Starting phenix.real_space_refine
on Thu Feb 13 16:25:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8exs_28661/02_2025/8exs_28661.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8exs_28661/02_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_28661/02_2025/8exs_28661.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8exs_28661/02_2025/8exs_28661.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8exs_28661/02_2025/8exs_28661.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8exs_28661/02_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-5592/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: 8.23, per 1000 atoms: 0.88
  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: 2.63
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 201 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 205 "
      pdb="  ZN B 701 "
        pdb="ZN    ZN B 701 " - pdb=" NE2 HIS B 201 "
        pdb="ZN    ZN B 701 " - pdb=" NE2 HIS B 205 "


  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: 0.88
  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: 2.80

  Time building geometry restraints manager: 2.96 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:             0.470
  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:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     27.730
  Find NCS groups from input model:        0.180
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.760
-------------------------------------------------------------------------------
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   0.122   9546  Z= 1.282
  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 

*********************** 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  : 1.212 
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: 0.2276
  time to fit residues: 106.1410
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  : 1.005 
-------------------------------------------------------------------------------
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   9546  Z= 0.226
  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 

*********************** 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  : 1.075 
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: 0.1998
  time to fit residues: 87.0263
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  : 1.245 
-------------------------------------------------------------------------------
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:    0.0270
   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:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.9042

-------------------------------------------------------------------------------
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
** A 436 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 = 0.4370 r_free = 0.4370 target = 0.158456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.110302 restraints weight = 22678.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.114162 restraints weight = 14091.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.116381 restraints weight = 10098.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6572
moved from start:          0.4545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9546  Z= 0.175
  Angle     :  0.558   6.479  12856  Z= 0.320
  Chirality :  0.043   0.220   1394
  Planarity :  0.004   0.036   1576
  Dihedral  :  4.567  14.843   1212
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.73 %
    Favored  : 98.17 %
  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:  0.74 (0.25), residues: 1104
  helix:  1.13 (0.20), residues: 598
  sheet:  0.15 (0.49), residues: 126
  loop : -0.26 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 424 
 HIS   0.003   0.001   HIS B 239 
 PHE   0.023   0.002   PHE B  22 
 TYR   0.024   0.002   TYR B 203 
 ARG   0.002   0.000   ARG A 444 

*********************** 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
  277 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 276
  time to evaluate  : 1.467 
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  142 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8845 (mt-10)
REVERT: A  152 ASN cc_start: 0.8306 (t0) cc_final: 0.8008 (m-40)
REVERT: A  173 PHE cc_start: 0.6392 (m-80) cc_final: 0.5445 (m-80)
REVERT: A  188 LYS cc_start: 0.7821 (tmtt) cc_final: 0.7598 (tmtt)
REVERT: A  195 LEU cc_start: 0.8109 (mm) cc_final: 0.7895 (mm)
REVERT: A  213 HIS cc_start: 0.8873 (m-70) cc_final: 0.8360 (m90)
REVERT: A  310 ILE cc_start: 0.8813 (mt) cc_final: 0.8597 (tp)
REVERT: A  434 MET cc_start: 0.6815 (tpp) cc_final: 0.5916 (tpp)
REVERT: B   14 PHE cc_start: 0.7833 (t80) cc_final: 0.7614 (t80)
REVERT: B   20 LEU cc_start: 0.9349 (mt) cc_final: 0.9145 (mt)
REVERT: B   37 LYS cc_start: 0.7721 (mtpt) cc_final: 0.7213 (mmtm)
REVERT: B  152 ASN cc_start: 0.8202 (t0) cc_final: 0.7908 (m-40)
REVERT: B  173 PHE cc_start: 0.6402 (m-80) cc_final: 0.5415 (m-80)
REVERT: B  188 LYS cc_start: 0.7851 (tmtt) cc_final: 0.7621 (tmtt)
REVERT: B  195 LEU cc_start: 0.8128 (mm) cc_final: 0.7624 (mm)
REVERT: B  213 HIS cc_start: 0.8873 (m-70) cc_final: 0.8374 (m90)
REVERT: B  310 ILE cc_start: 0.8858 (mt) cc_final: 0.8557 (tp)
REVERT: B  434 MET cc_start: 0.6808 (tpp) cc_final: 0.5911 (tpp)
  outliers start: 1
  outliers final: 1
  residues processed: 277
  average time/residue: 0.1947
  time to fit residues: 78.3349
Evaluate side-chains
  211 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 210
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 97 optimal weight:    0.4980
   chunk 81 optimal weight:    1.9990
   chunk 67 optimal weight:    9.9990
   chunk 77 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 22 optimal weight:    0.4980
   chunk 103 optimal weight:    0.4980
   chunk 83 optimal weight:    2.9990
   chunk 80 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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
** A 436 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 = 0.4379 r_free = 0.4379 target = 0.158337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.110453 restraints weight = 22452.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.114235 restraints weight = 13804.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.116739 restraints weight = 9821.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6602
moved from start:          0.5098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9546  Z= 0.169
  Angle     :  0.572   9.543  12856  Z= 0.316
  Chirality :  0.043   0.190   1394
  Planarity :  0.003   0.034   1576
  Dihedral  :  4.469  14.576   1212
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  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:  0.75 (0.25), residues: 1104
  helix:  1.13 (0.20), residues: 600
  sheet:  0.16 (0.49), residues: 126
  loop : -0.25 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 475 
 HIS   0.004   0.001   HIS A 205 
 PHE   0.025   0.002   PHE A 217 
 TYR   0.020   0.002   TYR B 203 
 ARG   0.003   0.000   ARG A 444 

