Starting phenix.real_space_refine
on Tue Mar 11 23:27:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yad_33709/03_2025/7yad_33709.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yad_33709/03_2025/7yad_33709.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yad_33709/03_2025/7yad_33709.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yad_33709/03_2025/7yad_33709.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yad_33709/03_2025/7yad_33709.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yad_33709/03_2025/7yad_33709.cif"
  }
  resolution = 2.66
  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=   0.001 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      29      5.16       5
     C    4267      2.51       5
     N    1141      2.21       5
     O    1291      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6728
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 966
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
    Chain: "B"
      Number of atoms: 787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 787
          Classifications: {'peptide': 105}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98}
    Chain: "M"
      Number of atoms: 1606
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1606
          Classifications: {'peptide': 200}
          Link IDs: {'PTRANS': 12, 'TRANS': 187}
    Chain: "C"
      Number of atoms: 979
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 979
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 3, 'TRANS': 122}
    Chain: "D"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 815
          Classifications: {'peptide': 108}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
    Chain: "E"
      Number of atoms: 1499
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 1499
          Classifications: {'peptide': 185}
          Link IDs: {'PTRANS': 10, 'TRANS': 174}
    Chain: "F"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "G"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 5.60, per 1000 atoms: 0.83
  Number of scatterers: 6728
  At special positions: 0
  Unit cell: (111.89, 136.01, 88.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      29     16.00
     O    1291      8.00
     N    1141      7.00
     C    4267      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS M 336 " - pdb=" SG  CYS M 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M 379 " - pdb=" SG  CYS M 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS M 480 " - pdb=" SG  CYS M 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
    BETA1-6
      " NAG F   1 " - " FUC F   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
      " NAG G   1 " - " FUC G   3 "
    NAG-ASN
      " NAG F   1 " - " ASN M 343 "
      " NAG G   1 " - " ASN E 343 "
  Time building additional restraints: 1.64
  Conformation dependent library (CDL) restraints added in 965.2 milliseconds
  

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1542

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 16 sheets defined
      11.7% alpha, 35.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 65
      removed outlier: 3.903A  pdb=" N   GLN A  65 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 62 through 65'
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 4.068A  pdb=" N   THR A  91 " --> pdb=" O   SER A  88 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 338 through 343
    Processing helix  chain 'M' and resid 349 through 353
      removed outlier: 3.967A  pdb=" N   TRP M 353 " --> pdb=" O   VAL M 350 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 365 through 370
      removed outlier: 3.879A  pdb=" N   TYR M 369 " --> pdb=" O   TYR M 365 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 384 through 390
      removed outlier: 4.332A  pdb=" N   ASN M 388 " --> pdb=" O   THR M 385 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   LEU M 390 " --> pdb=" O   LEU M 387 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 405 through 410
      removed outlier: 3.997A  pdb=" N   ARG M 408 " --> pdb=" O   ASP M 405 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 416 through 422
    Processing helix  chain 'M' and resid 438 through 443
      removed outlier: 3.553A  pdb=" N   SER M 443 " --> pdb=" O   ASN M 439 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 502 through 505
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.928A  pdb=" N   THR C  91 " --> pdb=" O   SER C  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 32
      No H-bonds generated for 'chain 'D' and resid 30 through 32'
    Processing helix  chain 'E' and resid 338 through 343
      removed outlier: 3.617A  pdb=" N   PHE E 342 " --> pdb=" O   PHE E 338 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ASN E 343 " --> pdb=" O   ASP E 339 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 338 through 343'
    Processing helix  chain 'E' and resid 383 through 390
      removed outlier: 3.769A  pdb=" N   LEU E 387 " --> pdb=" O   PRO E 384 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   ASN E 388 " --> pdb=" O   THR E 385 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU E 390 " --> pdb=" O   LEU E 387 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 403 through 410
      removed outlier: 3.921A  pdb=" N   VAL E 407 " --> pdb=" O   GLY E 404 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   ARG E 408 " --> pdb=" O   ASP E 405 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 416 through 422
    Processing helix  chain 'E' and resid 438 through 443
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60
      removed outlier: 6.761A  pdb=" N   TRP A  36 " --> pdb=" O   MET A  48 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   TRP A  50 " --> pdb=" O   ILE A  34 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   ILE A  34 " --> pdb=" O   TRP A  50 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLY A  33 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ASN A 116 " --> pdb=" O   ARG A  98 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60
      removed outlier: 6.761A  pdb=" N   TRP A  36 " --> pdb=" O   MET A  48 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   TRP A  50 " --> pdb=" O   ILE A  34 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   ILE A  34 " --> pdb=" O   TRP A  50 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLY A  33 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 5
      removed outlier: 5.702A  pdb=" N   THR B  70 " --> pdb=" O   ALA B  25 " (cutoff:3.500A)
      removed outlier: 10.633A  pdb=" N   GLN B  27 " --> pdb=" O   SER B  68 " (cutoff:3.500A)
      removed outlier: 10.006A  pdb=" N   SER B  68 " --> pdb=" O   GLN B  27 " (cutoff:3.500A)
      removed outlier: 11.802A  pdb=" N   VAL B  29 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
      removed outlier: 11.915A  pdb=" N   SER B  66 " --> pdb=" O   VAL B  29 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12
      removed outlier: 3.800A  pdb=" N   ILE B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   GLN B  38 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 5.765A  pdb=" N   LEU B  47 " --> pdb=" O   GLN B  38 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'M' and resid 354 through 358
      removed outlier: 3.625A  pdb=" N   ASN M 354 " --> pdb=" O   SER M 399 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   ASN M 394 " --> pdb=" O   GLU M 516 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   VAL M 433 " --> pdb=" O   LYS M 378 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   LYS M 378 " --> pdb=" O   VAL M 433 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'M' and resid 452 through 454
    Processing sheet with id=AA8, first strand: chain 'M' and resid 473 through 474
    Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 6
      removed outlier: 3.756A  pdb=" N   GLN C   3 " --> pdb=" O   SER C  25 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   SER C  25 " --> pdb=" O   GLN C   3 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU C  83 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   THR C  78 " --> pdb=" O   ASP C  73 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 58 through 60
      removed outlier: 6.716A  pdb=" N   TRP C  36 " --> pdb=" O   MET C  48 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   TRP C  50 " --> pdb=" O   ILE C  34 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   ILE C  34 " --> pdb=" O   TRP C  50 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLY C  33 " --> pdb=" O   ASP C  99 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   ASN C 116 " --> pdb=" O   ARG C  98 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 58 through 60
      removed outlier: 6.716A  pdb=" N   TRP C  36 " --> pdb=" O   MET C  48 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   TRP C  50 " --> pdb=" O   ILE C  34 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   ILE C  34 " --> pdb=" O   TRP C  50 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLY C  33 " --> pdb=" O   ASP C  99 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 4 through 6
      removed outlier: 3.845A  pdb=" N   ASP D  71 " --> pdb=" O   SER D  68 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 13
      removed outlier: 6.225A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   VAL D  86 " --> pdb=" O   GLN D  39 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ILE D  49 " --> pdb=" O   TRP D  36 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   GLN D  38 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
      removed outlier: 5.755A  pdb=" N   LEU D  47 " --> pdb=" O   GLN D  38 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 13
      removed outlier: 6.225A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLN D  91 " --> pdb=" O   THR D  97 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 354 through 358
      removed outlier: 3.959A  pdb=" N   ASN E 354 " --> pdb=" O   SER E 399 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   SER E 399 " --> pdb=" O   ASN E 354 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA E 397 " --> pdb=" O   LYS E 356 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ASN E 394 " --> pdb=" O   GLU E 516 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 452 through 454

