Starting phenix.real_space_refine
on Sat Aug 23 02:45:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8exq_28659/08_2025/8exq_28659.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8exq_28659/08_2025/8exq_28659.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8exq_28659/08_2025/8exq_28659.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8exq_28659/08_2025/8exq_28659.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8exq_28659/08_2025/8exq_28659.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8exq_28659/08_2025/8exq_28659.map"
  }
  resolution = 4.9
  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=   0.003 sd=   0.045
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
     Zn      2      6.06       5
     S      38      5.16       5
     C    6112      2.51       5
     N    1534      2.21       5
     O    1618      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 61 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: 9304
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 4651
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 554, 4651
          Classifications: {'peptide': 554}
          Link IDs: {'PTRANS': 11, 'TRANS': 542}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 4651
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 554, 4651
          Classifications: {'peptide': 554}
          Link IDs: {'PTRANS': 11, 'TRANS': 542}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.46, per 1000 atoms: 0.26
  Number of scatterers: 9304
  At special positions: 0
  Unit cell: (73.9927, 108.282, 135.353, 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)
     Zn      2     29.99
     S      38     16.00
     O    1618      8.00
     N    1534      7.00
     C    6112      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: 0.95
  Conformation dependent library (CDL) restraints added in 340.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 201 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 205 "
      pdb="  ZN B 701 "
        pdb="ZN    ZN B 701 " - pdb=" NE2 HIS B 201 "
        pdb="ZN    ZN B 701 " - pdb=" NE2 HIS B 205 "


  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2140

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 6 sheets defined
      57.5% alpha, 16.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'B' and resid 2 through 31
    Processing helix  chain 'B' and resid 35 through 38
    Processing helix  chain 'B' and resid 39 through 46
    Processing helix  chain 'B' and resid 99 through 133
      removed outlier: 3.571A  pdb=" N   ASP B 103 " --> pdb=" O   TRP B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 151
    Processing helix  chain 'B' and resid 184 through 189
    Processing helix  chain 'B' and resid 190 through 193
    Processing helix  chain 'B' and resid 194 through 208
    Processing helix  chain 'B' and resid 209 through 224
    Processing helix  chain 'B' and resid 229 through 251
      removed outlier: 3.969A  pdb=" N   ARG B 235 " --> pdb=" O   HIS B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 253
      No H-bonds generated for 'chain 'B' and resid 252 through 253'
    Processing helix  chain 'B' and resid 254 through 256
      No H-bonds generated for 'chain 'B' and resid 254 through 256'
    Processing helix  chain 'B' and resid 257 through 268
      removed outlier: 3.647A  pdb=" N   SER B 268 " --> pdb=" O   SER B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 300
    Processing helix  chain 'B' and resid 308 through 327
    Processing helix  chain 'B' and resid 332 through 337
    Processing helix  chain 'B' and resid 352 through 357
    Processing helix  chain 'B' and resid 377 through 382
    Processing helix  chain 'B' and resid 387 through 389
      No H-bonds generated for 'chain 'B' and resid 387 through 389'
    Processing helix  chain 'B' and resid 390 through 402
      removed outlier: 4.270A  pdb=" N   TYR B 394 " --> pdb=" O   THR B 390 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 425
    Processing helix  chain 'B' and resid 429 through 436
    Processing helix  chain 'B' and resid 438 through 448
    Processing helix  chain 'B' and resid 450 through 462
    Processing helix  chain 'B' and resid 483 through 497
    Processing helix  chain 'B' and resid 502 through 513
    Processing helix  chain 'B' and resid 564 through 579
    Processing helix  chain 'A' and resid 2 through 31
    Processing helix  chain 'A' and resid 35 through 38
    Processing helix  chain 'A' and resid 39 through 46
      removed outlier: 3.563A  pdb=" N   LEU A  43 " --> pdb=" O   TRP A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 51
    Processing helix  chain 'A' and resid 99 through 132
    Processing helix  chain 'A' and resid 139 through 152
      removed outlier: 4.659A  pdb=" N   ASN A 152 " --> pdb=" O   THR A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 187
      No H-bonds generated for 'chain 'A' and resid 185 through 187'
    Processing helix  chain 'A' and resid 194 through 208
    Processing helix  chain 'A' and resid 209 through 224
    Processing helix  chain 'A' and resid 228 through 233
    Processing helix  chain 'A' and resid 233 through 252
      removed outlier: 3.620A  pdb=" N   ASN A 252 " --> pdb=" O   PHE A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 256
      removed outlier: 5.426A  pdb=" N   ASN A 256 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 253 through 256'
    Processing helix  chain 'A' and resid 257 through 272
    Processing helix  chain 'A' and resid 289 through 300
    Processing helix  chain 'A' and resid 308 through 327
    Processing helix  chain 'A' and resid 333 through 337
    Processing helix  chain 'A' and resid 352 through 357
    Processing helix  chain 'A' and resid 377 through 382
    Processing helix  chain 'A' and resid 387 through 389
      No H-bonds generated for 'chain 'A' and resid 387 through 389'
    Processing helix  chain 'A' and resid 390 through 402
      removed outlier: 4.455A  pdb=" N   TYR A 394 " --> pdb=" O   THR A 390 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   MET A 397 " --> pdb=" O   ILE A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 425
    Processing helix  chain 'A' and resid 429 through 436
    Processing helix  chain 'A' and resid 438 through 449
    Processing helix  chain 'A' and resid 450 through 461
    Processing helix  chain 'A' and resid 483 through 497
    Processing helix  chain 'A' and resid 502 through 513
    Processing helix  chain 'A' and resid 564 through 579
    Processing sheet with id=AA1, first strand: chain 'B' and resid 90 through 94
      removed outlier: 6.686A  pdb=" N   PHE B  90 " --> pdb=" O   THR A 529 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   ILE A 531 " --> pdb=" O   PHE B  90 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   THR B  92 " --> pdb=" O   ILE A 531 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   VAL A 532 " --> pdb=" O   TYR A 536 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   TYR A 536 " --> pdb=" O   VAL A 532 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   ASP A 346 " --> pdb=" O   TYR A 373 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   ILE A 375 " --> pdb=" O   ASP A 346 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   GLN A 348 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 94
      removed outlier: 6.686A  pdb=" N   PHE B  90 " --> pdb=" O   THR A 529 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   ILE A 531 " --> pdb=" O   PHE B  90 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   THR B  92 " --> pdb=" O   ILE A 531 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   GLY A 525 " --> pdb=" O   LEU A 514 " (cutoff:3.500A)
      removed outlier: 5.673A  pdb=" N   LEU A 514 " --> pdb=" O   GLY A 525 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 164
      removed outlier: 6.457A  pdb=" N   VAL B 160 " --> pdb=" O   ILE B 180 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   ILE B 182 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   ARG B 162 " --> pdb=" O   ILE B 182 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 346 through 350
      removed outlier: 6.693A  pdb=" N   ASP B 346 " --> pdb=" O   TYR B 373 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   ILE B 375 " --> pdb=" O   ASP B 346 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   GLN B 348 " --> pdb=" O   ILE B 375 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   TYR B 536 " --> pdb=" O   VAL B 532 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   VAL B 532 " --> pdb=" O   TYR B 536 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   GLY B 525 " --> pdb=" O   LEU B 514 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   LEU B 514 " --> pdb=" O   GLY B 525 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 346 through 350
      removed outlier: 6.693A  pdb=" N   ASP B 346 " --> pdb=" O   TYR B 373 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   ILE B 375 " --> pdb=" O   ASP B 346 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   GLN B 348 " --> pdb=" O   ILE B 375 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   TYR B 536 " --> pdb=" O   VAL B 532 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   VAL B 532 " --> pdb=" O   TYR B 536 " (cutoff:3.500A)
      removed outlier: 8.784A  pdb=" N   THR A  92 " --> pdb=" O   THR B 527 " (cutoff:3.500A)
      removed outlier: 7.290A  pdb=" N   THR B 529 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   ILE A  94 " --> pdb=" O   THR B 529 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ILE B 531 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 136 through 137

    538 hydrogen bonds defined for protein.