*********************** 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
  284 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 284
  time to evaluate  : 1.066 
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  142 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8825 (mt-10)
REVERT: A  188 LYS cc_start: 0.7758 (tmtt) cc_final: 0.7545 (tmtt)
REVERT: A  195 LEU cc_start: 0.8083 (mm) cc_final: 0.7820 (mm)
REVERT: A  213 HIS cc_start: 0.8580 (m-70) cc_final: 0.8119 (m90)
REVERT: A  247 ARG cc_start: 0.7527 (mtp180) cc_final: 0.7149 (mtp85)
REVERT: A  310 ILE cc_start: 0.8812 (mt) cc_final: 0.8302 (tt)
REVERT: A  316 ILE cc_start: 0.8492 (tp) cc_final: 0.8281 (tp)
REVERT: A  434 MET cc_start: 0.6919 (tpp) cc_final: 0.6022 (tpp)
REVERT: A  486 GLU cc_start: 0.6491 (mt-10) cc_final: 0.5819 (mm-30)
REVERT: B   37 LYS cc_start: 0.7701 (mtpt) cc_final: 0.7316 (mmtm)
REVERT: B  195 LEU cc_start: 0.8120 (mm) cc_final: 0.7813 (mm)
REVERT: B  213 HIS cc_start: 0.8589 (m-70) cc_final: 0.8115 (m90)
REVERT: B  310 ILE cc_start: 0.8807 (mt) cc_final: 0.8307 (tt)
REVERT: B  316 ILE cc_start: 0.8528 (tp) cc_final: 0.8294 (tp)
REVERT: B  434 MET cc_start: 0.6890 (tpp) cc_final: 0.5998 (tpp)
REVERT: B  486 GLU cc_start: 0.6597 (mt-10) cc_final: 0.5888 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 284
  average time/residue: 0.1831
  time to fit residues: 75.4962
Evaluate side-chains
  202 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 1.241 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 92 optimal weight:    9.9990
   chunk 66 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 100 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 68 optimal weight:    0.3980
   chunk 65 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    2.2386

-------------------------------------------------------------------------------
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 327 GLN
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 134 GLN
B 252 ASN
B 327 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 = 0.4326 r_free = 0.4326 target = 0.154422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.107254 restraints weight = 23061.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.110790 restraints weight = 14512.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.113170 restraints weight = 10471.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6709
moved from start:          0.5645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9546  Z= 0.258
  Angle     :  0.621   7.239  12856  Z= 0.344
  Chirality :  0.045   0.174   1394
  Planarity :  0.004   0.044   1576
  Dihedral  :  4.642  15.574   1212
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.89 %
    Favored  : 97.01 %
  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:  0.31 (0.25), residues: 1104
  helix:  0.78 (0.20), residues: 594
  sheet:  0.04 (0.50), residues: 130
  loop : -0.48 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 475 
 HIS   0.005   0.001   HIS A 205 
 PHE   0.022   0.002   PHE B 274 
 TYR   0.025   0.002   TYR A 203 
 ARG   0.004   0.001   ARG B 247 

