Starting phenix.real_space_refine
on Thu Feb 13 18:19:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8exq_28659/02_2025/8exq_28659.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8exq_28659/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8exq_28659/02_2025/8exq_28659.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8exq_28659/02_2025/8exq_28659.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8exq_28659/02_2025/8exq_28659.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8exq_28659/02_2025/8exq_28659.cif"
  }
  resolution = 4.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.58, per 1000 atoms: 0.60
  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: 2.39
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  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: 1.23
  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: 3.20

  Time building geometry restraints manager: 2.74 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
Set refine NCS operators
  NCS operators will be refined.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.570
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.190
-------------------------------------------------------------------------------
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   9532  Z= 1.264
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (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
 TRP   0.075   0.013   TRP A 540 
 HIS   0.009   0.002   HIS A 153 
 PHE   0.037   0.007   PHE A 274 
 TYR   0.077   0.012   TYR A  36 
 ARG   0.007   0.001   ARG A 162 

*********************** 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  : 0.510 
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: 0.1906
  time to fit residues: 45.6162
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  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:   20.0000
   chunk 83 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0040
   chunk 28 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 44 optimal weight:   30.0000
   chunk 86 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   chunk 64 optimal weight:    0.4980
   chunk 99 optimal weight:    0.9990
   overall best weight:    1.2396
-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.186387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.144290 restraints weight = 12811.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.148875 restraints weight = 8638.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.152385 restraints weight = 6213.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.4127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6053
moved from start:          1.0546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9532  Z= 0.261
  Angle     :  0.774   9.122  12836  Z= 0.431
  Chirality :  0.048   0.156   1388
  Planarity :  0.005   0.042   1574
  Dihedral  :  5.727  29.939   1208
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 15.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  3.47 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.25), residues: 1100
  helix:  1.28 (0.21), residues: 562
  sheet:  0.24 (0.46), residues: 126
  loop : -0.78 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP B 414 
 HIS   0.009   0.002   HIS B 213 
 PHE   0.035   0.003   PHE A  14 
 TYR   0.030   0.002   TYR B 524 
 ARG   0.003   0.001   ARG B 293 

*********************** 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
  161 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 157
  time to evaluate  : 0.533 
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: A    7 MET cc_start: 0.8940 (tpt) cc_final: 0.8733 (tmm)
REVERT: A   27 LYS cc_start: 0.8648 (pttp) cc_final: 0.8085 (pttt)
REVERT: A   31 ASN cc_start: 0.9345 (m-40) cc_final: 0.8896 (p0)
REVERT: A   54 LYS cc_start: 0.9197 (mmmt) cc_final: 0.8960 (mmmt)
REVERT: A   92 THR cc_start: 0.6908 (p) cc_final: 0.6681 (t)
REVERT: A  110 TRP cc_start: 0.8533 (t60) cc_final: 0.7792 (t60)
REVERT: A  121 PHE cc_start: 0.9453 (t80) cc_final: 0.9081 (t80)
REVERT: A  126 LEU cc_start: 0.9403 (mt) cc_final: 0.9027 (mt)
REVERT: A  127 TYR cc_start: 0.9022 (t80) cc_final: 0.8696 (t80)
REVERT: A  147 ASP cc_start: 0.8607 (m-30) cc_final: 0.8382 (m-30)
REVERT: A  163 LYS cc_start: 0.6650 (pttt) cc_final: 0.6352 (tmmt)
REVERT: A  208 ASN cc_start: 0.8533 (m-40) cc_final: 0.7897 (m110)
REVERT: A  227 ASN cc_start: 0.8531 (t0) cc_final: 0.8063 (t0)