    1542 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.71

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 2085
        1.32 -     1.46: 3022
        1.46 -     1.59: 4346
        1.59 -     1.73: 11
        1.73 -     1.86: 68
  Bond restraints: 9532
  Sorted by residual:
  bond pdb=" CB  HIS B 201 "
       pdb=" CG  HIS B 201 "
    ideal  model  delta    sigma   weight residual
    1.497  1.397  0.100 1.40e-02 5.10e+03 5.14e+01
  bond pdb=" CB  HIS B 153 "
       pdb=" CG  HIS B 153 "
    ideal  model  delta    sigma   weight residual
    1.497  1.418  0.079 1.40e-02 5.10e+03 3.22e+01
  bond pdb=" CB  TYR B 552 "
       pdb=" CG  TYR B 552 "
    ideal  model  delta    sigma   weight residual
    1.512  1.397  0.115 2.20e-02 2.07e+03 2.75e+01
  bond pdb=" CB  PHE A  90 "
       pdb=" CG  PHE A  90 "
    ideal  model  delta    sigma   weight residual
    1.502  1.385  0.117 2.30e-02 1.89e+03 2.58e+01
  bond pdb=" CG  MET B 494 "
       pdb=" SD  MET B 494 "
    ideal  model  delta    sigma   weight residual
    1.803  1.678  0.125 2.50e-02 1.60e+03 2.52e+01
  ... (remaining 9527 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 10461
        2.06 -     4.11: 1944
        4.11 -     6.17: 331
        6.17 -     8.22: 79
        8.22 -    10.28: 21
  Bond angle restraints: 12836
  Sorted by residual:
  angle pdb=" CA  PHE A 313 "
        pdb=" CB  PHE A 313 "
        pdb=" CG  PHE A 313 "
      ideal   model   delta    sigma   weight residual
     113.80  105.83    7.97 1.00e+00 1.00e+00 6.36e+01
  angle pdb=" CA  ASP A 550 "
        pdb=" CB  ASP A 550 "
        pdb=" CG  ASP A 550 "
      ideal   model   delta    sigma   weight residual
     112.60  120.57   -7.97 1.00e+00 1.00e+00 6.36e+01
  angle pdb=" C   SER B 386 "
        pdb=" N   PRO B 387 "
        pdb=" CA  PRO B 387 "
      ideal   model   delta    sigma   weight residual
     119.56  127.47   -7.91 1.01e+00 9.80e-01 6.13e+01
  angle pdb=" C   TYR B 419 "
        pdb=" N   PRO B 420 "
        pdb=" CA  PRO B 420 "
      ideal   model   delta    sigma   weight residual
     119.56  127.53   -7.97 1.02e+00 9.61e-01 6.11e+01
  angle pdb=" C   TYR A 419 "
        pdb=" N   PRO A 420 "
        pdb=" CA  PRO A 420 "
      ideal   model   delta    sigma   weight residual
     119.56  127.44   -7.88 1.02e+00 9.61e-01 5.96e+01
  ... (remaining 12831 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 5476
       17.91 -    35.81: 176
       35.81 -    53.72: 26
       53.72 -    71.62: 9
       71.62 -    89.53: 7
  Dihedral angle restraints: 5694
    sinusoidal: 2374
      harmonic: 3320
  Sorted by residual:
  dihedral pdb=" C   ILE B  48 "
           pdb=" N   ILE B  48 "
           pdb=" CA  ILE B  48 "
           pdb=" CB  ILE B  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.80    9.80     0      2.50e+00 1.60e-01 1.54e+01
  dihedral pdb=" C   PHE B 501 "
           pdb=" N   PHE B 501 "
           pdb=" CA  PHE B 501 "
           pdb=" CB  PHE B 501 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.60   -9.00     0      2.50e+00 1.60e-01 1.30e+01
  dihedral pdb=" C   TYR B 385 "
           pdb=" N   TYR B 385 "
           pdb=" CA  TYR B 385 "
           pdb=" CB  TYR B 385 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.89   -8.71     0      2.50e+00 1.60e-01 1.21e+01
  ... (remaining 5691 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 923
       0.095 -    0.189: 364
       0.189 -    0.284: 87
       0.284 -    0.379: 13
       0.379 -    0.473: 1
  Chirality restraints: 1388
  Sorted by residual:
  chirality pdb=" CB  ILE B 531 "
            pdb=" CA  ILE B 531 "
            pdb=" CG1 ILE B 531 "
            pdb=" CG2 ILE B 531 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.17    0.47 2.00e-01 2.50e+01 5.60e+00
  chirality pdb=" CA  PHE A 313 "
            pdb=" N   PHE A 313 "
            pdb=" C   PHE A 313 "
            pdb=" CB  PHE A 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.54e+00
  chirality pdb=" CA  ASN B 436 "
            pdb=" N   ASN B 436 "
            pdb=" C   ASN B 436 "
            pdb=" CB  ASN B 436 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.25e+00
  ... (remaining 1385 not shown)

  Planarity restraints: 1574
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  36 "   -0.077 2.00e-02 2.50e+03   4.24e-02 3.60e+01
        pdb=" CG  TYR A  36 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  36 "    0.028 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  36 "    0.033 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  36 "    0.024 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  36 "    0.023 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  36 "    0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR A  36 "   -0.067 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 540 "   -0.075 2.00e-02 2.50e+03   3.64e-02 3.32e+01
        pdb=" CG  TRP A 540 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 540 "    0.035 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 540 "    0.030 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 540 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 540 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 540 "    0.038 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 540 "   -0.048 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 540 "    0.023 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 540 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 373 "    0.064 2.00e-02 2.50e+03   3.95e-02 3.12e+01
        pdb=" CG  TYR B 373 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 373 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 373 "   -0.026 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 373 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 373 "   -0.040 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 373 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR B 373 "    0.068 2.00e-02 2.50e+03
  ... (remaining 1571 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 67
        2.58 -     3.16: 8618
        3.16 -     3.74: 15153
        3.74 -     4.32: 22622
        4.32 -     4.90: 34188
  Nonbonded interactions: 80648
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 242 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.002 2.230
  nonbonded pdb=" OE2 GLU A 242 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.033 2.230
  nonbonded pdb=" OE2 GLU B 242 "
            pdb="ZN    ZN B 701 "
     model   vdw