*********************** 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
  238 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 237
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.8910 (mt) cc_final: 0.8665 (mt)
REVERT: A  142 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8785 (mt-10)
REVERT: A  171 ILE cc_start: 0.9319 (mm) cc_final: 0.8991 (tp)
REVERT: A  188 LYS cc_start: 0.7779 (tmtt) cc_final: 0.7563 (tmtt)
REVERT: A  195 LEU cc_start: 0.8277 (mm) cc_final: 0.8049 (mm)
REVERT: A  213 HIS cc_start: 0.8654 (m-70) cc_final: 0.8138 (m90)
REVERT: A  247 ARG cc_start: 0.7443 (mtp180) cc_final: 0.7150 (mtp85)
REVERT: A  309 LEU cc_start: 0.8248 (mt) cc_final: 0.7837 (pp)
REVERT: A  310 ILE cc_start: 0.8836 (mt) cc_final: 0.8268 (tp)
REVERT: A  486 GLU cc_start: 0.6488 (mt-10) cc_final: 0.5835 (mm-30)
REVERT: B   24 TYR cc_start: 0.6618 (t80) cc_final: 0.6345 (t80)
REVERT: B   37 LYS cc_start: 0.7883 (mtpt) cc_final: 0.7396 (mmtm)
REVERT: B   43 LEU cc_start: 0.8920 (mt) cc_final: 0.8705 (mt)
REVERT: B  142 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8934 (mt-10)
REVERT: B  171 ILE cc_start: 0.9295 (mm) cc_final: 0.8991 (tp)
REVERT: B  195 LEU cc_start: 0.8213 (mm) cc_final: 0.7981 (mm)
REVERT: B  213 HIS cc_start: 0.8679 (m-70) cc_final: 0.8155 (m90)
REVERT: B  309 LEU cc_start: 0.8335 (mt) cc_final: 0.7902 (pp)
REVERT: B  310 ILE cc_start: 0.8970 (mt) cc_final: 0.8288 (tt)
REVERT: B  486 GLU cc_start: 0.6421 (mt-10) cc_final: 0.5794 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 237
  average time/residue: 0.1864
  time to fit residues: 64.5951
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  : 1.167 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 6 optimal weight:   10.0000
   chunk 59 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 43 optimal weight:    7.9990
   chunk 88 optimal weight:    9.9990
   chunk 48 optimal weight:    0.0000
   chunk 47 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   overall best weight:    1.1388

-------------------------------------------------------------------------------
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 537 ASN
** B 227 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**
B 537 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.157318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.109518 restraints weight = 22916.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.113165 restraints weight = 14338.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.115652 restraints weight = 10309.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6688
moved from start:          0.5996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9546  Z= 0.186
  Angle     :  0.586  11.934  12856  Z= 0.324
  Chirality :  0.044   0.287   1394
  Planarity :  0.004   0.047   1576
  Dihedral  :  4.539  15.465   1212
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.64 %
    Favored  : 98.27 %
  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:  0.26 (0.25), residues: 1104
  helix:  0.72 (0.20), residues: 600
  sheet: -0.12 (0.49), residues: 130
  loop : -0.45 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 475 
 HIS   0.004   0.001   HIS A 205 
 PHE   0.028   0.002   PHE B 491 
 TYR   0.023   0.002   TYR A 203 
 ARG   0.004   0.000   ARG B 247 

