Starting phenix.real_space_refine
on Mon May 12 16:52:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8exs_28661/05_2025/8exs_28661.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8exs_28661/05_2025/8exs_28661.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8exs_28661/05_2025/8exs_28661.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8exs_28661/05_2025/8exs_28661.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8exs_28661/05_2025/8exs_28661.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8exs_28661/05_2025/8exs_28661.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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    6118      2.51       5
     N    1538      2.21       5
     O    1624      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9320
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 556, 4659
          Classifications: {'peptide': 556}
          Link IDs: {'PTRANS': 11, 'TRANS': 544}
          Chain breaks: 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}
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.33, per 1000 atoms: 0.89
  Number of scatterers: 9320
  At special positions: 0
  Unit cell: (90.015, 90.015, 122.844, 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    1624      8.00
     N    1538      7.00
     C    6118      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.36
  Conformation dependent library (CDL) restraints added in 982.9 milliseconds
  
  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 "


  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2148

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 4 sheets defined
      58.4% alpha, 10.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 31
    Processing helix  chain 'A' and resid 35 through 38
    Processing helix  chain 'A' and resid 39 through 46
    Processing helix  chain 'A' and resid 47 through 51
    Processing helix  chain 'A' and resid 99 through 134
      removed outlier: 4.522A  pdb=" N   ILE A 105 " --> pdb=" O   SER A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 152
      removed outlier: 5.088A  pdb=" N   LYS A 145 " --> pdb=" O   ASN A 141 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE A 146 " --> pdb=" O   GLU A 142 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   ASN A 152 " --> pdb=" O   THR A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 188
    Processing helix  chain 'A' and resid 193 through 208
    Processing helix  chain 'A' and resid 209 through 224
    Processing helix  chain 'A' and resid 228 through 252
    Processing helix  chain 'A' and resid 253 through 256
      removed outlier: 6.117A  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 271
      removed outlier: 3.632A  pdb=" N   VAL A 269 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 300
    Processing helix  chain 'A' and resid 307 through 327
      removed outlier: 4.298A  pdb=" N   LEU A 311 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 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 390
    Processing helix  chain 'A' and resid 391 through 402
    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
      removed outlier: 3.529A  pdb=" N   THR A 454 " --> pdb=" O   PRO A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 497
    Processing helix  chain 'A' and resid 502 through 513
      removed outlier: 3.616A  pdb=" N   SER A 512 " --> pdb=" O   GLN A 508 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU A 513 " --> pdb=" O   LEU A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 579
    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 47 through 51
    Processing helix  chain 'B' and resid 99 through 134
      removed outlier: 4.522A  pdb=" N   ILE B 105 " --> pdb=" O   SER B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 152
      removed outlier: 5.088A  pdb=" N   LYS B 145 " --> pdb=" O   ASN B 141 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE B 146 " --> pdb=" O   GLU B 142 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ASN B 152 " --> pdb=" O   THR B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 188
    Processing helix  chain 'B' and resid 193 through 208
    Processing helix  chain 'B' and resid 209 through 224
    Processing helix  chain 'B' and resid 228 through 252
    Processing helix  chain 'B' and resid 253 through 256
      removed outlier: 6.117A  pdb=" N   ASN B 256 " --> pdb=" O   ILE B 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 253 through 256'
    Processing helix  chain 'B' and resid 257 through 271
      removed outlier: 3.632A  pdb=" N   VAL B 269 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 300
    Processing helix  chain 'B' and resid 307 through 327
      removed outlier: 4.296A  pdb=" N   LEU B 311 " --> pdb=" O   SER B 307 " (cutoff:3.500A)
    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 390
    Processing helix  chain 'B' and resid 391 through 402
    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 449
    Processing helix  chain 'B' and resid 450 through 461
      removed outlier: 3.531A  pdb=" N   THR B 454 " --> pdb=" O   PRO B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 497
    Processing helix  chain 'B' and resid 502 through 513
      removed outlier: 3.617A  pdb=" N   SER B 512 " --> pdb=" O   GLN B 508 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU B 513 " --> pdb=" O   LEU B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 564 through 579
    Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 164
      removed outlier: 6.597A  pdb=" N   VAL A 160 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ARG A 162 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 350
      removed outlier: 6.898A  pdb=" N   ASP A 346 " --> pdb=" O   TYR A 373 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   ILE A 375 " --> pdb=" O   ASP A 346 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   GLN A 348 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   GLY A 530 " --> pdb=" O   ASN A 537 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   GLY A 539 " --> pdb=" O   GLY A 528 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   GLY A 528 " --> pdb=" O   GLY A 539 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   PHE A 541 " --> pdb=" O   LYS A 526 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   LYS A 526 " --> pdb=" O   PHE A 541 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   GLY A 543 " --> pdb=" O   TYR A 524 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   TYR A 524 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   VAL A 545 " --> pdb=" O   GLU A 522 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   GLU A 522 " --> pdb=" O   VAL A 545 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   TYR A 521 " --> pdb=" O   LYS A 517 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   LYS A 517 " --> pdb=" O   TYR A 521 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   LEU A 523 " --> pdb=" O   ILE A 515 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 164
      removed outlier: 6.596A  pdb=" N   VAL B 160 " --> pdb=" O   ILE B 180 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   ILE B 182 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 6.642A  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: 6.897A  pdb=" N   ASP B 346 " --> pdb=" O   TYR B 373 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   ILE B 375 " --> pdb=" O   ASP B 346 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   GLN B 348 " --> pdb=" O   ILE B 375 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   GLY B 530 " --> pdb=" O   ASN B 537 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   GLY B 539 " --> pdb=" O   GLY B 528 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   GLY B 528 " --> pdb=" O   GLY B 539 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   PHE B 541 " --> pdb=" O   LYS B 526 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   LYS B 526 " --> pdb=" O   PHE B 541 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   GLY B 543 " --> pdb=" O   TYR B 524 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   TYR B 524 " --> pdb=" O   GLY B 543 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   VAL B 545 " --> pdb=" O   GLU B 522 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   GLU B 522 " --> pdb=" O   VAL B 545 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   TYR B 521 " --> pdb=" O   LYS B 517 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   LYS B 517 " --> pdb=" O   TYR B 521 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU B 523 " --> pdb=" O   ILE B 515 " (cutoff:3.500A)

    489 hydrogen bonds defined for protein.