     2.044 2.230
  nonbonded pdb=" OE1 GLU B 242 "
            pdb="ZN    ZN B 701 "
     model   vdw
     2.061 2.230
  nonbonded pdb=" CD  GLU A 242 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.345 2.460
  ... (remaining 80643 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: 0.02
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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.120
  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:             0.020
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.760
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4707
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      :  0.020   0.130   9536  Z= 1.094
  Angle     :  1.739  10.276  12836  Z= 1.191
  Chirality :  0.104   0.473   1388
  Planarity :  0.009   0.044   1574
  Dihedral  : 10.285  89.529   3554
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 1.81
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.55 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.24), residues: 1100
  helix:  0.79 (0.20), residues: 534
  sheet: -0.15 (0.46), residues: 117
  loop : -0.21 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 162 
 TYR   0.077   0.012   TYR A  36 
 PHE   0.037   0.007   PHE A 274 
 TRP   0.075   0.013   TRP A 540 
 HIS   0.009   0.002   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.01975 ( 9532)
  covalent geometry    : angle       1.73869 (12836)
  hydrogen bonds       : bond        0.16429 (  508)
  hydrogen bonds       : angle       7.09006 ( 1542)
  metal coordination   : bond        0.04009 (    4)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 TYR cc_start: 0.8886 (t80) cc_final: 0.7920 (t80)
REVERT: A  131 LEU cc_start: 0.9043 (mt) cc_final: 0.8838 (mp)
REVERT: A  143 LYS cc_start: 0.8863 (tttm) cc_final: 0.8445 (tmtt)
REVERT: A  147 ASP cc_start: 0.8624 (m-30) cc_final: 0.8340 (m-30)
REVERT: A  149 ILE cc_start: 0.9315 (mt) cc_final: 0.8812 (mm)
REVERT: A  180 ILE cc_start: 0.8271 (mt) cc_final: 0.7615 (mt)
REVERT: A  181 LEU cc_start: 0.9043 (mp) cc_final: 0.8751 (mp)
REVERT: A  208 ASN cc_start: 0.9097 (m-40) cc_final: 0.7563 (m110)
REVERT: A  215 ILE cc_start: 0.8958 (mt) cc_final: 0.8726 (mt)
REVERT: A  216 ILE cc_start: 0.9672 (mt) cc_final: 0.9248 (mt)
REVERT: A  220 PHE cc_start: 0.7931 (m-10) cc_final: 0.7512 (m-80)
REVERT: A  227 ASN cc_start: 0.8976 (t0) cc_final: 0.8402 (t0)
REVERT: A  248 PHE cc_start: 0.6596 (m-80) cc_final: 0.6072 (m-80)
REVERT: A  292 LYS cc_start: 0.8466 (tptt) cc_final: 0.7860 (tttm)
REVERT: A  296 ILE cc_start: 0.9503 (mt) cc_final: 0.9228 (mm)
REVERT: A  297 ASN cc_start: 0.8594 (m-40) cc_final: 0.8230 (m110)
REVERT: A  311 LEU cc_start: 0.9239 (pp) cc_final: 0.8840 (mp)
REVERT: A  368 MET cc_start: -0.2061 (tpt) cc_final: -0.2607 (ttm)
REVERT: A  462 ASN cc_start: 0.5872 (t0) cc_final: 0.5219 (m-40)
REVERT: A  553 TYR cc_start: 0.3296 (m-80) cc_final: 0.1548 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.0813
  time to fit residues: 19.5905
Evaluate side-chains
  114 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    0.0470
   overall best weight:    2.1484
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 241 ASN
A 567 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.182762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.141619 restraints weight = 13168.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.146119 restraints weight = 8885.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.149614 restraints weight = 6420.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.152325 restraints weight = 4812.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.154207 restraints weight = 3739.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.4140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6063
moved from start:          1.0435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   9536  Z= 0.209
  Angle     :  0.794  11.126  12836  Z= 0.441
  Chirality :  0.048   0.150   1388
  Planarity :  0.005   0.036   1574
  Dihedral  :  5.628  27.397   1208
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 18.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  3.67 %
    Favored  : 95.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.25), residues: 1100
  helix:  1.28 (0.21), residues: 562
  sheet:  0.27 (0.47), residues: 126
  loop : -0.67 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 293 
 TYR   0.030   0.003   TYR A 524 
 PHE   0.037   0.003   PHE A  14 
 TRP   0.035   0.003   TRP B 414 
 HIS   0.008   0.001   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 9532)
  covalent geometry    : angle       0.79350 (12836)
  hydrogen bonds       : bond        0.07449 (  508)
  hydrogen bonds       : angle       5.44562 ( 1542)
  metal coordination   : bond        0.00104 (    4)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 156
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 LYS cc_start: 0.8661 (pttp) cc_final: 0.8098 (pttt)
REVERT: A   31 ASN cc_start: 0.9338 (m-40) cc_final: 0.8882 (p0)
REVERT: A   54 LYS cc_start: 0.9179 (mmmt) cc_final: 0.8944 (mmmt)
REVERT: A  110 TRP cc_start: 0.8500 (t60) cc_final: 0.7703 (t60)
REVERT: A  121 PHE cc_start: 0.9443 (t80) cc_final: 0.9059 (t80)
REVERT: A  123 LYS cc_start: 0.9094 (mmmt) cc_final: 0.8838 (ptpp)
REVERT: A  126 LEU cc_start: 0.9436 (mt) cc_final: 0.9100 (mt)
REVERT: A  127 TYR cc_start: 0.9004 (t80) cc_final: 0.8698 (t80)
REVERT: A  147 ASP cc_start: 0.8592 (m-30) cc_final: 0.8371 (m-30)
REVERT: A  202 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8748 (mt-10)
REVERT: A  212 LEU cc_start: 0.9532 (tp) cc_final: 0.9230 (tp)
REVERT: A  227 ASN cc_start: 0.8629 (t0) cc_final: 0.8145 (t0)
REVERT: A  233 VAL cc_start: 0.8853 (m) cc_final: 0.8507 (m)
REVERT: A  241 ASN cc_start: 0.9373 (m110) cc_final: 0.9108 (t0)
REVERT: A  244 GLU cc_start: 0.8710 (mm-30) cc_final: 0.7798 (mm-30)
REVERT: A  248 PHE cc_start: 0.8093 (m-80) cc_final: 0.7493 (m-80)
REVERT: A  282 HIS cc_start: 0.7595 (m-70) cc_final: 0.7069 (m-70)
REVERT: A  295 LEU cc_start: 0.9478 (mt) cc_final: 0.9181 (mt)
REVERT: A  297 ASN cc_start: 0.9083 (m-40) cc_final: 0.8619 (m110)
REVERT: A  320 LEU cc_start: 0.9415 (mt) cc_final: 0.9188 (mt)
REVERT: A  494 MET cc_start: 0.6120 (ptt) cc_final: 0.5697 (ptt)
REVERT: A  495 MET cc_start: 0.6790 (mmt) cc_final: 0.6361 (mmm)
  outliers start: 3
  outliers final: 1
  residues processed: 157
  average time/residue: 0.0776
  time to fit residues: 15.4383
Evaluate side-chains