REVERT: A  233 VAL cc_start: 0.8816 (m) cc_final: 0.8476 (m)
REVERT: A  244 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8030 (mm-30)
REVERT: A  248 PHE cc_start: 0.7993 (m-80) cc_final: 0.7347 (m-80)
REVERT: A  275 PHE cc_start: 0.8042 (t80) cc_final: 0.7819 (t80)
REVERT: A  295 LEU cc_start: 0.9505 (mt) cc_final: 0.9219 (mt)
REVERT: A  297 ASN cc_start: 0.9090 (m-40) cc_final: 0.8587 (m-40)
  outliers start: 4
  outliers final: 1
  residues processed: 159
  average time/residue: 0.1787
  time to fit residues: 35.7735
Evaluate side-chains
  126 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 6 optimal weight:    0.4980
   chunk 3 optimal weight:    0.2980
   chunk 25 optimal weight:    8.9990
   chunk 91 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 80 optimal weight:    8.9990
   chunk 103 optimal weight:    4.9990
   chunk 106 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 83 optimal weight:    0.7980
   overall best weight:    0.6380
-------------------------------------------------------------------------------
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 557 HIS
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 = 0.4532 r_free = 0.4532 target = 0.184539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.146649 restraints weight = 13209.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.150603 restraints weight = 9180.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.153309 restraints weight = 6779.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6172
moved from start:          1.1260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9532  Z= 0.198
  Angle     :  0.665   8.676  12836  Z= 0.367
  Chirality :  0.043   0.144   1388
  Planarity :  0.004   0.044   1574
  Dihedral  :  5.238  21.232   1208
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 14.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.90 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.25), residues: 1100
  helix:  0.64 (0.21), residues: 564
  sheet:  0.25 (0.46), residues: 126
  loop : -0.96 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 414 
 HIS   0.004   0.001   HIS B 201 
 PHE   0.046   0.002   PHE A  14 
 TYR   0.021   0.002   TYR A 524 
 ARG   0.002   0.000   ARG B 247 

*********************** 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: 1
    poor density    : 146
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LEU cc_start: 0.9004 (tp) cc_final: 0.8529 (pp)
REVERT: A  110 TRP cc_start: 0.8431 (t60) cc_final: 0.7705 (t60)
REVERT: A  116 ILE cc_start: 0.9467 (mm) cc_final: 0.9245 (pt)
REVERT: A  121 PHE cc_start: 0.9291 (t80) cc_final: 0.9027 (t80)
REVERT: A  126 LEU cc_start: 0.9252 (mt) cc_final: 0.8929 (mt)
REVERT: A  141 ASN cc_start: 0.9496 (m-40) cc_final: 0.9123 (m-40)
REVERT: A  198 ILE cc_start: 0.8953 (pt) cc_final: 0.8710 (pt)
REVERT: A  199 ILE cc_start: 0.9762 (mm) cc_final: 0.9515 (mm)
REVERT: A  208 ASN cc_start: 0.8482 (m-40) cc_final: 0.8190 (m110)
REVERT: A  212 LEU cc_start: 0.9608 (tt) cc_final: 0.9229 (tp)
REVERT: A  213 HIS cc_start: 0.8927 (m90) cc_final: 0.8555 (m90)
REVERT: A  215 ILE cc_start: 0.9143 (tp) cc_final: 0.8824 (pt)
REVERT: A  218 ASN cc_start: 0.9268 (t0) cc_final: 0.8387 (t0)
REVERT: A  222 ILE cc_start: 0.8999 (pt) cc_final: 0.8790 (pt)
REVERT: A  227 ASN cc_start: 0.8474 (t0) cc_final: 0.7864 (t0)
REVERT: A  233 VAL cc_start: 0.8804 (m) cc_final: 0.8390 (m)
REVERT: A  237 ILE cc_start: 0.9577 (mt) cc_final: 0.9353 (mt)
REVERT: A  244 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8376 (mm-30)
REVERT: A  248 PHE cc_start: 0.7886 (m-80) cc_final: 0.7255 (m-10)
REVERT: A  292 LYS cc_start: 0.8595 (tptt) cc_final: 0.8176 (ttmt)
REVERT: A  295 LEU cc_start: 0.9399 (mt) cc_final: 0.9152 (mt)
REVERT: A  297 ASN cc_start: 0.8906 (m-40) cc_final: 0.8512 (m110)
REVERT: A  302 ASN cc_start: 0.9095 (t0) cc_final: 0.8747 (t0)
REVERT: A  553 TYR cc_start: 0.7271 (m-80) cc_final: 0.6909 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 147
  average time/residue: 0.1769
  time to fit residues: 32.7072
Evaluate side-chains
  119 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 3 optimal weight:    0.5980
   chunk 89 optimal weight:    0.1980
   chunk 43 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0270
   chunk 37 optimal weight:   20.0000
   chunk 13 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 100 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    0.4438