    1401 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.79

  Time building geometry restraints manager: 2.73 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1464
        1.30 -     1.43: 2855
        1.43 -     1.57: 5100
        1.57 -     1.70: 57
        1.70 -     1.84: 70
  Bond restraints: 9546
  Sorted by residual:
  bond pdb=" CB  HIS A 201 "
       pdb=" CG  HIS A 201 "
    ideal  model  delta    sigma   weight residual
    1.497  1.388  0.109 1.40e-02 5.10e+03 6.08e+01
  bond pdb=" CB  HIS B 201 "
       pdb=" CG  HIS B 201 "
    ideal  model  delta    sigma   weight residual
    1.497  1.389  0.108 1.40e-02 5.10e+03 6.00e+01
  bond pdb=" CB  PHE B 501 "
       pdb=" CG  PHE B 501 "
    ideal  model  delta    sigma   weight residual
    1.502  1.380  0.122 2.30e-02 1.89e+03 2.84e+01
  bond pdb=" CB  PHE A 501 "
       pdb=" CG  PHE A 501 "
    ideal  model  delta    sigma   weight residual
    1.502  1.381  0.121 2.30e-02 1.89e+03 2.78e+01
  bond pdb=" CB  HIS A 549 "
       pdb=" CG  HIS A 549 "
    ideal  model  delta    sigma   weight residual
    1.497  1.562 -0.065 1.40e-02 5.10e+03 2.17e+01
  ... (remaining 9541 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 11080
        2.38 -     4.77: 1540
        4.77 -     7.15: 194
        7.15 -     9.54: 36
        9.54 -    11.92: 6
  Bond angle restraints: 12856
  Sorted by residual:
  angle pdb=" C   SER A 386 "
        pdb=" N   PRO A 387 "
        pdb=" CA  PRO A 387 "
      ideal   model   delta    sigma   weight residual
     119.56  128.94   -9.38 1.02e+00 9.61e-01 8.46e+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  128.84   -9.28 1.02e+00 9.61e-01 8.29e+01
  angle pdb=" N   ILE A 222 "
        pdb=" CA  ILE A 222 "
        pdb=" C   ILE A 222 "
      ideal   model   delta    sigma   weight residual
     111.45  103.71    7.74 9.30e-01 1.16e+00 6.93e+01
  angle pdb=" N   ILE B 222 "
        pdb=" CA  ILE B 222 "
        pdb=" C   ILE B 222 "
      ideal   model   delta    sigma   weight residual
     111.45  103.78    7.67 9.30e-01 1.16e+00 6.81e+01
  angle pdb=" N   TYR A 521 "
        pdb=" CA  TYR A 521 "
        pdb=" C   TYR A 521 "
      ideal   model   delta    sigma   weight residual
     108.60  120.52  -11.92 1.46e+00 4.69e-01 6.67e+01
  ... (remaining 12851 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.28: 5462
       16.28 -    32.57: 183
       32.57 -    48.85: 37
       48.85 -    65.13: 20
       65.13 -    81.41: 6
  Dihedral angle restraints: 5708
    sinusoidal: 2376
      harmonic: 3332
  Sorted by residual:
  dihedral pdb=" C   ASN A 406 "
           pdb=" N   ASN A 406 "
           pdb=" CA  ASN A 406 "
           pdb=" CB  ASN A 406 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.18    9.58     0      2.50e+00 1.60e-01 1.47e+01
  dihedral pdb=" C   ASN B 406 "
           pdb=" N   ASN B 406 "
           pdb=" CA  ASN B 406 "
           pdb=" CB  ASN B 406 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.11    9.51     0      2.50e+00 1.60e-01 1.45e+01
  dihedral pdb=" CA  GLU A 202 "
           pdb=" CB  GLU A 202 "
           pdb=" CG  GLU A 202 "
           pdb=" CD  GLU A 202 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    4.59   55.41     3      1.50e+01 4.44e-03 9.35e+00
  ... (remaining 5705 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 765
       0.076 -    0.153: 463
       0.153 -    0.229: 148
       0.229 -    0.305: 10
       0.305 -    0.381: 8
  Chirality restraints: 1394
  Sorted by residual:
  chirality pdb=" CA  PHE A 220 "
            pdb=" N   PHE A 220 "
            pdb=" C   PHE A 220 "
            pdb=" CB  PHE A 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.64e+00
  chirality pdb=" CA  PHE B 220 "
            pdb=" N   PHE B 220 "
            pdb=" C   PHE B 220 "
            pdb=" CB  PHE B 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.63e+00
  chirality pdb=" CA  ILE B 515 "
            pdb=" N   ILE B 515 "
            pdb=" C   ILE B 515 "
            pdb=" CB  ILE B 515 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.80   -0.37 2.00e-01 2.50e+01 3.37e+00
  ... (remaining 1391 not shown)

  Planarity restraints: 1576
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 419 "    0.062 2.00e-02 2.50e+03   3.23e-02 2.09e+01
        pdb=" CG  TYR A 419 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 419 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 419 "   -0.023 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 419 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 419 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 419 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 419 "    0.045 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 419 "   -0.061 2.00e-02 2.50e+03   3.20e-02 2.05e+01
        pdb=" CG  TYR B 419 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 419 "    0.027 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 419 "    0.024 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 419 "    0.016 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 419 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 419 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B 419 "   -0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 540 "    0.056 2.00e-02 2.50e+03   2.68e-02 1.79e+01
        pdb=" CG  TRP B 540 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 540 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 540 "   -0.025 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 540 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 540 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 540 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 540 "    0.035 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 540 "   -0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 540 "    0.022 2.00e-02 2.50e+03
  ... (remaining 1573 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.36: 13