  120 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 18 optimal weight:    7.9990
   chunk 90 optimal weight:    9.9990
   chunk 7 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 80 optimal weight:    7.9990
   chunk 15 optimal weight:    8.9990
   chunk 106 optimal weight:    0.0170
   chunk 51 optimal weight:    0.0170
   chunk 77 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.7860
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 500 HIS
A 518 ASN
A 557 HIS
A 567 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.180594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.141158 restraints weight = 13336.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.145120 restraints weight = 9204.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.148320 restraints weight = 6801.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.150576 restraints weight = 5249.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.152285 restraints weight = 4205.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.4145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6264
moved from start:          1.1211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9536  Z= 0.149
  Angle     :  0.682  11.014  12836  Z= 0.377
  Chirality :  0.044   0.145   1388
  Planarity :  0.004   0.045   1574
  Dihedral  :  5.319  21.271   1208
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 15.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.24), residues: 1100
  helix:  0.51 (0.21), residues: 568
  sheet:  0.16 (0.44), residues: 126
  loop : -1.09 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 247 
 TYR   0.025   0.002   TYR B 524 
 PHE   0.037   0.002   PHE B  14 
 TRP   0.026   0.002   TRP A 414 
 HIS   0.007   0.001   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9532)
  covalent geometry    : angle       0.68209 (12836)
  hydrogen bonds       : bond        0.05790 (  508)
  hydrogen bonds       : angle       5.10332 ( 1542)
  metal coordination   : bond        0.00187 (    4)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 LEU cc_start: 0.9175 (mt) cc_final: 0.8635 (pp)
REVERT: A  110 TRP cc_start: 0.8452 (t60) cc_final: 0.7678 (t60)
REVERT: A  116 ILE cc_start: 0.9479 (mm) cc_final: 0.9168 (pt)
REVERT: A  121 PHE cc_start: 0.9250 (t80) cc_final: 0.8962 (t80)
REVERT: A  126 LEU cc_start: 0.9191 (mt) cc_final: 0.8777 (mt)
REVERT: A  137 TYR cc_start: 0.8473 (p90) cc_final: 0.8147 (p90)
REVERT: A  141 ASN cc_start: 0.9517 (m-40) cc_final: 0.9161 (m-40)
REVERT: A  199 ILE cc_start: 0.9736 (mm) cc_final: 0.9452 (mm)
REVERT: A  202 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8680 (mt-10)
REVERT: A  208 ASN cc_start: 0.9121 (m110) cc_final: 0.8335 (m110)
REVERT: A  215 ILE cc_start: 0.9146 (tp) cc_final: 0.8871 (pt)
REVERT: A  218 ASN cc_start: 0.9308 (t0) cc_final: 0.8459 (t0)
REVERT: A  227 ASN cc_start: 0.8695 (t0) cc_final: 0.7991 (t0)
REVERT: A  233 VAL cc_start: 0.8962 (m) cc_final: 0.8578 (m)
REVERT: A  237 ILE cc_start: 0.9626 (mt) cc_final: 0.9394 (mt)
REVERT: A  241 ASN cc_start: 0.9527 (m110) cc_final: 0.9233 (t0)
REVERT: A  244 GLU cc_start: 0.8879 (mm-30) cc_final: 0.7353 (mm-30)
REVERT: A  247 ARG cc_start: 0.9336 (ttp-170) cc_final: 0.8853 (ttp-170)
REVERT: A  248 PHE cc_start: 0.8225 (m-80) cc_final: 0.7270 (m-10)
REVERT: A  292 LYS cc_start: 0.8770 (tptt) cc_final: 0.8353 (ttmt)
REVERT: A  295 LEU cc_start: 0.9442 (mt) cc_final: 0.9181 (mt)
REVERT: A  297 ASN cc_start: 0.8886 (m-40) cc_final: 0.8533 (m110)
REVERT: A  302 ASN cc_start: 0.9133 (t0) cc_final: 0.8852 (t0)
REVERT: A  322 MET cc_start: 0.9384 (mpp) cc_final: 0.9151 (mmt)
REVERT: A  495 MET cc_start: 0.7299 (mmt) cc_final: 0.6775 (mmt)
REVERT: A  553 TYR cc_start: 0.7051 (m-80) cc_final: 0.6376 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.0740
  time to fit residues: 13.8874
Evaluate side-chains
  119 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 100 optimal weight:    5.9990
   chunk 96 optimal weight:    0.6980
   chunk 104 optimal weight:    0.0970
   chunk 49 optimal weight:    0.0970
   chunk 5 optimal weight:    8.9990
   chunk 71 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 64 optimal weight:    0.0970
   chunk 31 optimal weight:    0.4980
   chunk 68 optimal weight:    0.4980
   overall best weight:    0.2574
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 239 HIS
A 285 ASN
A 567 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.185651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.144202 restraints weight = 13503.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.148540 restraints weight = 9421.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.151820 restraints weight = 6953.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.154211 restraints weight = 5295.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.155869 restraints weight = 4181.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.4197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6223
moved from start:          1.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9536  Z= 0.139
  Angle     :  0.705  19.280  12836  Z= 0.374
  Chirality :  0.042   0.139   1388
  Planarity :  0.004   0.036   1574
  Dihedral  :  5.149  26.287   1208
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 15.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.25), residues: 1100
  helix:  0.67 (0.21), residues: 568
  sheet:  0.26 (0.45), residues: 126
  loop : -1.27 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 162 
 TYR   0.023   0.002   TYR B 544 
 PHE   0.040   0.002   PHE B  22 
 TRP   0.018   0.002   TRP A 414 
 HIS   0.006   0.001   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9532)
  covalent geometry    : angle       0.70515 (12836)
  hydrogen bonds       : bond        0.05252 (  508)
  hydrogen bonds       : angle       5.06877 ( 1542)
  metal coordination   : bond        0.00042 (    4)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 ARG cc_start: 0.8366 (tpt90) cc_final: 0.7806 (tpt90)
REVERT: A   34 LEU cc_start: 0.9022 (tp) cc_final: 0.8647 (pp)
REVERT: A  110 TRP cc_start: 0.8375 (t60) cc_final: 0.7679 (t60)
REVERT: A  116 ILE cc_start: 0.9403 (mm) cc_final: 0.9159 (pt)
REVERT: A  121 PHE cc_start: 0.9525 (t80) cc_final: 0.9005 (t80)
REVERT: A  122 LEU cc_start: 0.9407 (tp) cc_final: 0.9192 (tp)
REVERT: A  126 LEU cc_start: 0.9299 (mt) cc_final: 0.8824 (mt)
REVERT: A  141 ASN cc_start: 0.9338 (m-40) cc_final: 0.9015 (m-40)
REVERT: A  147 ASP cc_start: 0.8630 (m-30) cc_final: 0.8393 (m-30)