-------------------------------------------------------------------------------
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 = 0.4561 r_free = 0.4561 target = 0.185873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.145408 restraints weight = 13708.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.149720 restraints weight = 9571.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.152812 restraints weight = 7041.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.4149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6231
moved from start:          1.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9532  Z= 0.180
  Angle     :  0.650   6.419  12836  Z= 0.360
  Chirality :  0.042   0.170   1388
  Planarity :  0.004   0.037   1574
  Dihedral  :  4.891  19.331   1208
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 13.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.24), residues: 1100
  helix:  0.39 (0.20), residues: 568
  sheet:  0.06 (0.42), residues: 136
  loop : -1.24 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 414 
 HIS   0.007   0.001   HIS B 201 
 PHE   0.032   0.002   PHE A  14 
 TYR   0.023   0.002   TYR A 544 
 ARG   0.006   0.000   ARG B 247 

*********************** 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
  143 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5993 (mtt) cc_final: 0.5793 (mtt)
REVERT: A    7 MET cc_start: 0.9269 (mtm) cc_final: 0.9002 (tpt)
REVERT: A   22 PHE cc_start: 0.8981 (m-80) cc_final: 0.8775 (m-80)
REVERT: A   28 ARG cc_start: 0.8168 (tpt90) cc_final: 0.7487 (tpt90)
REVERT: A   34 LEU cc_start: 0.8974 (tp) cc_final: 0.8595 (pp)
REVERT: A  110 TRP cc_start: 0.8414 (t60) cc_final: 0.7747 (t60)
REVERT: A  120 LYS cc_start: 0.9379 (mttt) cc_final: 0.9175 (tttt)
REVERT: A  121 PHE cc_start: 0.9440 (t80) cc_final: 0.9041 (t80)
REVERT: A  126 LEU cc_start: 0.9289 (mt) cc_final: 0.8917 (mt)
REVERT: A  127 TYR cc_start: 0.8939 (t80) cc_final: 0.8244 (t80)
REVERT: A  141 ASN cc_start: 0.9362 (m-40) cc_final: 0.9048 (m-40)
REVERT: A  147 ASP cc_start: 0.8656 (m-30) cc_final: 0.8440 (m-30)
REVERT: A  153 HIS cc_start: 0.8707 (m90) cc_final: 0.8448 (m90)
REVERT: A  174 TRP cc_start: 0.8751 (t60) cc_final: 0.8529 (t60)
REVERT: A  198 ILE cc_start: 0.9234 (pt) cc_final: 0.8976 (pt)
REVERT: A  199 ILE cc_start: 0.9737 (mm) cc_final: 0.9457 (mm)
REVERT: A  202 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8974 (mt-10)
REVERT: A  208 ASN cc_start: 0.8803 (m-40) cc_final: 0.8191 (m110)
REVERT: A  212 LEU cc_start: 0.9584 (tt) cc_final: 0.9185 (mt)
REVERT: A  213 HIS cc_start: 0.8889 (m90) cc_final: 0.8540 (m90)
REVERT: A  215 ILE cc_start: 0.9137 (tp) cc_final: 0.8892 (pt)
REVERT: A  218 ASN cc_start: 0.9352 (t0) cc_final: 0.8464 (t0)
REVERT: A  227 ASN cc_start: 0.8450 (t0) cc_final: 0.7799 (t0)
REVERT: A  233 VAL cc_start: 0.8777 (m) cc_final: 0.8325 (m)
REVERT: A  240 ASP cc_start: 0.9449 (m-30) cc_final: 0.9163 (m-30)
REVERT: A  241 ASN cc_start: 0.9354 (t0) cc_final: 0.8930 (t0)
REVERT: A  248 PHE cc_start: 0.7813 (m-80) cc_final: 0.7469 (m-10)
REVERT: A  275 PHE cc_start: 0.8233 (t80) cc_final: 0.7960 (t80)
REVERT: A  295 LEU cc_start: 0.9465 (mt) cc_final: 0.9243 (mt)
REVERT: A  297 ASN cc_start: 0.8977 (m-40) cc_final: 0.8621 (m110)
REVERT: A  320 LEU cc_start: 0.9376 (mm) cc_final: 0.9130 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1467
  time to fit residues: 27.3066
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  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 96 optimal weight:    0.0670
   chunk 92 optimal weight:    0.1980
   chunk 4 optimal weight:    0.8980
   chunk 26 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0980
   chunk 53 optimal weight:    0.6980
   chunk 87 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0370
   overall best weight:    0.2196
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 231 HIS
A 239 HIS
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 = 0.4588 r_free = 0.4588 target = 0.187994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.146640 restraints weight = 14166.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.151031 restraints weight = 9709.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.154309 restraints weight = 7034.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.4177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6237