        2.36 -     2.99: 5681
        2.99 -     3.63: 14462
        3.63 -     4.26: 24287
        4.26 -     4.90: 37307
  Nonbonded interactions: 81750
  Sorted by model distance:
  nonbonded pdb=" CB  ASP A 422 "
            pdb=" CB  ASP B 422 "
     model   vdw
     1.722 3.840
  nonbonded pdb=" O   ALA A  91 "
            pdb=" CZ  PHE B 421 "
     model   vdw
     1.923 3.340
  nonbonded pdb=" CZ  PHE A 421 "
            pdb=" O   ALA B  91 "
     model   vdw
     1.924 3.340
  nonbonded pdb=" OE2 GLU B 242 "
            pdb="ZN    ZN B 701 "
     model   vdw
     2.099 2.230
  nonbonded pdb=" OE2 GLU A 242 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.099 2.230
  ... (remaining 81745 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
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     27.300
  Find NCS groups from input model:        0.170
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5053
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   0.227   9551  Z= 1.150
  Angle     :  1.722  11.922  12856  Z= 1.186
  Chirality :  0.099   0.381   1394
  Planarity :  0.009   0.041   1576
  Dihedral  : 10.181  81.415   3560
  Min Nonbonded Distance : 1.722

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  0.77 %
    Favored  : 98.65 %
  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:  0.10 (0.23), residues: 1104
  helix:  0.31 (0.19), residues: 594
  sheet:  0.08 (0.47), residues: 124
  loop : -0.07 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.008   TRP B 540 
 HIS   0.010   0.002   HIS A 205 
 PHE   0.047   0.006   PHE A 274 
 TYR   0.062   0.010   TYR A 419 
 ARG   0.003   0.001   ARG B 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16118 (  489)
  hydrogen bonds       : angle       7.39130 ( 1401)
  metal coordination   : bond        0.02375 (    4)
  covalent geometry    : bond        0.01995 ( 9546)
  covalent geometry    : angle       1.72157 (12856)
  Misc. bond           : bond        0.22736 (    1)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 341
  time to evaluate  : 1.051 
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  173 PHE cc_start: 0.4322 (m-80) cc_final: 0.3598 (m-80)
REVERT: A  316 ILE cc_start: 0.7263 (tp) cc_final: 0.6910 (tp)
REVERT: A  320 LEU cc_start: 0.8007 (mt) cc_final: 0.7510 (tp)
REVERT: A  412 MET cc_start: 0.2881 (tpp) cc_final: 0.1904 (tpp)
REVERT: A  434 MET cc_start: 0.4727 (tpp) cc_final: 0.4362 (tpp)
REVERT: B  173 PHE cc_start: 0.4309 (m-80) cc_final: 0.3592 (m-80)
REVERT: B  316 ILE cc_start: 0.7205 (tp) cc_final: 0.6845 (tp)
REVERT: B  320 LEU cc_start: 0.8018 (mt) cc_final: 0.7504 (tp)
REVERT: B  412 MET cc_start: 0.3080 (tpp) cc_final: 0.2131 (tpp)
REVERT: B  434 MET cc_start: 0.4728 (tpp) cc_final: 0.4340 (tpp)
  outliers start: 6
  outliers final: 2
  residues processed: 343
  average time/residue: 0.2319
  time to fit residues: 108.6170
Evaluate side-chains
  202 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 200
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 52 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 152 ASN
A 252 ASN
A 297 ASN
A 538 ASN
B 152 ASN
B 252 ASN
B 297 ASN
B 538 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.160054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.111972 restraints weight = 22459.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.115865 restraints weight = 13902.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.118612 restraints weight = 9909.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6579
moved from start:          0.3637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9551  Z= 0.175
  Angle     :  0.648   5.772  12856  Z= 0.373
  Chirality :  0.045   0.182   1394
  Planarity :  0.004   0.031   1576
  Dihedral  :  4.807  19.818   1212
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  2.22 %
    Favored  : 97.40 %
  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:  0.72 (0.24), residues: 1104
  helix:  1.12 (0.20), residues: 588
  sheet:  0.14 (0.48), residues: 128
  loop : -0.25 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 424 
 HIS   0.004   0.001   HIS B 239 
 PHE   0.030   0.002   PHE B  22 
 TYR   0.025   0.002   TYR A 203 
 ARG   0.003   0.001   ARG A  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06059 (  489)
  hydrogen bonds       : angle       5.64163 ( 1401)
  metal coordination   : bond        0.00398 (    4)
  covalent geometry    : bond        0.00359 ( 9546)
  covalent geometry    : angle       0.64835 (12856)
  Misc. bond           : bond        0.00363 (    1)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 299
  time to evaluate  : 1.142 
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   24 TYR cc_start: 0.7083 (t80) cc_final: 0.6800 (t80)
REVERT: A  142 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8828 (mt-10)
REVERT: A  152 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.8151 (m-40)
REVERT: A  173 PHE cc_start: 0.6167 (m-80) cc_final: 0.5334 (m-80)
REVERT: A  188 LYS cc_start: 0.7748 (tmtt) cc_final: 0.7522 (tmtt)
REVERT: A  195 LEU cc_start: 0.7960 (mm) cc_final: 0.7744 (mm)
REVERT: A  213 HIS cc_start: 0.8756 (m-70) cc_final: 0.8367 (m90)
REVERT: A  310 ILE cc_start: 0.8880 (mt) cc_final: 0.8404 (tp)
REVERT: A  323 VAL cc_start: 0.9319 (t) cc_final: 0.9104 (t)
REVERT: A  391 TYR cc_start: 0.8118 (t80) cc_final: 0.7538 (t80)
REVERT: A  434 MET cc_start: 0.7049 (tpp) cc_final: 0.6117 (tpp)
REVERT: A  476 MET cc_start: 0.5232 (ptm) cc_final: 0.4691 (ptt)
REVERT: B   24 TYR cc_start: 0.7006 (t80) cc_final: 0.6797 (t80)
REVERT: B  152 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.8095 (m-40)
REVERT: B  173 PHE cc_start: 0.6188 (m-80) cc_final: 0.5334 (m-80)
REVERT: B  188 LYS cc_start: 0.7847 (tmtt) cc_final: 0.7612 (tmtt)
REVERT: B  195 LEU cc_start: 0.7987 (mm) cc_final: 0.7771 (mm)
REVERT: B  213 HIS cc_start: 0.8739 (m-70) cc_final: 0.8271 (m90)