*********************** 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
  258 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 257
  time to evaluate  : 1.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8807 (mt-10)
REVERT: A  171 ILE cc_start: 0.9264 (mm) cc_final: 0.9018 (tp)
REVERT: A  188 LYS cc_start: 0.7744 (tmtt) cc_final: 0.7524 (tmtt)
REVERT: A  195 LEU cc_start: 0.8282 (mm) cc_final: 0.7845 (mm)
REVERT: A  213 HIS cc_start: 0.8524 (m-70) cc_final: 0.8031 (m90)
REVERT: A  247 ARG cc_start: 0.7342 (mtp180) cc_final: 0.6976 (mtp85)
REVERT: A  278 ASN cc_start: 0.7149 (t0) cc_final: 0.6874 (t0)
REVERT: A  309 LEU cc_start: 0.8215 (mt) cc_final: 0.7715 (pp)
REVERT: A  310 ILE cc_start: 0.8763 (mt) cc_final: 0.8219 (tt)
REVERT: A  434 MET cc_start: 0.6820 (tpp) cc_final: 0.5979 (tpp)
REVERT: A  486 GLU cc_start: 0.6289 (mt-10) cc_final: 0.5641 (mm-30)
REVERT: B   37 LYS cc_start: 0.7771 (mtpt) cc_final: 0.7373 (mmtm)
REVERT: B  142 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8961 (mt-10)
REVERT: B  171 ILE cc_start: 0.9238 (mm) cc_final: 0.9013 (tp)
REVERT: B  195 LEU cc_start: 0.8229 (mm) cc_final: 0.7767 (mm)
REVERT: B  213 HIS cc_start: 0.8551 (m-70) cc_final: 0.8051 (m90)
REVERT: B  278 ASN cc_start: 0.7146 (t0) cc_final: 0.6867 (t0)
REVERT: B  309 LEU cc_start: 0.8239 (mt) cc_final: 0.7775 (pp)
REVERT: B  310 ILE cc_start: 0.8786 (mt) cc_final: 0.8284 (tt)
REVERT: B  434 MET cc_start: 0.6826 (tpp) cc_final: 0.5981 (tpp)
REVERT: B  486 GLU cc_start: 0.6296 (mt-10) cc_final: 0.5644 (mm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 257
  average time/residue: 0.1999
  time to fit residues: 72.7833
Evaluate side-chains
  200 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 199
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 41 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 106 optimal weight:    7.9990
   chunk 79 optimal weight:    9.9990
   chunk 68 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   chunk 75 optimal weight:    0.0570
   overall best weight:    2.2104

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 ASN
A 327 GLN
** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 252 ASN
B 327 GLN
** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 567 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 = 0.4319 r_free = 0.4319 target = 0.153788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.106911 restraints weight = 23417.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.110395 restraints weight = 14781.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.112864 restraints weight = 10702.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6747
moved from start:          0.6439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9546  Z= 0.267
  Angle     :  0.666  11.500  12856  Z= 0.366
  Chirality :  0.046   0.171   1394
  Planarity :  0.004   0.048   1576
  Dihedral  :  4.698  17.247   1212
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    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: -0.04 (0.24), residues: 1104
  helix:  0.52 (0.20), residues: 596
  sheet: -0.03 (0.50), residues: 130
  loop : -0.74 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 174 
 HIS   0.005   0.002   HIS A 282 
 PHE   0.019   0.002   PHE B 274 
 TYR   0.019   0.002   TYR A 391 
 ARG   0.003   0.000   ARG B 294 