moved from start:          1.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9532  Z= 0.182
  Angle     :  0.637   9.100  12836  Z= 0.352
  Chirality :  0.041   0.145   1388
  Planarity :  0.004   0.036   1574
  Dihedral  :  4.804  18.249   1208
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.67 %
    Favored  : 96.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.24), residues: 1100
  helix:  0.34 (0.20), residues: 568
  sheet:  0.06 (0.42), residues: 136
  loop : -1.45 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP B 424 
 HIS   0.006   0.001   HIS B 231 
 PHE   0.025   0.002   PHE B  16 
 TYR   0.019   0.001   TYR B 544 
 ARG   0.003   0.000   ARG B 194 

*********************** 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
  141 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 MET cc_start: 0.9319 (mtm) cc_final: 0.8958 (tpt)
REVERT: A   28 ARG cc_start: 0.8224 (tpt90) cc_final: 0.7766 (tpt90)
REVERT: A   34 LEU cc_start: 0.9013 (tp) cc_final: 0.8612 (pp)
REVERT: A  110 TRP cc_start: 0.8420 (t60) cc_final: 0.7774 (t60)
REVERT: A  117 LEU cc_start: 0.9086 (mt) cc_final: 0.8844 (mt)
REVERT: A  121 PHE cc_start: 0.9599 (t80) cc_final: 0.9137 (t80)
REVERT: A  122 LEU cc_start: 0.9476 (tp) cc_final: 0.9266 (tp)
REVERT: A  126 LEU cc_start: 0.9219 (mt) cc_final: 0.8934 (mt)
REVERT: A  131 LEU cc_start: 0.9076 (mt) cc_final: 0.8733 (mt)
REVERT: A  141 ASN cc_start: 0.9291 (m-40) cc_final: 0.8567 (p0)
REVERT: A  172 THR cc_start: 0.8756 (m) cc_final: 0.8370 (m)
REVERT: A  178 TYR cc_start: 0.6978 (m-80) cc_final: 0.5936 (m-80)
REVERT: A  198 ILE cc_start: 0.9193 (pt) cc_final: 0.8910 (pt)
REVERT: A  199 ILE cc_start: 0.9733 (mm) cc_final: 0.9517 (mm)
REVERT: A  202 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8918 (mt-10)
REVERT: A  208 ASN cc_start: 0.8520 (m-40) cc_final: 0.7804 (m110)
REVERT: A  212 LEU cc_start: 0.9381 (tt) cc_final: 0.9126 (tp)
REVERT: A  213 HIS cc_start: 0.8835 (m90) cc_final: 0.8540 (m90)
REVERT: A  215 ILE cc_start: 0.9167 (tp) cc_final: 0.8881 (pt)
REVERT: A  218 ASN cc_start: 0.9237 (t0) cc_final: 0.8557 (t0)
REVERT: A  227 ASN cc_start: 0.8432 (t0) cc_final: 0.7740 (t0)
REVERT: A  233 VAL cc_start: 0.8743 (m) cc_final: 0.8328 (m)
REVERT: A  248 PHE cc_start: 0.6331 (m-10) cc_final: 0.5770 (m-10)
REVERT: A  267 ASP cc_start: 0.9243 (m-30) cc_final: 0.8774 (m-30)
REVERT: A  275 PHE cc_start: 0.8279 (t80) cc_final: 0.7792 (t80)
REVERT: A  295 LEU cc_start: 0.9426 (mt) cc_final: 0.9183 (mt)
REVERT: A  297 ASN cc_start: 0.8976 (m-40) cc_final: 0.8636 (m110)
REVERT: A  325 GLN cc_start: 0.9144 (pm20) cc_final: 0.8875 (pm20)
REVERT: A  495 MET cc_start: 0.6649 (mmp) cc_final: 0.6441 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1535
  time to fit residues: 28.0947
Evaluate side-chains
  116 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 12 optimal weight:    0.0870
   chunk 96 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0870
   chunk 8 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 97 optimal weight:    0.8980
   chunk 81 optimal weight:    8.9990
   chunk 77 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.6138
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 285 ASN
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 = 0.4575 r_free = 0.4575 target = 0.187255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.144979 restraints weight = 13428.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.149342 restraints weight = 9287.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.152594 restraints weight = 6815.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.4162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6267
moved from start:          1.2163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9532  Z= 0.174
  Angle     :  0.626   7.541  12836  Z= 0.345
  Chirality :  0.041   0.157   1388
  Planarity :  0.004   0.037   1574
  Dihedral  :  4.723  19.837   1208
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.24), residues: 1100
  helix:  0.34 (0.20), residues: 566
  sheet:  0.18 (0.43), residues: 136
  loop : -1.40 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP B 174 
 HIS   0.008   0.001   HIS A 418 
 PHE   0.035   0.002   PHE B  22 
 TYR   0.018   0.001   TYR A 441 
 ARG   0.002   0.000   ARG B 411 