REVERT: B  310 ILE cc_start: 0.8882 (mt) cc_final: 0.8267 (tp)
REVERT: B  323 VAL cc_start: 0.9313 (t) cc_final: 0.9107 (t)
REVERT: B  391 TYR cc_start: 0.8114 (t80) cc_final: 0.7538 (t80)
REVERT: B  434 MET cc_start: 0.7056 (tpp) cc_final: 0.6118 (tpp)
REVERT: B  476 MET cc_start: 0.5241 (ptm) cc_final: 0.4701 (ptt)
  outliers start: 4
  outliers final: 2
  residues processed: 303
  average time/residue: 0.1911
  time to fit residues: 83.2906
Evaluate side-chains
  222 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 218
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 37 optimal weight:    9.9990
   chunk 13 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 39 optimal weight:    0.7980
   chunk 100 optimal weight:    7.9990
   chunk 64 optimal weight:    2.9990
   chunk 44 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    1.4984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 252 ASN
A 327 GLN
A 428 GLN
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 252 ASN
B 327 GLN
B 428 GLN
** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.156667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.108141 restraints weight = 23203.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.111882 restraints weight = 14794.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.114405 restraints weight = 10696.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6615
moved from start:          0.4637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9551  Z= 0.166
  Angle     :  0.581   6.484  12856  Z= 0.333
  Chirality :  0.044   0.159   1394
  Planarity :  0.004   0.035   1576
  Dihedral  :  4.652  14.790   1212
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.83 %
    Favored  : 98.07 %
  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:  0.55 (0.25), residues: 1104
  helix:  0.99 (0.20), residues: 596
  sheet:  0.10 (0.48), residues: 126
  loop : -0.38 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 424 
 HIS   0.005   0.001   HIS B 282 
 PHE   0.023   0.002   PHE B  22 
 TYR   0.022   0.002   TYR B 203 
 ARG   0.002   0.000   ARG A 444 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05163 (  489)
  hydrogen bonds       : angle       5.29007 ( 1401)
  metal coordination   : bond        0.00076 (    4)
  covalent geometry    : bond        0.00338 ( 9546)
  covalent geometry    : angle       0.58135 (12856)
  Misc. bond           : bond        0.00230 (    1)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 280
  time to evaluate  : 1.070 
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  142 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8853 (mt-10)
REVERT: A  152 ASN cc_start: 0.8444 (t0) cc_final: 0.8138 (m-40)
REVERT: A  173 PHE cc_start: 0.6555 (m-80) cc_final: 0.5437 (m-80)
REVERT: A  188 LYS cc_start: 0.7832 (tmtt) cc_final: 0.7613 (tmtt)
REVERT: A  195 LEU cc_start: 0.8101 (mm) cc_final: 0.7878 (mm)
REVERT: A  202 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8320 (mm-30)
REVERT: A  213 HIS cc_start: 0.8886 (m-70) cc_final: 0.8357 (m90)
REVERT: A  307 SER cc_start: 0.8453 (t) cc_final: 0.8186 (t)
REVERT: A  310 ILE cc_start: 0.8814 (mt) cc_final: 0.8465 (tp)
REVERT: A  434 MET cc_start: 0.6844 (tpp) cc_final: 0.5965 (tpp)
REVERT: A  486 GLU cc_start: 0.6552 (mt-10) cc_final: 0.5836 (mm-30)
REVERT: B   12 PHE cc_start: 0.8760 (t80) cc_final: 0.8527 (t80)
REVERT: B   14 PHE cc_start: 0.7899 (t80) cc_final: 0.7635 (t80)
REVERT: B   37 LYS cc_start: 0.7844 (mtpt) cc_final: 0.7320 (mmtm)
REVERT: B  142 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8934 (mt-10)
REVERT: B  152 ASN cc_start: 0.8246 (t0) cc_final: 0.7943 (m-40)
REVERT: B  173 PHE cc_start: 0.6547 (m-80) cc_final: 0.5434 (m-80)
REVERT: B  188 LYS cc_start: 0.7821 (tmtt) cc_final: 0.7605 (tmtt)
REVERT: B  195 LEU cc_start: 0.8172 (mm) cc_final: 0.7671 (mm)
REVERT: B  213 HIS cc_start: 0.8889 (m-70) cc_final: 0.8369 (m90)
REVERT: B  247 ARG cc_start: 0.7837 (mtp85) cc_final: 0.7527 (mtp85)
REVERT: B  309 LEU cc_start: 0.8378 (mt) cc_final: 0.7951 (pp)
REVERT: B  310 ILE cc_start: 0.8886 (mt) cc_final: 0.8345 (tp)
REVERT: B  434 MET cc_start: 0.6824 (tpp) cc_final: 0.5951 (tpp)
REVERT: B  486 GLU cc_start: 0.6538 (mt-10) cc_final: 0.5922 (mm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 281
  average time/residue: 0.1812
  time to fit residues: 73.0691
Evaluate side-chains
  202 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 201
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 44 optimal weight:    7.9990
   chunk 97 optimal weight:    7.9990
   chunk 81 optimal weight:    2.9990
   chunk 67 optimal weight:    8.9990
   chunk 77 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 103 optimal weight:   10.0000
   chunk 83 optimal weight:    0.7980
   chunk 80 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    2.0986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 ASN
A 327 GLN
B 252 ASN
B 327 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.152393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.105908 restraints weight = 22829.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.109049 restraints weight = 15105.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.111164 restraints weight = 11282.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6697
moved from start:          0.5288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9551  Z= 0.185
  Angle     :  0.625  10.338  12856  Z= 0.345
  Chirality :  0.045   0.207   1394
  Planarity :  0.004   0.039   1576
  Dihedral  :  4.713  15.019   1212
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 14.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  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:  0.32 (0.24), residues: 1104
  helix:  0.75 (0.20), residues: 600
  sheet:  0.07 (0.49), residues: 126
  loop : -0.44 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 475 