*********************** 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
  230 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ILE cc_start: 0.9384 (mm) cc_final: 0.9167 (mm)
REVERT: A  142 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8802 (mt-10)
REVERT: A  171 ILE cc_start: 0.9323 (mm) cc_final: 0.9090 (tp)
REVERT: A  188 LYS cc_start: 0.7821 (tmtt) cc_final: 0.7604 (tmtt)
REVERT: A  195 LEU cc_start: 0.8235 (mm) cc_final: 0.8002 (mm)
REVERT: A  213 HIS cc_start: 0.8706 (m-70) cc_final: 0.8120 (m90)
REVERT: A  247 ARG cc_start: 0.7540 (mtp180) cc_final: 0.7261 (mtp85)
REVERT: A  309 LEU cc_start: 0.8338 (mt) cc_final: 0.7861 (pp)
REVERT: A  310 ILE cc_start: 0.8810 (mt) cc_final: 0.8294 (tt)
REVERT: A  486 GLU cc_start: 0.6392 (mt-10) cc_final: 0.5776 (mm-30)
REVERT: B   15 ILE cc_start: 0.9344 (mm) cc_final: 0.9046 (mm)
REVERT: B  142 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8850 (mt-10)
REVERT: B  171 ILE cc_start: 0.9332 (mm) cc_final: 0.9118 (tp)
REVERT: B  194 ARG cc_start: 0.8910 (ttm170) cc_final: 0.8647 (ttp-110)
REVERT: B  195 LEU cc_start: 0.8221 (mm) cc_final: 0.7995 (mm)
REVERT: B  213 HIS cc_start: 0.8722 (m-70) cc_final: 0.8127 (m90)
REVERT: B  246 ASP cc_start: 0.8592 (m-30) cc_final: 0.8342 (m-30)
REVERT: B  247 ARG cc_start: 0.8718 (ptm-80) cc_final: 0.7834 (ptp-110)
REVERT: B  310 ILE cc_start: 0.8854 (mt) cc_final: 0.8617 (tt)
REVERT: B  486 GLU cc_start: 0.6454 (mt-10) cc_final: 0.5842 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.1939
  time to fit residues: 64.2000
Evaluate side-chains
  184 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 1.226 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 12 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 31 optimal weight:    0.4980
   chunk 92 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0020
   chunk 68 optimal weight:    0.9990
   chunk 94 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.6990

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 ASN
A 327 GLN
A 428 GLN
** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 252 ASN
B 327 GLN
** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.160095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.112132 restraints weight = 23402.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.115721 restraints weight = 14872.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.118239 restraints weight = 10816.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6687
moved from start:          0.6663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9546  Z= 0.177
  Angle     :  0.687  28.833  12856  Z= 0.366
  Chirality :  0.044   0.230   1394
  Planarity :  0.004   0.047   1576
  Dihedral  :  4.522  19.477   1212
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Cbeta Deviations :  0.09 %
  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:  0.20 (0.25), residues: 1104
  helix:  0.73 (0.20), residues: 592
  sheet: -0.23 (0.48), residues: 130
  loop : -0.51 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 424 
 HIS   0.004   0.001   HIS A 239 
 PHE   0.036   0.002   PHE A 274 
 TYR   0.024   0.002   TYR A 337 
 ARG   0.004   0.000   ARG B 247 