REVERT: A  180 ILE cc_start: 0.8783 (mp) cc_final: 0.7569 (mp)
REVERT: A  208 ASN cc_start: 0.8852 (m110) cc_final: 0.8202 (m-40)
REVERT: A  213 HIS cc_start: 0.8892 (m90) cc_final: 0.8542 (m90)
REVERT: A  215 ILE cc_start: 0.9093 (tp) cc_final: 0.8813 (pt)
REVERT: A  218 ASN cc_start: 0.9270 (t0) cc_final: 0.8352 (t0)
REVERT: A  227 ASN cc_start: 0.8521 (t0) cc_final: 0.7763 (t0)
REVERT: A  233 VAL cc_start: 0.8859 (m) cc_final: 0.8482 (m)
REVERT: A  239 HIS cc_start: 0.8934 (m90) cc_final: 0.8276 (m90)
REVERT: A  244 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8354 (mm-30)
REVERT: A  247 ARG cc_start: 0.9285 (ttp-170) cc_final: 0.8975 (tmm-80)
REVERT: A  275 PHE cc_start: 0.8513 (t80) cc_final: 0.8111 (t80)
REVERT: A  295 LEU cc_start: 0.9457 (mt) cc_final: 0.9231 (mt)
REVERT: A  297 ASN cc_start: 0.8991 (m-40) cc_final: 0.8640 (m110)
REVERT: A  320 LEU cc_start: 0.9360 (mm) cc_final: 0.9083 (mm)
REVERT: A  322 MET cc_start: 0.9333 (mpp) cc_final: 0.9120 (mpp)
REVERT: A  325 GLN cc_start: 0.9257 (pm20) cc_final: 0.9035 (pm20)
REVERT: A  553 TYR cc_start: 0.6604 (m-80) cc_final: 0.6116 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.0656
  time to fit residues: 12.5875
Evaluate side-chains
  118 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0020
   chunk 45 optimal weight:    7.9990
   chunk 31 optimal weight:    6.9990
   chunk 83 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0770
   chunk 47 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.5546
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 231 HIS
A 567 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4559 r_free = 0.4559 target = 0.184889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.143585 restraints weight = 14002.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.148105 restraints weight = 9551.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.151310 restraints weight = 6903.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.153633 restraints weight = 5249.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.155380 restraints weight = 4140.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.4183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6259
moved from start:          1.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9536  Z= 0.135
  Angle     :  0.659   7.290  12836  Z= 0.364
  Chirality :  0.041   0.136   1388
  Planarity :  0.004   0.039   1574
  Dihedral  :  4.946  18.676   1208
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.24), residues: 1100
  helix:  0.68 (0.21), residues: 568
  sheet:  0.23 (0.43), residues: 136
  loop : -1.38 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 194 
 TYR   0.020   0.002   TYR A 544 
 PHE   0.058   0.002   PHE A  14 
 TRP   0.034   0.003   TRP A 414 
 HIS   0.006   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9532)
  covalent geometry    : angle       0.65950 (12836)
  hydrogen bonds       : bond        0.05092 (  508)
  hydrogen bonds       : angle       4.98537 ( 1542)
  metal coordination   : bond        0.00031 (    4)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5564 (mtt) cc_final: 0.5120 (mtt)
REVERT: A   28 ARG cc_start: 0.8327 (tpt90) cc_final: 0.7807 (tpt90)
REVERT: A   34 LEU cc_start: 0.8971 (tp) cc_final: 0.8651 (pp)
REVERT: A  110 TRP cc_start: 0.8288 (t60) cc_final: 0.7552 (t60)
REVERT: A  116 ILE cc_start: 0.9298 (mm) cc_final: 0.9032 (pt)
REVERT: A  117 LEU cc_start: 0.9199 (mt) cc_final: 0.8952 (mt)
REVERT: A  121 PHE cc_start: 0.9537 (t80) cc_final: 0.9059 (t80)
REVERT: A  122 LEU cc_start: 0.9416 (tp) cc_final: 0.9170 (tp)
REVERT: A  126 LEU cc_start: 0.9234 (mt) cc_final: 0.8930 (mt)
REVERT: A  141 ASN cc_start: 0.9334 (m-40) cc_final: 0.8937 (m-40)
REVERT: A  153 HIS cc_start: 0.8418 (m90) cc_final: 0.8193 (m90)
REVERT: A  198 ILE cc_start: 0.9259 (pt) cc_final: 0.8981 (pt)
REVERT: A  199 ILE cc_start: 0.9751 (mm) cc_final: 0.9446 (mm)
REVERT: A  202 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8924 (mt-10)
REVERT: A  208 ASN cc_start: 0.8805 (m110) cc_final: 0.8131 (m110)
REVERT: A  213 HIS cc_start: 0.8803 (m90) cc_final: 0.8551 (m90)
REVERT: A  215 ILE cc_start: 0.9162 (tp) cc_final: 0.8885 (pt)
REVERT: A  218 ASN cc_start: 0.9324 (t0) cc_final: 0.8413 (t0)
REVERT: A  233 VAL cc_start: 0.8815 (m) cc_final: 0.8439 (m)
REVERT: A  247 ARG cc_start: 0.9328 (ttp-170) cc_final: 0.8724 (ttp-170)
REVERT: A  248 PHE cc_start: 0.8139 (m-80) cc_final: 0.6989 (m-10)
REVERT: A  275 PHE cc_start: 0.8573 (t80) cc_final: 0.8043 (t80)
REVERT: A  295 LEU cc_start: 0.9400 (mt) cc_final: 0.9095 (mt)
REVERT: A  297 ASN cc_start: 0.9008 (m-40) cc_final: 0.8669 (m110)
REVERT: A  320 LEU cc_start: 0.9415 (mm) cc_final: 0.8959 (mm)
REVERT: A  462 ASN cc_start: 0.5085 (m-40) cc_final: 0.4801 (t0)
REVERT: A  495 MET cc_start: 0.6306 (mmt) cc_final: 0.6087 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.0587
  time to fit residues: 10.6468
Evaluate side-chains
  115 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 65 optimal weight:    0.2980
   chunk 3 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 52 optimal weight:    0.7980
   chunk 85 optimal weight:    0.3980
   chunk 75 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 79 optimal weight:   20.0000
   overall best weight:    0.6580
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 567 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.185297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.143256 restraints weight = 13607.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.147702 restraints weight = 9358.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.150842 restraints weight = 6896.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.153171 restraints weight = 5340.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.154986 restraints weight = 4287.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.4179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6308
moved from start:          1.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9536  Z= 0.135
  Angle     :  0.656   7.123  12836  Z= 0.358
  Chirality :  0.042   0.182   1388
  Planarity :  0.004   0.036   1574
  Dihedral  :  4.774  16.322   1208
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.24), residues: 1100
  helix:  0.60 (0.21), residues: 568
  sheet:  0.47 (0.44), residues: 136
  loop : -1.43 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 194 
 TYR   0.017   0.002   TYR B 544 