 HIS   0.005   0.001   HIS A 557 
 PHE   0.023   0.002   PHE A 274 
 TYR   0.016   0.002   TYR A 203 
 ARG   0.002   0.000   ARG A 444 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05009 (  489)
  hydrogen bonds       : angle       5.28531 ( 1401)
  metal coordination   : bond        0.00487 (    4)
  covalent geometry    : bond        0.00390 ( 9546)
  covalent geometry    : angle       0.62495 (12856)
  Misc. bond           : bond        0.00800 (    1)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 1.146 
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  142 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8764 (mt-10)
REVERT: A  173 PHE cc_start: 0.6583 (m-80) cc_final: 0.5338 (m-80)
REVERT: A  188 LYS cc_start: 0.7755 (tmtt) cc_final: 0.7538 (tmtt)
REVERT: A  195 LEU cc_start: 0.8261 (mm) cc_final: 0.8026 (mm)
REVERT: A  213 HIS cc_start: 0.8681 (m-70) cc_final: 0.8223 (m90)
REVERT: A  278 ASN cc_start: 0.6949 (t0) cc_final: 0.6683 (t0)
REVERT: A  309 LEU cc_start: 0.8507 (mt) cc_final: 0.7853 (pp)
REVERT: A  310 ILE cc_start: 0.8852 (mt) cc_final: 0.8287 (tp)
REVERT: A  311 LEU cc_start: 0.8468 (mt) cc_final: 0.8103 (pp)
REVERT: A  486 GLU cc_start: 0.6564 (mt-10) cc_final: 0.5872 (mm-30)
REVERT: B   37 LYS cc_start: 0.7812 (mtpt) cc_final: 0.7396 (mmtm)
REVERT: B  142 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8834 (mt-10)
REVERT: B  188 LYS cc_start: 0.7773 (tmtt) cc_final: 0.7569 (tmtt)
REVERT: B  195 LEU cc_start: 0.8327 (mm) cc_final: 0.8049 (mm)
REVERT: B  213 HIS cc_start: 0.8699 (m-70) cc_final: 0.8252 (m90)
REVERT: B  278 ASN cc_start: 0.6954 (t0) cc_final: 0.6706 (t0)
REVERT: B  309 LEU cc_start: 0.8586 (mt) cc_final: 0.8076 (pp)
REVERT: B  310 ILE cc_start: 0.8910 (mt) cc_final: 0.8355 (tp)
REVERT: B  486 GLU cc_start: 0.6530 (mt-10) cc_final: 0.5874 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 259
  average time/residue: 0.1932
  time to fit residues: 74.3580
Evaluate side-chains
  192 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 92 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0000
   chunk 3 optimal weight:    2.9990
   chunk 100 optimal weight:    8.9990
   chunk 9 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 68 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0980
   overall best weight:    0.5186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 252 ASN
A 327 GLN
A 537 ASN
B 252 ASN
B 327 GLN
B 537 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.154529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.108223 restraints weight = 22603.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.111528 restraints weight = 14808.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.113902 restraints weight = 10952.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6629
moved from start:          0.5706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9551  Z= 0.127
  Angle     :  0.547   6.796  12856  Z= 0.304
  Chirality :  0.043   0.195   1394
  Planarity :  0.004   0.043   1576
  Dihedral  :  4.503  15.507   1212
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.83 %
    Favored  : 98.07 %
  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 (0.25), residues: 1104
  helix:  0.84 (0.20), residues: 596
  sheet:  0.17 (0.49), residues: 126
  loop : -0.25 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 424 
 HIS   0.004   0.001   HIS A 239 
 PHE   0.024   0.002   PHE B 217 
 TYR   0.020   0.001   TYR B 203 
 ARG   0.006   0.001   ARG A 444 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04502 (  489)
  hydrogen bonds       : angle       5.10589 ( 1401)
  metal coordination   : bond        0.00083 (    4)
  covalent geometry    : bond        0.00263 ( 9546)
  covalent geometry    : angle       0.54657 (12856)
  Misc. bond           : bond        0.00661 (    1)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 262
  time to evaluate  : 1.132 
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  142 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8823 (mt-10)
REVERT: A  152 ASN cc_start: 0.8313 (t0) cc_final: 0.8101 (m-40)
REVERT: A  195 LEU cc_start: 0.8141 (mm) cc_final: 0.7681 (mm)
REVERT: A  213 HIS cc_start: 0.8685 (m-70) cc_final: 0.8182 (m90)
REVERT: A  309 LEU cc_start: 0.8442 (mt) cc_final: 0.7897 (pp)
REVERT: A  310 ILE cc_start: 0.8798 (mt) cc_final: 0.8248 (tt)
REVERT: A  486 GLU cc_start: 0.6414 (mt-10) cc_final: 0.5775 (mm-30)
REVERT: B   37 LYS cc_start: 0.7802 (mtpt) cc_final: 0.7355 (mmtm)
REVERT: B  142 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8879 (mt-10)
REVERT: B  171 ILE cc_start: 0.9214 (mm) cc_final: 0.8788 (tp)
REVERT: B  188 LYS cc_start: 0.7732 (tmtt) cc_final: 0.7527 (tmtt)
REVERT: B  195 LEU cc_start: 0.8238 (mm) cc_final: 0.7810 (mm)
REVERT: B  213 HIS cc_start: 0.8654 (m-70) cc_final: 0.8134 (m90)
REVERT: B  247 ARG cc_start: 0.7607 (mtp85) cc_final: 0.7086 (mtp85)
REVERT: B  307 SER cc_start: 0.8248 (t) cc_final: 0.7981 (p)
REVERT: B  309 LEU cc_start: 0.8527 (mt) cc_final: 0.7921 (pp)
REVERT: B  310 ILE cc_start: 0.8831 (mt) cc_final: 0.8288 (tt)
REVERT: B  486 GLU cc_start: 0.6393 (mt-10) cc_final: 0.5762 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 262
  average time/residue: 0.1862
  time to fit residues: 70.5541
Evaluate side-chains
  213 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 95 optimal weight:    0.9980
   chunk 6 optimal weight:   10.0000
   chunk 59 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0060
   chunk 88 optimal weight:    7.9990
   chunk 48 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 46 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.2002

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 252 ASN
A 327 GLN
** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 252 ASN
B 327 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.154328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.107252 restraints weight = 23119.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.110604 restraints weight = 15049.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.113017 restraints weight = 11042.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6680
moved from start:          0.6024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9551  Z= 0.142
  Angle     :  0.595  13.651  12856  Z= 0.324
  Chirality :  0.043   0.177   1394
  Planarity :  0.004   0.043   1576
  Dihedral  :  4.566  20.811   1212
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.93 %
    Favored  : 97.88 %
  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 (0.25), residues: 1104
  helix:  0.79 (0.20), residues: 594
  sheet:  0.02 (0.49), residues: 130
  loop : -0.29 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 475 
 HIS   0.004   0.001   HIS B 205 
 PHE   0.020   0.002   PHE B 217 
 TYR   0.025   0.002   TYR B 337 
 ARG   0.001   0.000   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04368 (  489)
  hydrogen bonds       : angle       5.12669 ( 1401)
  metal coordination   : bond        0.00305 (    4)
  covalent geometry    : bond        0.00300 ( 9546)
  covalent geometry    : angle       0.59506 (12856)
  Misc. bond           : bond        0.01261 (    1)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 253
  time to evaluate  : 1.752 
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   43 LEU cc_start: 0.8901 (mt) cc_final: 0.8558 (mt)
REVERT: A  142 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8834 (mt-10)
REVERT: A  152 ASN cc_start: 0.8309 (t0) cc_final: 0.8094 (m-40)
REVERT: A  213 HIS cc_start: 0.8662 (m-70) cc_final: 0.8151 (m90)
REVERT: A  278 ASN cc_start: 0.7049 (t0) cc_final: 0.6738 (t0)
REVERT: A  309 LEU cc_start: 0.8428 (mt) cc_final: 0.7854 (pp)
REVERT: A  310 ILE cc_start: 0.8763 (mt) cc_final: 0.8264 (tt)
REVERT: A  486 GLU cc_start: 0.6426 (mt-10) cc_final: 0.5783 (mm-30)
REVERT: B   43 LEU cc_start: 0.8972 (mt) cc_final: 0.8771 (mt)
REVERT: B  142 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8850 (mt-10)
REVERT: B  171 ILE cc_start: 0.9241 (mm) cc_final: 0.8999 (tp)
REVERT: B  188 LYS cc_start: 0.7707 (tmtt) cc_final: 0.7497 (tmtt)
REVERT: B  194 ARG cc_start: 0.8801 (ttm170) cc_final: 0.8561 (ttp-110)
REVERT: B  195 LEU cc_start: 0.8244 (mm) cc_final: 0.7969 (mm)
REVERT: B  213 HIS cc_start: 0.8620 (m-70) cc_final: 0.8084 (m90)
REVERT: B  247 ARG cc_start: 0.7464 (mtp85) cc_final: 0.7134 (mtp85)
REVERT: B  278 ASN cc_start: 0.7152 (t0) cc_final: 0.6886 (t0)
REVERT: B  310 ILE cc_start: 0.8741 (mt) cc_final: 0.8395 (tt)
REVERT: B  486 GLU cc_start: 0.6434 (mt-10) cc_final: 0.5833 (mm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 253
  average time/residue: 0.1877
  time to fit residues: 68.0206
Evaluate side-chains
  213 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 212
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 41 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 106 optimal weight:    5.9990
   chunk 79 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0070
   chunk 55 optimal weight:    0.6980
   chunk 83 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 75 optimal weight:    0.5980
   overall best weight:    0.5798

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 252 ASN
A 327 GLN
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 252 ASN
B 327 GLN
** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.155353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.109440 restraints weight = 22797.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.112705 restraints weight = 14895.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.115022 restraints weight = 10980.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6641
moved from start:          0.6298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9551  Z= 0.125
  Angle     :  0.593  12.336  12856  Z= 0.322
  Chirality :  0.043   0.172   1394
  Planarity :  0.004   0.046   1576
  Dihedral  :  4.505  19.652   1212
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  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:  0.53 (0.25), residues: 1104
  helix:  0.93 (0.20), residues: 582
  sheet:  0.14 (0.49), residues: 130
  loop : -0.31 (0.33), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 424 
 HIS   0.005   0.001   HIS B 239 
 PHE   0.025   0.002   PHE A 217 
 TYR   0.023   0.001   TYR B 337 
 ARG   0.001   0.000   ARG B  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04314 (  489)
  hydrogen bonds       : angle       5.15927 ( 1401)
  metal coordination   : bond        0.00109 (    4)
  covalent geometry    : bond        0.00267 ( 9546)
  covalent geometry    : angle       0.59287 (12856)
  Misc. bond           : bond        0.00305 (    1)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 1.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.8786 (mt) cc_final: 0.8529 (mt)
REVERT: A  152 ASN cc_start: 0.8304 (t0) cc_final: 0.8086 (m-40)
REVERT: A  213 HIS cc_start: 0.8689 (m-70) cc_final: 0.8109 (m90)
REVERT: A  310 ILE cc_start: 0.8784 (mt) cc_final: 0.8441 (tt)
REVERT: A  330 MET cc_start: 0.5117 (mpp) cc_final: 0.4902 (mpp)
REVERT: A  434 MET cc_start: 0.6872 (tpp) cc_final: 0.6039 (tpp)
REVERT: A  486 GLU cc_start: 0.6417 (mt-10) cc_final: 0.5809 (mm-30)
REVERT: B   15 ILE cc_start: 0.9308 (mm) cc_final: 0.9017 (mm)
REVERT: B  142 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8890 (mt-10)
REVERT: B  152 ASN cc_start: 0.8386 (m110) cc_final: 0.8056 (m-40)
REVERT: B  171 ILE cc_start: 0.9254 (mm) cc_final: 0.8872 (tp)
REVERT: B  213 HIS cc_start: 0.8681 (m-70) cc_final: 0.8173 (m-70)
REVERT: B  247 ARG cc_start: 0.7415 (mtp85) cc_final: 0.7108 (mtp85)
REVERT: B  310 ILE cc_start: 0.8802 (mt) cc_final: 0.8480 (tt)
REVERT: B  434 MET cc_start: 0.6942 (tpp) cc_final: 0.6123 (tpp)
REVERT: B  486 GLU cc_start: 0.6329 (mt-10) cc_final: 0.5737 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 258