*********************** 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
  136 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 MET cc_start: 0.9329 (mtm) cc_final: 0.8836 (tmm)
REVERT: A   28 ARG cc_start: 0.8155 (tpt90) cc_final: 0.7775 (tpt90)
REVERT: A  110 TRP cc_start: 0.8433 (t60) cc_final: 0.7765 (t60)
REVERT: A  121 PHE cc_start: 0.9553 (t80) cc_final: 0.9172 (t80)
REVERT: A  126 LEU cc_start: 0.9180 (mt) cc_final: 0.8774 (mt)
REVERT: A  138 LEU cc_start: 0.7594 (mt) cc_final: 0.7185 (mt)
REVERT: A  141 ASN cc_start: 0.9363 (m-40) cc_final: 0.8809 (p0)
REVERT: A  153 HIS cc_start: 0.8953 (m90) cc_final: 0.8629 (m90)
REVERT: A  178 TYR cc_start: 0.7087 (m-80) cc_final: 0.6043 (m-80)
REVERT: A  180 ILE cc_start: 0.8823 (mp) cc_final: 0.8307 (mp)
REVERT: A  208 ASN cc_start: 0.8548 (m-40) cc_final: 0.7856 (m110)
REVERT: A  212 LEU cc_start: 0.9403 (tt) cc_final: 0.9007 (mt)
REVERT: A  213 HIS cc_start: 0.8855 (m90) cc_final: 0.8530 (m90)
REVERT: A  215 ILE cc_start: 0.9179 (tp) cc_final: 0.8859 (pt)
REVERT: A  218 ASN cc_start: 0.9270 (t0) cc_final: 0.8524 (t0)
REVERT: A  227 ASN cc_start: 0.8642 (t0) cc_final: 0.8048 (t0)
REVERT: A  233 VAL cc_start: 0.8755 (m) cc_final: 0.8375 (m)
REVERT: A  239 HIS cc_start: 0.9050 (m90) cc_final: 0.8706 (m-70)
REVERT: A  248 PHE cc_start: 0.6948 (m-10) cc_final: 0.6581 (m-10)
REVERT: A  267 ASP cc_start: 0.9212 (m-30) cc_final: 0.8736 (m-30)
REVERT: A  275 PHE cc_start: 0.8457 (t80) cc_final: 0.7932 (t80)
REVERT: A  295 LEU cc_start: 0.9444 (mt) cc_final: 0.9196 (mt)
REVERT: A  297 ASN cc_start: 0.8971 (m-40) cc_final: 0.8654 (m110)
REVERT: A  317 PHE cc_start: 0.8962 (m-10) cc_final: 0.8512 (m-80)
REVERT: A  319 PHE cc_start: 0.9583 (t80) cc_final: 0.9325 (t80)
REVERT: A  320 LEU cc_start: 0.9452 (mm) cc_final: 0.8966 (mm)
REVERT: A  330 MET cc_start: 0.0266 (tpp) cc_final: 0.0013 (tpp)
REVERT: A  412 MET cc_start: 0.3275 (mmt) cc_final: 0.2768 (mmt)
REVERT: A  495 MET cc_start: 0.6770 (mmp) cc_final: 0.6564 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1470
  time to fit residues: 26.1111
Evaluate side-chains
  107 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 107 optimal weight:    3.9990
   chunk 46 optimal weight:    0.3980
   chunk 54 optimal weight:    0.0670
   chunk 44 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0970
   chunk 94 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9990
   chunk 12 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.7120
-------------------------------------------------------------------------------
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 = 0.4581 r_free = 0.4581 target = 0.186948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.145586 restraints weight = 13531.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.149983 restraints weight = 9318.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.153287 restraints weight = 6839.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.4115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6287
moved from start:          1.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9532  Z= 0.172
  Angle     :  0.623   9.956  12836  Z= 0.342
  Chirality :  0.042   0.187   1388
  Planarity :  0.004   0.041   1574
  Dihedral  :  4.397  15.300   1208
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.24), residues: 1100
  helix:  0.31 (0.20), residues: 568
  sheet:  0.43 (0.43), residues: 136
  loop : -1.47 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 174 
 HIS   0.005   0.001   HIS A 201 
 PHE   0.030   0.001   PHE B  14 
 TYR   0.018   0.001   TYR A 441 
 ARG   0.004   0.000   ARG A 294 

*********************** 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
  138 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 MET cc_start: 0.9301 (mtm) cc_final: 0.8736 (tmm)
REVERT: A   28 ARG cc_start: 0.8364 (tpt90) cc_final: 0.7875 (tpt90)
REVERT: A   34 LEU cc_start: 0.8882 (tp) cc_final: 0.8672 (tp)
REVERT: A  110 TRP cc_start: 0.8327 (t60) cc_final: 0.7676 (t60)
REVERT: A  121 PHE cc_start: 0.9528 (t80) cc_final: 0.9168 (t80)
REVERT: A  126 LEU cc_start: 0.9114 (mt) cc_final: 0.8817 (mt)
REVERT: A  138 LEU cc_start: 0.7403 (mt) cc_final: 0.7108 (mt)
REVERT: A  141 ASN cc_start: 0.9326 (m-40) cc_final: 0.8636 (p0)
REVERT: A  178 TYR cc_start: 0.7162 (m-80) cc_final: 0.6289 (m-80)
REVERT: A  198 ILE cc_start: 0.9318 (pt) cc_final: 0.9044 (pt)
REVERT: A  199 ILE cc_start: 0.9725 (mm) cc_final: 0.9427 (mm)
REVERT: A  202 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8883 (mt-10)