 PHE   0.030   0.002   PHE B  14 
 TRP   0.031   0.003   TRP B 414 
 HIS   0.004   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 9532)
  covalent geometry    : angle       0.65611 (12836)
  hydrogen bonds       : bond        0.04978 (  508)
  hydrogen bonds       : angle       5.07851 ( 1542)
  metal coordination   : bond        0.00053 (    4)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 PHE cc_start: 0.8898 (m-80) cc_final: 0.8688 (m-80)
REVERT: A   28 ARG cc_start: 0.8242 (tpt90) cc_final: 0.7811 (tpt90)
REVERT: A   43 LEU cc_start: 0.9305 (mt) cc_final: 0.9105 (mt)
REVERT: A   44 LEU cc_start: 0.9676 (mt) cc_final: 0.9393 (pp)
REVERT: A  110 TRP cc_start: 0.8260 (t60) cc_final: 0.7530 (t60)
REVERT: A  116 ILE cc_start: 0.9324 (mm) cc_final: 0.9093 (pt)
REVERT: A  121 PHE cc_start: 0.9473 (t80) cc_final: 0.8981 (t80)
REVERT: A  126 LEU cc_start: 0.9087 (mt) cc_final: 0.8773 (mt)
REVERT: A  138 LEU cc_start: 0.7526 (mt) cc_final: 0.7288 (mt)
REVERT: A  141 ASN cc_start: 0.9384 (m-40) cc_final: 0.8863 (p0)
REVERT: A  178 TYR cc_start: 0.7003 (m-80) cc_final: 0.5863 (m-80)
REVERT: A  198 ILE cc_start: 0.9219 (pt) cc_final: 0.8913 (pt)
REVERT: A  199 ILE cc_start: 0.9727 (mm) cc_final: 0.9411 (mm)
REVERT: A  202 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8893 (mt-10)
REVERT: A  208 ASN cc_start: 0.8812 (m110) cc_final: 0.8493 (m110)
REVERT: A  212 LEU cc_start: 0.9507 (tp) cc_final: 0.9259 (mt)
REVERT: A  213 HIS cc_start: 0.8739 (m90) cc_final: 0.8535 (m170)
REVERT: A  218 ASN cc_start: 0.9330 (t0) cc_final: 0.8436 (t0)
REVERT: A  233 VAL cc_start: 0.8838 (m) cc_final: 0.8422 (m)
REVERT: A  247 ARG cc_start: 0.9246 (ttp-170) cc_final: 0.8816 (ttp-170)
REVERT: A  295 LEU cc_start: 0.9484 (mt) cc_final: 0.9235 (mt)
REVERT: A  297 ASN cc_start: 0.9004 (m-40) cc_final: 0.8663 (m110)
REVERT: A  320 LEU cc_start: 0.9497 (mm) cc_final: 0.9070 (mm)
REVERT: A  462 ASN cc_start: 0.5218 (m-40) cc_final: 0.4950 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.0621
  time to fit residues: 11.5087
Evaluate side-chains
  114 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 96 optimal weight:    0.1980
   chunk 19 optimal weight:    3.9990
   chunk 64 optimal weight:    8.9990
   chunk 27 optimal weight:    0.0170
   chunk 81 optimal weight:    6.9990
   chunk 13 optimal weight:    0.5980
   chunk 57 optimal weight:    5.9990
   chunk 92 optimal weight:    0.0050
   chunk 58 optimal weight:    0.0070
   chunk 23 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.1650
-------------------------------------------------------------------------------
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 = 0.4547 r_free = 0.4547 target = 0.185461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.144794 restraints weight = 13846.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.149034 restraints weight = 9534.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.152132 restraints weight = 7037.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.154603 restraints weight = 5438.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.156512 restraints weight = 4374.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.4193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6183
moved from start:          1.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9536  Z= 0.131
  Angle     :  0.637   7.029  12836  Z= 0.349
  Chirality :  0.042   0.155   1388
  Planarity :  0.004   0.040   1574
  Dihedral  :  4.691  17.700   1208
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.27 (0.24), residues: 1100
  helix:  0.64 (0.20), residues: 570
  sheet:  0.53 (0.44), residues: 136
  loop : -1.61 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 294 
 TYR   0.019   0.002   TYR A 544 
 PHE   0.023   0.002   PHE A  16 
 TRP   0.029   0.002   TRP B 414 
 HIS   0.004   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9532)
  covalent geometry    : angle       0.63651 (12836)
  hydrogen bonds       : bond        0.04830 (  508)
  hydrogen bonds       : angle       4.93191 ( 1542)
  metal coordination   : bond        0.00024 (    4)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 PHE cc_start: 0.9562 (t80) cc_final: 0.8936 (t80)
REVERT: A   28 ARG cc_start: 0.8252 (tpt90) cc_final: 0.7718 (tpt90)
REVERT: A   34 LEU cc_start: 0.8904 (tp) cc_final: 0.8606 (pp)
REVERT: A  110 TRP cc_start: 0.8251 (t60) cc_final: 0.7562 (t60)
REVERT: A  116 ILE cc_start: 0.9355 (mm) cc_final: 0.9131 (pt)
REVERT: A  121 PHE cc_start: 0.9533 (t80) cc_final: 0.9260 (t80)
REVERT: A  126 LEU cc_start: 0.8994 (mt) cc_final: 0.8742 (mt)
REVERT: A  138 LEU cc_start: 0.7311 (mt) cc_final: 0.6980 (mt)
REVERT: A  141 ASN cc_start: 0.9425 (m-40) cc_final: 0.8547 (p0)
REVERT: A  145 LYS cc_start: 0.9626 (mttm) cc_final: 0.9276 (mttm)
REVERT: A  178 TYR cc_start: 0.7333 (m-80) cc_final: 0.6254 (m-80)
REVERT: A  198 ILE cc_start: 0.9213 (pt) cc_final: 0.8969 (pt)
REVERT: A  199 ILE cc_start: 0.9697 (mm) cc_final: 0.9443 (mm)
REVERT: A  208 ASN cc_start: 0.8753 (m110) cc_final: 0.8143 (m110)
REVERT: A  212 LEU cc_start: 0.9604 (tp) cc_final: 0.9303 (mt)
REVERT: A  213 HIS cc_start: 0.8673 (m90) cc_final: 0.8368 (m90)
REVERT: A  218 ASN cc_start: 0.9320 (t0) cc_final: 0.8557 (t0)
REVERT: A  233 VAL cc_start: 0.8779 (m) cc_final: 0.8372 (m)
REVERT: A  247 ARG cc_start: 0.9323 (ttp-170) cc_final: 0.9039 (ttp-170)
REVERT: A  248 PHE cc_start: 0.8051 (m-80) cc_final: 0.7528 (m-10)
REVERT: A  267 ASP cc_start: 0.9235 (m-30) cc_final: 0.8777 (m-30)
REVERT: A  275 PHE cc_start: 0.9048 (t80) cc_final: 0.8620 (t80)
REVERT: A  291 LEU cc_start: 0.8937 (tp) cc_final: 0.8503 (tp)
REVERT: A  295 LEU cc_start: 0.9422 (mt) cc_final: 0.9082 (mt)
REVERT: A  297 ASN cc_start: 0.9111 (m-40) cc_final: 0.8771 (m110)
REVERT: A  317 PHE cc_start: 0.9357 (m-80) cc_final: 0.8828 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0609
  time to fit residues: 10.9371
Evaluate side-chains
  109 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 28 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 89 optimal weight:    0.2980
   chunk 88 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   chunk 51 optimal weight:    8.9990
   chunk 72 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0870
   overall best weight:    0.5958
-------------------------------------------------------------------------------