*********************** 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
  248 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5562 (mmt) cc_final: 0.5166 (mmp)
REVERT: A   15 ILE cc_start: 0.9314 (mm) cc_final: 0.9053 (mm)
REVERT: A   43 LEU cc_start: 0.8824 (mt) cc_final: 0.8580 (mt)
REVERT: A  142 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8870 (mt-10)
REVERT: A  171 ILE cc_start: 0.9266 (mm) cc_final: 0.9010 (tp)
REVERT: A  213 HIS cc_start: 0.8698 (m-70) cc_final: 0.8093 (m90)
REVERT: A  247 ARG cc_start: 0.7436 (mtp180) cc_final: 0.7063 (mtp85)
REVERT: A  309 LEU cc_start: 0.8339 (mt) cc_final: 0.7905 (pp)
REVERT: A  310 ILE cc_start: 0.8706 (mt) cc_final: 0.8200 (tt)
REVERT: A  486 GLU cc_start: 0.6334 (mt-10) cc_final: 0.5720 (mm-30)
REVERT: B    1 MET cc_start: 0.6051 (mmt) cc_final: 0.5649 (mmp)
REVERT: B   15 ILE cc_start: 0.9321 (mm) cc_final: 0.8924 (mm)
REVERT: B   43 LEU cc_start: 0.8883 (mt) cc_final: 0.8645 (mt)
REVERT: B  142 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8924 (mt-10)
REVERT: B  171 ILE cc_start: 0.9265 (mm) cc_final: 0.9021 (tp)
REVERT: B  195 LEU cc_start: 0.8177 (mm) cc_final: 0.7951 (mm)
REVERT: B  213 HIS cc_start: 0.8724 (m-70) cc_final: 0.8130 (m90)
REVERT: B  246 ASP cc_start: 0.8507 (m-30) cc_final: 0.8279 (m-30)
REVERT: B  247 ARG cc_start: 0.8649 (ptm-80) cc_final: 0.7830 (ptp-110)
REVERT: B  264 SER cc_start: 0.8612 (p) cc_final: 0.8267 (p)
REVERT: B  310 ILE cc_start: 0.8827 (mt) cc_final: 0.8610 (tt)
REVERT: B  311 LEU cc_start: 0.8465 (mt) cc_final: 0.8077 (pp)
REVERT: B  434 MET cc_start: 0.6779 (tpp) cc_final: 0.5903 (tpp)
REVERT: B  486 GLU cc_start: 0.6323 (mt-10) cc_final: 0.5717 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 248
  average time/residue: 0.2047
  time to fit residues: 71.4128
Evaluate side-chains
  190 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 83 optimal weight:    5.9990
   chunk 88 optimal weight:   30.0000
   chunk 57 optimal weight:    0.9990
   chunk 82 optimal weight:    4.9990
   chunk 27 optimal weight:    8.9990
   chunk 44 optimal weight:   10.0000
   chunk 46 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 327 GLN
A 345 ASN
** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 227 ASN
** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 327 GLN
** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 567 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 = 0.4293 r_free = 0.4293 target = 0.153286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.105977 restraints weight = 23990.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.109239 restraints weight = 15656.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.111537 restraints weight = 11598.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6845
moved from start:          0.7019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077   9546  Z= 0.412
  Angle     :  0.847  20.129  12856  Z= 0.451
  Chirality :  0.050   0.181   1394
  Planarity :  0.005   0.049   1576
  Dihedral  :  5.288  20.575   1212
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 18.05
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.89 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  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: -0.88 (0.24), residues: 1104
  helix: -0.11 (0.19), residues: 594
  sheet: -0.90 (0.50), residues: 120
  loop : -1.00 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP B 424 
 HIS   0.009   0.002   HIS A 282 
 PHE   0.030   0.003   PHE A 274 
 TYR   0.024   0.003   TYR B 553 
 ARG   0.005   0.001   ARG B 235 

*********************** 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
  223 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 LYS cc_start: 0.7980 (mtmt) cc_final: 0.7500 (mppt)
REVERT: A  142 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8813 (mt-10)
REVERT: A  202 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8540 (mm-30)
REVERT: A  213 HIS cc_start: 0.8757 (m-70) cc_final: 0.8189 (m90)
REVERT: A  309 LEU cc_start: 0.8360 (mt) cc_final: 0.7889 (pp)
REVERT: A  310 ILE cc_start: 0.8739 (mt) cc_final: 0.8259 (tt)
REVERT: A  327 GLN cc_start: 0.4931 (tm130) cc_final: 0.4583 (tm-30)
REVERT: A  363 PHE cc_start: 0.7412 (t80) cc_final: 0.6900 (t80)
REVERT: A  486 GLU cc_start: 0.6397 (mt-10) cc_final: 0.5801 (mm-30)
REVERT: B   43 LEU cc_start: 0.8933 (mt) cc_final: 0.8730 (mt)
REVERT: B  130 TYR cc_start: 0.7631 (t80) cc_final: 0.7401 (t80)
REVERT: B  142 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8861 (mt-10)
REVERT: B  202 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8499 (mm-30)
REVERT: B  213 HIS cc_start: 0.8780 (m-70) cc_final: 0.8190 (m90)
REVERT: B  264 SER cc_start: 0.8777 (p) cc_final: 0.8376 (p)
REVERT: B  310 ILE cc_start: 0.8833 (mt) cc_final: 0.8560 (tt)
REVERT: B  363 PHE cc_start: 0.7293 (t80) cc_final: 0.6826 (t80)
REVERT: B  486 GLU cc_start: 0.6387 (mt-10) cc_final: 0.5788 (mm-30)
REVERT: B  562 LYS cc_start: 0.4991 (pttm) cc_final: 0.4684 (ttpp)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.1823
  time to fit residues: 59.3758
Evaluate side-chains
  177 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 1.550 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 98 optimal weight:    7.9990
   chunk 108 optimal weight:    3.9990
   chunk 81 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 93 optimal weight:    4.9990
   chunk 47 optimal weight:    9.9990
   chunk 15 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 ASN
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 359 ASN
B 252 ASN
** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.153400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.106680 restraints weight = 23602.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.110124 restraints weight = 15220.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.112546 restraints weight = 11147.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6751
moved from start:          0.7152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9546  Z= 0.217
  Angle     :  0.689  16.675  12856  Z= 0.371
  Chirality :  0.045   0.246   1394
  Planarity :  0.004   0.058   1576
  Dihedral  :  4.936  19.585   1212
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 15.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.24), residues: 1104
  helix:  0.26 (0.20), residues: 592
  sheet: -0.48 (0.47), residues: 126
  loop : -0.90 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 424 
 HIS   0.006   0.001   HIS B 239 
 PHE   0.028   0.002   PHE B 151 
 TYR   0.045   0.002   TYR B 203 
 ARG   0.004   0.000   ARG B 247 