REVERT: A  208 ASN cc_start: 0.8488 (m-40) cc_final: 0.7874 (m110)
REVERT: A  215 ILE cc_start: 0.9187 (tp) cc_final: 0.8893 (pt)
REVERT: A  218 ASN cc_start: 0.9242 (t0) cc_final: 0.8515 (t0)
REVERT: A  233 VAL cc_start: 0.8757 (m) cc_final: 0.8385 (m)
REVERT: A  239 HIS cc_start: 0.9082 (m90) cc_final: 0.8762 (m90)
REVERT: A  248 PHE cc_start: 0.6954 (m-10) cc_final: 0.6544 (m-10)
REVERT: A  255 LYS cc_start: 0.9656 (mtmm) cc_final: 0.9428 (mtmm)
REVERT: A  267 ASP cc_start: 0.9193 (m-30) cc_final: 0.8688 (m-30)
REVERT: A  275 PHE cc_start: 0.8556 (t80) cc_final: 0.8005 (t80)
REVERT: A  291 LEU cc_start: 0.8891 (tp) cc_final: 0.8450 (tp)
REVERT: A  295 LEU cc_start: 0.9455 (mt) cc_final: 0.9099 (mt)
REVERT: A  317 PHE cc_start: 0.9024 (m-10) cc_final: 0.8569 (m-80)
REVERT: A  320 LEU cc_start: 0.9559 (mm) cc_final: 0.9198 (mm)
REVERT: A  328 PHE cc_start: 0.8467 (m-80) cc_final: 0.7942 (t80)
REVERT: A  330 MET cc_start: 0.1015 (tpp) cc_final: 0.0607 (tpp)
REVERT: A  412 MET cc_start: 0.2215 (mmt) cc_final: 0.1758 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1514
  time to fit residues: 27.5459
Evaluate side-chains
  106 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 95 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   chunk 107 optimal weight:    0.0370
   chunk 47 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0770
   chunk 0 optimal weight:   10.0000
   chunk 55 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 77 optimal weight:    4.9990
   chunk 92 optimal weight:    0.2980
   chunk 66 optimal weight:    3.9990
   overall best weight:    1.0818
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 487 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.185529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.143950 restraints weight = 13596.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.148268 restraints weight = 9463.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.151334 restraints weight = 6957.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.4098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6344
moved from start:          1.2576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9532  Z= 0.177
  Angle     :  0.638   9.182  12836  Z= 0.348
  Chirality :  0.042   0.199   1388
  Planarity :  0.004   0.041   1574
  Dihedral  :  4.426  16.353   1208
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 14.15
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.24), residues: 1100
  helix:  0.36 (0.20), residues: 572
  sheet:  0.48 (0.44), residues: 136
  loop : -1.58 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 540 
 HIS   0.004   0.001   HIS A 201 
 PHE   0.038   0.002   PHE A  14 
 TYR   0.019   0.001   TYR A 544 
 ARG   0.007   0.001   ARG B 294 

*********************** 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
  134 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.544 
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    7 MET cc_start: 0.9202 (mtm) cc_final: 0.8989 (tmm)
REVERT: A   12 PHE cc_start: 0.9484 (t80) cc_final: 0.8923 (t80)
REVERT: A   28 ARG cc_start: 0.8364 (tpt90) cc_final: 0.7848 (tpt90)
REVERT: A  110 TRP cc_start: 0.8332 (t60) cc_final: 0.7702 (t60)
REVERT: A  126 LEU cc_start: 0.9136 (mt) cc_final: 0.8890 (mt)
REVERT: A  138 LEU cc_start: 0.7387 (mt) cc_final: 0.7112 (mt)
REVERT: A  141 ASN cc_start: 0.9234 (m-40) cc_final: 0.8604 (p0)
REVERT: A  198 ILE cc_start: 0.9348 (pt) cc_final: 0.9051 (pt)
REVERT: A  199 ILE cc_start: 0.9723 (mm) cc_final: 0.9427 (mm)
REVERT: A  202 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8775 (mt-10)
REVERT: A  212 LEU cc_start: 0.9592 (tt) cc_final: 0.9271 (mt)
REVERT: A  213 HIS cc_start: 0.8848 (m90) cc_final: 0.8614 (m90)
REVERT: A  218 ASN cc_start: 0.9227 (t0) cc_final: 0.8778 (t0)
REVERT: A  222 ILE cc_start: 0.9246 (pt) cc_final: 0.8354 (pt)
REVERT: A  233 VAL cc_start: 0.8808 (m) cc_final: 0.8470 (m)
REVERT: A  239 HIS cc_start: 0.9025 (m90) cc_final: 0.8732 (m90)
REVERT: A  248 PHE cc_start: 0.7445 (m-10) cc_final: 0.6893 (m-10)
REVERT: A  255 LYS cc_start: 0.9642 (mtmm) cc_final: 0.9428 (mtmm)
REVERT: A  267 ASP cc_start: 0.9117 (m-30) cc_final: 0.8547 (m-30)
REVERT: A  275 PHE cc_start: 0.8579 (t80) cc_final: 0.8012 (t80)
REVERT: A  291 LEU cc_start: 0.8827 (tp) cc_final: 0.8305 (tp)
REVERT: A  294 ARG cc_start: 0.8945 (mmm-85) cc_final: 0.8739 (mmt90)