  average time/residue: 0.1909
  time to fit residues: 70.2102
Evaluate side-chains
  205 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 86 optimal weight:    0.2980
   chunk 31 optimal weight:    8.9990
   chunk 92 optimal weight:    7.9990
   chunk 24 optimal weight:    0.3980
   chunk 68 optimal weight:    3.9990
   chunk 94 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  95 HIS
A 252 ASN
A 327 GLN
B 153 HIS
B 227 ASN
B 327 GLN
** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.156582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.110096 restraints weight = 22853.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.113585 restraints weight = 14686.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.115976 restraints weight = 10642.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6663
moved from start:          0.6473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9551  Z= 0.130
  Angle     :  0.591  13.949  12856  Z= 0.319
  Chirality :  0.044   0.181   1394
  Planarity :  0.004   0.045   1576
  Dihedral  :  4.423  17.351   1212
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  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 (0.25), residues: 1104
  helix:  1.02 (0.20), residues: 576
  sheet:  0.08 (0.50), residues: 130
  loop : -0.39 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 424 
 HIS   0.005   0.001   HIS B 239 
 PHE   0.028   0.002   PHE B 217 
 TYR   0.016   0.001   TYR B 203 
 ARG   0.006   0.000   ARG A 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04389 (  489)
  hydrogen bonds       : angle       5.11194 ( 1401)
  metal coordination   : bond        0.00194 (    4)
  covalent geometry    : bond        0.00282 ( 9546)
  covalent geometry    : angle       0.59131 (12856)
  Misc. bond           : bond        0.00714 (    1)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.8867 (mt) cc_final: 0.8596 (mt)
REVERT: A  122 LEU cc_start: 0.8923 (mt) cc_final: 0.8688 (mt)
REVERT: A  213 HIS cc_start: 0.8728 (m-70) cc_final: 0.8175 (m90)
REVERT: A  310 ILE cc_start: 0.8789 (mt) cc_final: 0.8462 (tt)
REVERT: A  434 MET cc_start: 0.6864 (tpp) cc_final: 0.6041 (tpp)
REVERT: A  486 GLU cc_start: 0.6410 (mt-10) cc_final: 0.5838 (mm-30)
REVERT: B   15 ILE cc_start: 0.9356 (mm) cc_final: 0.8884 (mm)
REVERT: B   43 LEU cc_start: 0.9017 (mt) cc_final: 0.8807 (mt)
REVERT: B  130 TYR cc_start: 0.7559 (t80) cc_final: 0.7341 (t80)
REVERT: B  142 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8891 (mt-10)
REVERT: B  171 ILE cc_start: 0.9255 (mm) cc_final: 0.8861 (tp)
REVERT: B  213 HIS cc_start: 0.8653 (m-70) cc_final: 0.8202 (m-70)
REVERT: B  247 ARG cc_start: 0.7364 (mtp85) cc_final: 0.7063 (mtp85)
REVERT: B  264 SER cc_start: 0.8578 (p) cc_final: 0.8290 (p)
REVERT: B  310 ILE cc_start: 0.8787 (mt) cc_final: 0.8505 (tt)
REVERT: B  434 MET cc_start: 0.6957 (tpp) cc_final: 0.6154 (tpp)
REVERT: B  486 GLU cc_start: 0.6311 (mt-10) cc_final: 0.5751 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 236
  average time/residue: 0.1729
  time to fit residues: 59.6862
Evaluate side-chains
  196 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 83 optimal weight:    0.6980
   chunk 88 optimal weight:   10.0000
   chunk 57 optimal weight:    1.9990
   chunk 82 optimal weight:    0.4980
   chunk 27 optimal weight:    0.5980
   chunk 44 optimal weight:    0.3980
   chunk 46 optimal weight:    1.9990
   chunk 61 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9980
   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 252 ASN
A 327 GLN
** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 153 HIS
B 327 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.156860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.111167 restraints weight = 22322.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.114206 restraints weight = 15067.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.116490 restraints weight = 11267.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6656
moved from start:          0.6684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   9551  Z= 0.132
  Angle     :  0.594  10.654  12856  Z= 0.324
  Chirality :  0.044   0.218   1394
  Planarity :  0.004   0.048   1576
  Dihedral  :  4.447  24.963   1212
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  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:  0.66 (0.25), residues: 1104
  helix:  1.15 (0.21), residues: 572
  sheet:  0.10 (0.49), residues: 130
  loop : -0.37 (0.33), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 424 
 HIS   0.005   0.001   HIS B 239 
 PHE   0.029   0.002   PHE B 217 
 TYR   0.017   0.001   TYR A 203 
 ARG   0.003   0.000   ARG A 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04464 (  489)
  hydrogen bonds       : angle       5.15894 ( 1401)
  metal coordination   : bond        0.00179 (    4)
  covalent geometry    : bond        0.00288 ( 9546)
  covalent geometry    : angle       0.59415 (12856)
  Misc. bond           : bond        0.01365 (    1)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 PHE cc_start: 0.8433 (m-10) cc_final: 0.7920 (m-80)
REVERT: A   43 LEU cc_start: 0.8709 (mt) cc_final: 0.8490 (mt)
REVERT: A  202 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7524 (mm-30)
REVERT: A  213 HIS cc_start: 0.8468 (m-70) cc_final: 0.8037 (m90)
REVERT: A  310 ILE cc_start: 0.8675 (mt) cc_final: 0.8344 (tt)
REVERT: A  368 MET cc_start: 0.7523 (ppp) cc_final: 0.6985 (ppp)
REVERT: A  374 TYR cc_start: 0.3431 (m-80) cc_final: 0.2045 (m-80)
REVERT: A  434 MET cc_start: 0.6847 (tpp) cc_final: 0.6035 (tpp)
REVERT: A  486 GLU cc_start: 0.6421 (mt-10) cc_final: 0.5842 (mm-30)
REVERT: B  171 ILE cc_start: 0.9101 (mm) cc_final: 0.8882 (tp)
REVERT: B  213 HIS cc_start: 0.8292 (m-70) cc_final: 0.8021 (m-70)
REVERT: B  247 ARG cc_start: 0.7020 (mtp85) cc_final: 0.6771 (mtp85)
REVERT: B  264 SER cc_start: 0.8579 (p) cc_final: 0.8092 (p)