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 = 0.4580 r_free = 0.4580 target = 0.186622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.144489 restraints weight = 13242.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.148948 restraints weight = 9107.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.152271 restraints weight = 6649.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.154731 restraints weight = 5078.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.156400 restraints weight = 4033.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.4199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6280
moved from start:          1.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9536  Z= 0.125
  Angle     :  0.637   9.441  12836  Z= 0.345
  Chirality :  0.042   0.179   1388
  Planarity :  0.004   0.039   1574
  Dihedral  :  4.513  17.079   1208
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.24), residues: 1100
  helix:  0.63 (0.20), residues: 570
  sheet:  0.36 (0.44), residues: 136
  loop : -1.60 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 294 
 TYR   0.015   0.001   TYR B 441 
 PHE   0.033   0.002   PHE A  14 
 TRP   0.031   0.003   TRP B 414 
 HIS   0.005   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 9532)
  covalent geometry    : angle       0.63714 (12836)
  hydrogen bonds       : bond        0.04636 (  508)
  hydrogen bonds       : angle       4.93798 ( 1542)
  metal coordination   : bond        0.00018 (    4)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 PHE cc_start: 0.9484 (t80) cc_final: 0.8917 (t80)
REVERT: A   28 ARG cc_start: 0.8392 (tpt90) cc_final: 0.7857 (tpt90)
REVERT: A   34 LEU cc_start: 0.8986 (tp) cc_final: 0.8653 (tp)
REVERT: A   39 TRP cc_start: 0.8757 (m100) cc_final: 0.7122 (m-90)
REVERT: A   42 THR cc_start: 0.9394 (p) cc_final: 0.9180 (p)
REVERT: A  110 TRP cc_start: 0.8351 (t60) cc_final: 0.7540 (t60)
REVERT: A  116 ILE cc_start: 0.9333 (mm) cc_final: 0.9106 (pt)
REVERT: A  121 PHE cc_start: 0.9470 (t80) cc_final: 0.9256 (t80)
REVERT: A  126 LEU cc_start: 0.9125 (mt) cc_final: 0.8920 (mt)
REVERT: A  138 LEU cc_start: 0.7221 (mt) cc_final: 0.6929 (mt)
REVERT: A  141 ASN cc_start: 0.9354 (m-40) cc_final: 0.8753 (p0)
REVERT: A  178 TYR cc_start: 0.7288 (m-80) cc_final: 0.6216 (m-80)
REVERT: A  198 ILE cc_start: 0.9336 (pt) cc_final: 0.9024 (pt)
REVERT: A  199 ILE cc_start: 0.9752 (mm) cc_final: 0.9408 (mm)
REVERT: A  208 ASN cc_start: 0.8755 (m110) cc_final: 0.8098 (m110)
REVERT: A  212 LEU cc_start: 0.9606 (tp) cc_final: 0.9239 (mt)
REVERT: A  213 HIS cc_start: 0.8645 (m90) cc_final: 0.8369 (m90)
REVERT: A  215 ILE cc_start: 0.9199 (tp) cc_final: 0.8851 (pt)
REVERT: A  218 ASN cc_start: 0.9316 (t0) cc_final: 0.8606 (t0)
REVERT: A  233 VAL cc_start: 0.8836 (m) cc_final: 0.8306 (m)
REVERT: A  240 ASP cc_start: 0.9336 (m-30) cc_final: 0.8998 (m-30)
REVERT: A  241 ASN cc_start: 0.9289 (t0) cc_final: 0.9057 (t0)
REVERT: A  244 GLU cc_start: 0.9102 (mm-30) cc_final: 0.6799 (mm-30)
REVERT: A  247 ARG cc_start: 0.9211 (ttp-170) cc_final: 0.8954 (ttp-110)
REVERT: A  248 PHE cc_start: 0.7972 (m-80) cc_final: 0.7270 (m-10)
REVERT: A  267 ASP cc_start: 0.9141 (m-30) cc_final: 0.8658 (m-30)
REVERT: A  275 PHE cc_start: 0.9109 (t80) cc_final: 0.8815 (t80)
REVERT: A  291 LEU cc_start: 0.8953 (tp) cc_final: 0.8496 (tp)
REVERT: A  295 LEU cc_start: 0.9433 (mt) cc_final: 0.9069 (mt)
REVERT: A  317 PHE cc_start: 0.9371 (m-80) cc_final: 0.8846 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0654
  time to fit residues: 11.3741
Evaluate side-chains
  115 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 104 optimal weight:    4.9990
   chunk 67 optimal weight:    0.1980
   chunk 37 optimal weight:    0.5980
   chunk 71 optimal weight:    0.6980
   chunk 23 optimal weight:    5.9990
   chunk 83 optimal weight:    0.9990
   chunk 88 optimal weight:    8.9990
   chunk 74 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 70 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   overall best weight:    0.8984
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.186202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.145004 restraints weight = 13483.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.149268 restraints weight = 9278.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.152314 restraints weight = 6802.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.154395 restraints weight = 5235.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.156222 restraints weight = 4226.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.4192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6317
moved from start:          1.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9536  Z= 0.125
  Angle     :  0.622   9.127  12836  Z= 0.339
  Chirality :  0.041   0.140   1388
  Planarity :  0.004   0.034   1574
  Dihedral  :  4.526  17.658   1208
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 14.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.24), residues: 1100
  helix:  0.65 (0.20), residues: 574
  sheet:  0.38 (0.44), residues: 136
  loop : -1.57 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 294 
 TYR   0.016   0.001   TYR A 544 
 PHE   0.048   0.002   PHE B  14 
 TRP   0.033   0.002   TRP A 414 
 HIS   0.004   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 9532)
  covalent geometry    : angle       0.62236 (12836)
  hydrogen bonds       : bond        0.04356 (  508)
  hydrogen bonds       : angle       4.95222 ( 1542)
  metal coordination   : bond        0.00017 (    4)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 PHE cc_start: 0.9498 (t80) cc_final: 0.8961 (t80)
REVERT: A   28 ARG cc_start: 0.8486 (tpt90) cc_final: 0.8021 (tpt90)
REVERT: A  110 TRP cc_start: 0.8488 (t60) cc_final: 0.7578 (t60)
REVERT: A  116 ILE cc_start: 0.9305 (mm) cc_final: 0.9046 (pt)
REVERT: A  126 LEU cc_start: 0.9113 (mt) cc_final: 0.8858 (mt)
REVERT: A  138 LEU cc_start: 0.6561 (mt) cc_final: 0.6228 (mt)
REVERT: A  141 ASN cc_start: 0.9288 (m-40) cc_final: 0.8879 (m-40)
REVERT: A  178 TYR cc_start: 0.7325 (m-80) cc_final: 0.6297 (m-80)
REVERT: A  198 ILE cc_start: 0.9269 (pt) cc_final: 0.8914 (pt)
REVERT: A  199 ILE cc_start: 0.9748 (mm) cc_final: 0.9412 (mm)
REVERT: A  208 ASN cc_start: 0.8761 (m110) cc_final: 0.8225 (m110)
REVERT: A  212 LEU cc_start: 0.9624 (tp) cc_final: 0.9216 (mt)
REVERT: A  213 HIS cc_start: 0.8643 (m90) cc_final: 0.8375 (m90)
REVERT: A  215 ILE cc_start: 0.9216 (tp) cc_final: 0.8862 (pt)
REVERT: A  218 ASN cc_start: 0.9284 (t0) cc_final: 0.8564 (t0)
REVERT: A  233 VAL cc_start: 0.8850 (m) cc_final: 0.8478 (m)