REVERT: A  295 LEU cc_start: 0.9472 (mt) cc_final: 0.9119 (mt)
REVERT: A  317 PHE cc_start: 0.9245 (m-10) cc_final: 0.8753 (m-80)
REVERT: A  412 MET cc_start: 0.2271 (mmt) cc_final: 0.1949 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1559
  time to fit residues: 27.0095
Evaluate side-chains
  111 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 4 optimal weight:    0.0570
   chunk 39 optimal weight:    0.1980
   chunk 46 optimal weight:    0.9990
   chunk 103 optimal weight:   10.0000
   chunk 51 optimal weight:    0.0770
   chunk 70 optimal weight:    4.9990
   chunk 105 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 16 optimal weight:    0.4980
   chunk 95 optimal weight:    7.9990
   chunk 102 optimal weight:    0.9990
   overall best weight:    0.2856
-------------------------------------------------------------------------------
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 = 0.4591 r_free = 0.4591 target = 0.187661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.145778 restraints weight = 13701.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.150271 restraints weight = 9399.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.153344 restraints weight = 6898.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.4170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6305
moved from start:          1.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9532  Z= 0.169
  Angle     :  0.647   9.678  12836  Z= 0.347
  Chirality :  0.042   0.171   1388
  Planarity :  0.004   0.040   1574
  Dihedral  :  4.433  19.588   1208
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.24), residues: 1100
  helix:  0.42 (0.20), residues: 572
  sheet:  0.49 (0.44), residues: 136
  loop : -1.65 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP B 424 
 HIS   0.004   0.001   HIS A 201 
 PHE   0.040   0.002   PHE B  14 
 TYR   0.017   0.001   TYR B 544 
 ARG   0.006   0.001   ARG B 294 

*********************** 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
  140 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 MET cc_start: 0.9261 (mtm) cc_final: 0.9040 (tmm)
REVERT: A   12 PHE cc_start: 0.9464 (t80) cc_final: 0.8695 (t80)
REVERT: A   28 ARG cc_start: 0.8320 (tpt90) cc_final: 0.7822 (tpt90)
REVERT: A   39 TRP cc_start: 0.8664 (m100) cc_final: 0.6999 (m-90)
REVERT: A  121 PHE cc_start: 0.8577 (m-80) cc_final: 0.8166 (m-80)
REVERT: A  126 LEU cc_start: 0.9176 (mt) cc_final: 0.8901 (mt)
REVERT: A  138 LEU cc_start: 0.6807 (mt) cc_final: 0.6436 (mt)
REVERT: A  198 ILE cc_start: 0.9315 (pt) cc_final: 0.9030 (pt)
REVERT: A  199 ILE cc_start: 0.9726 (mm) cc_final: 0.9449 (mm)
REVERT: A  202 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8865 (mt-10)
REVERT: A  208 ASN cc_start: 0.8433 (m-40) cc_final: 0.7805 (m110)
REVERT: A  212 LEU cc_start: 0.9607 (tt) cc_final: 0.9351 (mt)
REVERT: A  222 ILE cc_start: 0.9337 (pt) cc_final: 0.8910 (pt)
REVERT: A  233 VAL cc_start: 0.8768 (m) cc_final: 0.8328 (m)
REVERT: A  240 ASP cc_start: 0.9389 (m-30) cc_final: 0.9094 (m-30)
REVERT: A  248 PHE cc_start: 0.7430 (m-10) cc_final: 0.6852 (m-10)
REVERT: A  267 ASP cc_start: 0.9142 (m-30) cc_final: 0.8610 (m-30)
REVERT: A  275 PHE cc_start: 0.8413 (t80) cc_final: 0.8191 (t80)
REVERT: A  292 LYS cc_start: 0.8258 (tptt) cc_final: 0.7741 (ttpp)
REVERT: A  297 ASN cc_start: 0.9035 (m-40) cc_final: 0.8705 (m110)
REVERT: A  317 PHE cc_start: 0.9285 (m-10) cc_final: 0.8913 (m-80)
REVERT: A  330 MET cc_start: 0.1227 (tpp) cc_final: 0.0908 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1436
  time to fit residues: 26.2860
Evaluate side-chains
  107 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 102 optimal weight:    0.9980
   chunk 105 optimal weight:    0.0770
   chunk 50 optimal weight:    0.0770
   chunk 9 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   chunk 103 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 101 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.4296
-------------------------------------------------------------------------------
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 = 0.4595 r_free = 0.4595 target = 0.188641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.147861 restraints weight = 13389.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.152028 restraints weight = 9350.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.155119 restraints weight = 6939.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.4184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6292
