04 %
    Allowed  :  6.05 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.45 %

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: -0.42 (0.27), residues: 958
  helix:  1.02 (0.28), residues: 334
  sheet: -0.50 (0.42), residues: 152
  loop : -1.14 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 126 
 TYR   0.048   0.004   TYR B 201 
 PHE   0.008   0.001   PHE A 155 
 TRP   0.018   0.002   TRP A 426 
 HIS   0.005   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 7482)
  covalent geometry    : angle       0.86445 (10196)
  hydrogen bonds       : bond        0.15360 (  297)
  hydrogen bonds       : angle       7.61851 (  831)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.9031 (ppp) cc_final: 0.8495 (ppp)
REVERT: A  163 PHE cc_start: 0.9578 (m-10) cc_final: 0.9331 (m-10)
REVERT: A  180 MET cc_start: 0.8112 (pmm) cc_final: 0.7873 (pmm)
REVERT: A  370 MET cc_start: 0.9780 (pmm) cc_final: 0.9564 (pmm)
REVERT: A  476 ARG cc_start: 0.9719 (ppt170) cc_final: 0.9483 (tmm160)
REVERT: A  485 PHE cc_start: 0.8743 (m-80) cc_final: 0.8499 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.0627
  time to fit residues: 3.6943
Evaluate side-chains
  35 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 88 optimal weight:    0.6980
   chunk 50 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0020
   chunk 91 optimal weight:    0.0050
   chunk 9 optimal weight:    0.0870
   chunk 66 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 25 optimal weight:    8.9990
   chunk 86 optimal weight:    0.0570
   chunk 87 optimal weight:    4.9990
   chunk 32 optimal weight:   30.0000
   overall best weight:    0.1698
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.064118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.051389 restraints weight = 39958.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.052617 restraints weight = 23578.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.053532 restraints weight = 16369.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.054170 restraints weight = 12352.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.054507 restraints weight = 9959.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6790
moved from start:          2.3875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7482  Z= 0.196
  Angle     :  0.869  11.221  10196  Z= 0.483
  Chirality :  0.046   0.222   1158
  Planarity :  0.006   0.068   1342
  Dihedral  :  6.306  65.137   1058
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 19.98
  Ramachandran Plot:
    Outliers :  1.04 %
    Allowed  :  5.85 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.45 %

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: -0.40 (0.27), residues: 958
  helix:  1.04 (0.28), residues: 334
  sheet: -0.50 (0.42), residues: 152
  loop : -1.12 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 203 
 TYR   0.029   0.003   TYR B 398 
 PHE   0.014   0.002   PHE B 460 
 TRP   0.017   0.002   TRP A 426 
 HIS   0.004   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 7482)
  covalent geometry    : angle       0.86884 (10196)
  hydrogen bonds       : bond        0.15320 (  297)
  hydrogen bonds       : angle       7.57800 (  831)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 865.83 seconds
wall clock time: 15 minutes 44.69 seconds (944.69 seconds total)