REVERT: B  310 ILE cc_start: 0.8656 (mt) cc_final: 0.8394 (tt)
REVERT: B  329 LEU cc_start: 0.3805 (tp) cc_final: 0.3523 (mt)
REVERT: B  434 MET cc_start: 0.6841 (tpp) cc_final: 0.6072 (tpp)
REVERT: B  486 GLU cc_start: 0.6358 (mt-10) cc_final: 0.5788 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 232
  average time/residue: 0.1676
  time to fit residues: 56.8937
Evaluate side-chains
  186 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0020
   chunk 10 optimal weight:    0.0030
   chunk 98 optimal weight:    2.9990
   chunk 108 optimal weight:    2.9990
   chunk 81 optimal weight:    0.0670
   chunk 77 optimal weight:    0.9990
   chunk 93 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 80 optimal weight:    6.9990
   overall best weight:    0.4138

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
A 252 ASN
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 153 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.157780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.111987 restraints weight = 22664.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.115296 restraints weight = 14948.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.117644 restraints weight = 11033.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6623
moved from start:          0.6930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9551  Z= 0.123
  Angle     :  0.611  17.438  12856  Z= 0.323
  Chirality :  0.044   0.192   1394
  Planarity :  0.004   0.048   1576
  Dihedral  :  4.392  19.699   1212
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  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:  0.68 (0.26), residues: 1104
  helix:  1.15 (0.21), residues: 572
  sheet:  0.13 (0.49), residues: 130
  loop : -0.32 (0.33), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 424 
 HIS   0.003   0.001   HIS B 205 
 PHE   0.030   0.002   PHE B 217 
 TYR   0.018   0.001   TYR A 337 
 ARG   0.003   0.000   ARG A 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04340 (  489)
  hydrogen bonds       : angle       5.13766 ( 1401)
  metal coordination   : bond        0.00133 (    4)
  covalent geometry    : bond        0.00259 ( 9546)
  covalent geometry    : angle       0.61083 (12856)
  Misc. bond           : bond        0.00904 (    1)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 1.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 TYR cc_start: 0.6121 (t80) cc_final: 0.5897 (t80)
REVERT: A   43 LEU cc_start: 0.8809 (mt) cc_final: 0.8497 (mt)
REVERT: A  173 PHE cc_start: 0.6547 (m-80) cc_final: 0.6143 (m-80)
REVERT: A  202 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7797 (mm-30)
REVERT: A  213 HIS cc_start: 0.8700 (m-70) cc_final: 0.8130 (m90)
REVERT: A  263 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7569 (mm-30)
REVERT: A  310 ILE cc_start: 0.8814 (mt) cc_final: 0.8513 (tt)
REVERT: A  368 MET cc_start: 0.7562 (ppp) cc_final: 0.7138 (ppp)
REVERT: A  374 TYR cc_start: 0.3507 (m-80) cc_final: 0.2225 (m-80)
REVERT: A  434 MET cc_start: 0.6768 (tpp) cc_final: 0.6083 (tpp)
REVERT: A  486 GLU cc_start: 0.6425 (mt-10) cc_final: 0.5804 (mm-30)
REVERT: B   43 LEU cc_start: 0.8978 (mt) cc_final: 0.8761 (mt)
REVERT: B  171 ILE cc_start: 0.9149 (mm) cc_final: 0.8892 (tp)
REVERT: B  213 HIS cc_start: 0.8562 (m-70) cc_final: 0.8142 (m-70)
REVERT: B  226 TYR cc_start: 0.7659 (p90) cc_final: 0.7442 (p90)
REVERT: B  247 ARG cc_start: 0.7264 (mtp85) cc_final: 0.6952 (mtp85)
REVERT: B  310 ILE cc_start: 0.8745 (mt) cc_final: 0.8474 (tt)
REVERT: B  434 MET cc_start: 0.6863 (tpp) cc_final: 0.6201 (tpp)
REVERT: B  486 GLU cc_start: 0.6447 (mt-10) cc_final: 0.5839 (mm-30)
REVERT: B  566 LYS cc_start: 0.6898 (mmtm) cc_final: 0.6670 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 226
  average time/residue: 0.1680
  time to fit residues: 56.1482
Evaluate side-chains
  189 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 53 optimal weight:    0.0070
   chunk 8 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 101 optimal weight:    1.9990
   chunk 80 optimal weight:    6.9990
   chunk 84 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 69 optimal weight:    0.4980
   chunk 66 optimal weight:    0.5980
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.5398

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 252 ASN
A 327 GLN
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 134 GLN
B 327 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.160207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.115311 restraints weight = 22069.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.118519 restraints weight = 14697.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.120732 restraints weight = 10881.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6626
moved from start:          0.7122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9551  Z= 0.120
  Angle     :  0.594  11.407  12856  Z= 0.319
  Chirality :  0.043   0.157   1394
  Planarity :  0.004   0.048   1576
  Dihedral  :  4.326  19.366   1212
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  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:  0.71 (0.26), residues: 1104
  helix:  1.13 (0.21), residues: 576
  sheet:  0.16 (0.49), residues: 130
  loop : -0.26 (0.33), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 540 
 HIS   0.031   0.002   HIS B 153 
 PHE   0.030   0.002   PHE B 217 
 TYR   0.016   0.001   TYR B 203 
 ARG   0.003   0.000   ARG A 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04062 (  489)
  hydrogen bonds       : angle       5.11364 ( 1401)
  metal coordination   : bond        0.00162 (    4)
  covalent geometry    : bond        0.00254 ( 9546)
  covalent geometry    : angle       0.59416 (12856)
  Misc. bond           : bond        0.00303 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3257.28 seconds
wall clock time: 58 minutes 7.89 seconds (3487.89 seconds total)