REVERT: A  241 ASN cc_start: 0.9229 (t0) cc_final: 0.9021 (t0)
REVERT: A  244 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8924 (mm-30)
REVERT: A  247 ARG cc_start: 0.9162 (ttp-170) cc_final: 0.8922 (ttp80)
REVERT: A  267 ASP cc_start: 0.9169 (m-30) cc_final: 0.8714 (m-30)
REVERT: A  295 LEU cc_start: 0.9379 (mt) cc_final: 0.9136 (mt)
REVERT: A  297 ASN cc_start: 0.9012 (m-40) cc_final: 0.8694 (m110)
REVERT: A  317 PHE cc_start: 0.9391 (m-80) cc_final: 0.8791 (m-80)
REVERT: A  322 MET cc_start: 0.9310 (mpp) cc_final: 0.9104 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.0635
  time to fit residues: 11.1400
Evaluate side-chains
  108 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 49 optimal weight:    0.4980
   chunk 105 optimal weight:    0.3980
   chunk 106 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 72 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0050
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.5394
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.188301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.146214 restraints weight = 13695.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.150495 restraints weight = 9394.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.153743 restraints weight = 6901.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.155957 restraints weight = 5319.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.157797 restraints weight = 4263.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.4204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6296
moved from start:          1.2958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9536  Z= 0.121
  Angle     :  0.619   9.459  12836  Z= 0.337
  Chirality :  0.041   0.142   1388
  Planarity :  0.004   0.034   1574
  Dihedral  :  4.476  18.069   1208
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.24), residues: 1100
  helix:  0.67 (0.20), residues: 578
  sheet:  0.46 (0.45), residues: 136
  loop : -1.64 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 294 
 TYR   0.015   0.001   TYR A 441 
 PHE   0.044   0.002   PHE A  14 
 TRP   0.034   0.002   TRP B 414 
 HIS   0.004   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 9532)
  covalent geometry    : angle       0.61856 (12836)
  hydrogen bonds       : bond        0.04359 (  508)
  hydrogen bonds       : angle       4.89976 ( 1542)
  metal coordination   : bond        0.00020 (    4)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 PHE cc_start: 0.9451 (t80) cc_final: 0.9071 (t80)
REVERT: A   28 ARG cc_start: 0.8453 (tpt90) cc_final: 0.8040 (tpt90)
REVERT: A   39 TRP cc_start: 0.8752 (m100) cc_final: 0.7211 (m-90)
REVERT: A  110 TRP cc_start: 0.8440 (t60) cc_final: 0.7666 (t60)
REVERT: A  116 ILE cc_start: 0.9301 (mm) cc_final: 0.9006 (pt)
REVERT: A  121 PHE cc_start: 0.9481 (t80) cc_final: 0.9213 (m-80)
REVERT: A  126 LEU cc_start: 0.9092 (mt) cc_final: 0.8818 (mt)
REVERT: A  138 LEU cc_start: 0.6755 (mt) cc_final: 0.6377 (mt)
REVERT: A  141 ASN cc_start: 0.9289 (m-40) cc_final: 0.8882 (m110)
REVERT: A  178 TYR cc_start: 0.7278 (m-80) cc_final: 0.6352 (m-80)
REVERT: A  198 ILE cc_start: 0.9330 (pt) cc_final: 0.9004 (pt)
REVERT: A  199 ILE cc_start: 0.9753 (mm) cc_final: 0.9410 (mm)
REVERT: A  208 ASN cc_start: 0.8740 (m110) cc_final: 0.8110 (m110)
REVERT: A  213 HIS cc_start: 0.8731 (m90) cc_final: 0.8235 (m90)
REVERT: A  222 ILE cc_start: 0.9209 (pt) cc_final: 0.8918 (pt)
REVERT: A  233 VAL cc_start: 0.8856 (m) cc_final: 0.8327 (m)
REVERT: A  240 ASP cc_start: 0.9280 (m-30) cc_final: 0.9016 (m-30)
REVERT: A  241 ASN cc_start: 0.9265 (t0) cc_final: 0.8963 (t0)
REVERT: A  244 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8165 (mm-30)
REVERT: A  247 ARG cc_start: 0.9191 (ttp-170) cc_final: 0.8361 (tmm160)
REVERT: A  248 PHE cc_start: 0.8024 (m-80) cc_final: 0.7209 (m-10)
REVERT: A  267 ASP cc_start: 0.9162 (m-30) cc_final: 0.8699 (m-30)
REVERT: A  295 LEU cc_start: 0.9364 (mt) cc_final: 0.9119 (mt)
REVERT: A  297 ASN cc_start: 0.8999 (m-40) cc_final: 0.8693 (m110)
REVERT: A  317 PHE cc_start: 0.9390 (m-80) cc_final: 0.8878 (m-80)
REVERT: A  320 LEU cc_start: 0.9563 (tp) cc_final: 0.9334 (pp)
REVERT: A  330 MET cc_start: 0.0621 (mmt) cc_final: 0.0138 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0666
  time to fit residues: 11.5816
Evaluate side-chains
  104 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 90 optimal weight:    0.0170
   chunk 41 optimal weight:    3.9990
   chunk 107 optimal weight:    0.0370
   chunk 11 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 42 optimal weight:    4.9990
   chunk 69 optimal weight:    0.2980
   chunk 78 optimal weight:    9.9990
   chunk 4 optimal weight:    0.0470
   chunk 88 optimal weight:    0.0570
   overall best weight:    0.0912
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS
** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 487 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.189110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.150554 restraints weight = 13879.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.154296 restraints weight = 9978.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.157312 restraints weight = 7525.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.159615 restraints weight = 5856.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.161170 restraints weight = 4719.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.4241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6254
moved from start:          1.3189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9536  Z= 0.121
  Angle     :  0.608   9.759  12836  Z= 0.333
  Chirality :  0.041   0.140   1388
  Planarity :  0.004   0.035   1574
  Dihedral  :  4.319  17.492   1208
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.24), residues: 1100
  helix:  0.65 (0.20), residues: 578
  sheet:  0.45 (0.46), residues: 136
  loop : -1.69 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 294 
 TYR   0.015   0.001   TYR B 441 
 PHE   0.042   0.002   PHE A  14 
 TRP   0.031   0.002   TRP B 414 
 HIS   0.006   0.001   HIS A 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 9532)
  covalent geometry    : angle       0.60801 (12836)
  hydrogen bonds       : bond        0.04264 (  508)
  hydrogen bonds       : angle       4.82090 ( 1542)
  metal coordination   : bond        0.00046 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1323.36 seconds
wall clock time: 23 minutes 59.15 seconds (1439.15 seconds total)