********************** 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
  239 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 1.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5331 (mmt) cc_final: 0.4945 (mmp)
REVERT: A   15 ILE cc_start: 0.9351 (mm) cc_final: 0.8989 (mm)
REVERT: A   43 LEU cc_start: 0.8868 (mt) cc_final: 0.8601 (mt)
REVERT: A  142 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8857 (mt-10)
REVERT: A  202 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8251 (mm-30)
REVERT: A  213 HIS cc_start: 0.8769 (m-70) cc_final: 0.8149 (m90)
REVERT: A  247 ARG cc_start: 0.7492 (mtp180) cc_final: 0.7154 (mtp85)
REVERT: A  309 LEU cc_start: 0.8396 (mt) cc_final: 0.7887 (pp)
REVERT: A  310 ILE cc_start: 0.8706 (mt) cc_final: 0.8209 (tt)
REVERT: A  363 PHE cc_start: 0.7192 (t80) cc_final: 0.6958 (t80)
REVERT: A  486 GLU cc_start: 0.6395 (mt-10) cc_final: 0.5750 (mm-30)
REVERT: B   15 ILE cc_start: 0.9322 (mm) cc_final: 0.8945 (mm)
REVERT: B   43 LEU cc_start: 0.8914 (mt) cc_final: 0.8578 (mt)
REVERT: B  142 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8899 (mt-10)
REVERT: B  202 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8350 (mm-30)
REVERT: B  213 HIS cc_start: 0.8756 (m-70) cc_final: 0.8108 (m90)
REVERT: B  246 ASP cc_start: 0.8540 (m-30) cc_final: 0.8328 (m-30)
REVERT: B  247 ARG cc_start: 0.8675 (ptm-80) cc_final: 0.7671 (ptp-110)
REVERT: B  264 SER cc_start: 0.8619 (p) cc_final: 0.8122 (p)
REVERT: B  310 ILE cc_start: 0.8781 (mt) cc_final: 0.8575 (tt)
REVERT: B  486 GLU cc_start: 0.6405 (mt-10) cc_final: 0.5755 (mm-30)
REVERT: B  569 GLU cc_start: 0.7922 (pt0) cc_final: 0.7371 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 0.1842
  time to fit residues: 63.6916
Evaluate side-chains
  191 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 ASN
A 327 GLN
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 252 ASN
** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 327 GLN
B 359 ASN
** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.154740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.107951 restraints weight = 23058.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.111467 restraints weight = 14921.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.113830 restraints weight = 10955.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6717
moved from start:          0.7318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   9546  Z= 0.199
  Angle     :  0.668  15.836  12856  Z= 0.359
  Chirality :  0.045   0.294   1394
  Planarity :  0.004   0.056   1576
  Dihedral  :  4.776  19.664   1212
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 14.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  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: -0.12 (0.25), residues: 1104
  helix:  0.53 (0.20), residues: 594
  sheet: -0.50 (0.47), residues: 130
  loop : -0.73 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 424 
 HIS   0.005   0.001   HIS B 239 
 PHE   0.028   0.002   PHE A 121 
 TYR   0.034   0.002   TYR B 203 
 ARG   0.003   0.000   ARG B 247 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3090.55 seconds
wall clock time: 56 minutes 35.12 seconds (3395.12 seconds total)