moved from start:          1.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9532  Z= 0.176
  Angle     :  0.678  10.864  12836  Z= 0.358
  Chirality :  0.042   0.163   1388
  Planarity :  0.004   0.039   1574
  Dihedral  :  4.395  18.517   1208
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.24), residues: 1100
  helix:  0.33 (0.20), residues: 572
  sheet:  0.64 (0.44), residues: 136
  loop : -1.63 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP B 174 
 HIS   0.004   0.001   HIS A 201 
 PHE   0.041   0.002   PHE B  14 
 TYR   0.017   0.001   TYR A 441 
 ARG   0.006   0.001   ARG B 294 

********************** 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
  137 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.572 
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    7 MET cc_start: 0.9292 (mtm) cc_final: 0.9061 (tmm)
REVERT: A   12 PHE cc_start: 0.9505 (t80) cc_final: 0.8833 (t80)
REVERT: A   20 LEU cc_start: 0.9741 (mt) cc_final: 0.9338 (mt)
REVERT: A   39 TRP cc_start: 0.8726 (m100) cc_final: 0.7133 (m-90)
REVERT: A   42 THR cc_start: 0.9384 (p) cc_final: 0.9173 (p)
REVERT: A  110 TRP cc_start: 0.8030 (t60) cc_final: 0.7507 (t60)
REVERT: A  121 PHE cc_start: 0.8550 (m-80) cc_final: 0.8123 (m-80)
REVERT: A  126 LEU cc_start: 0.9161 (mt) cc_final: 0.8911 (mt)
REVERT: A  138 LEU cc_start: 0.6935 (mt) cc_final: 0.6292 (mt)
REVERT: A  141 ASN cc_start: 0.9493 (m-40) cc_final: 0.9241 (m-40)
REVERT: A  153 HIS cc_start: 0.8428 (m90) cc_final: 0.8165 (m-70)
REVERT: A  174 TRP cc_start: 0.8327 (t60) cc_final: 0.8096 (t-100)
REVERT: A  198 ILE cc_start: 0.9309 (pt) cc_final: 0.9047 (pt)
REVERT: A  199 ILE cc_start: 0.9729 (mm) cc_final: 0.9439 (mm)
REVERT: A  202 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8913 (mt-10)
REVERT: A  208 ASN cc_start: 0.8396 (m-40) cc_final: 0.7815 (m110)
REVERT: A  213 HIS cc_start: 0.8926 (m90) cc_final: 0.8626 (m90)
REVERT: A  222 ILE cc_start: 0.9337 (pt) cc_final: 0.9050 (pt)
REVERT: A  233 VAL cc_start: 0.8775 (m) cc_final: 0.8304 (m)
REVERT: A  240 ASP cc_start: 0.9322 (m-30) cc_final: 0.9027 (m-30)
REVERT: A  248 PHE cc_start: 0.7485 (m-10) cc_final: 0.6875 (m-10)
REVERT: A  275 PHE cc_start: 0.8602 (t80) cc_final: 0.8342 (t80)
REVERT: A  291 LEU cc_start: 0.8867 (tp) cc_final: 0.8362 (tp)
REVERT: A  294 ARG cc_start: 0.8877 (mmm-85) cc_final: 0.8668 (mmm-85)
REVERT: A  295 LEU cc_start: 0.9229 (mt) cc_final: 0.8850 (mt)
REVERT: A  317 PHE cc_start: 0.9155 (m-10) cc_final: 0.8683 (m-80)
REVERT: A  330 MET cc_start: 0.1342 (tpp) cc_final: 0.0964 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1454
  time to fit residues: 26.2517
Evaluate side-chains
  113 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 69 optimal weight:    3.9990
   chunk 76 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   chunk 102 optimal weight:    0.1980
   chunk 86 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   overall best weight:    0.7780
-------------------------------------------------------------------------------
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 = 0.4587 r_free = 0.4587 target = 0.187836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.145935 restraints weight = 13489.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.150145 restraints weight = 9524.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.153203 restraints weight = 7102.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.4163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6332
moved from start:          1.3121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9532  Z= 0.165
  Angle     :  0.673  12.713  12836  Z= 0.354
  Chirality :  0.042   0.172   1388
  Planarity :  0.004   0.039   1574
  Dihedral  :  4.340  17.056   1208
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 15.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.24), residues: 1100
  helix:  0.23 (0.20), residues: 574
  sheet:  0.54 (0.46), residues: 124
  loop : -1.62 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP A 414 
 HIS   0.004   0.001   HIS A 201 
 PHE   0.046   0.002   PHE A  14 
 TYR   0.017   0.001   TYR B 441 
 ARG   0.006   0.001   ARG A 294 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2264.65 seconds
wall clock time: 42 minutes 0.08 seconds (2520.08 seconds total)