    209 hydrogen bonds defined for protein.
    525 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.65

  Time building geometry restraints manager: 1.94 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2149
        1.35 -     1.47: 1932
        1.47 -     1.60: 2784
        1.60 -     1.72: 0
        1.72 -     1.84: 35
  Bond restraints: 6900
  Sorted by residual:
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.69e+00
  bond pdb=" CA  ALA M 520 "
       pdb=" CB  ALA M 520 "
    ideal  model  delta    sigma   weight residual
    1.522  1.531 -0.008 7.00e-03 2.04e+04 1.45e+00
  bond pdb=" C5  NAG G   2 "
       pdb=" O5  NAG G   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.29e+00
  bond pdb=" C5  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.17e+00
  bond pdb=" C1  NAG G   2 "
       pdb=" O5  NAG G   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.427 -0.021 2.00e-02 2.50e+03 1.13e+00
  ... (remaining 6895 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 9169
        1.59 -     3.19: 171
        3.19 -     4.78: 28
        4.78 -     6.38: 5
        6.38 -     7.97: 1
  Bond angle restraints: 9374
  Sorted by residual:
  angle pdb=" C   LEU D  13 "
        pdb=" N   SER D  14 "
        pdb=" CA  SER D  14 "
      ideal   model   delta    sigma   weight residual
     120.49  128.46   -7.97 1.42e+00 4.96e-01 3.15e+01
  angle pdb=" CA  LYS E 386 "
        pdb=" CB  LYS E 386 "
        pdb=" CG  LYS E 386 "
      ideal   model   delta    sigma   weight residual
     114.10  120.35   -6.25 2.00e+00 2.50e-01 9.75e+00
  angle pdb=" C   HIS E 505 "
        pdb=" N   GLN E 506 "
        pdb=" CA  GLN E 506 "
      ideal   model   delta    sigma   weight residual
     120.68  125.29   -4.61 1.52e+00 4.33e-01 9.19e+00
  angle pdb=" CA  PRO D  81 "
        pdb=" N   PRO D  81 "
        pdb=" CD  PRO D  81 "
      ideal   model   delta    sigma   weight residual
     112.00  108.19    3.81 1.40e+00 5.10e-01 7.40e+00
  angle pdb=" CA  CYS M 379 "
        pdb=" CB  CYS M 379 "
        pdb=" SG  CYS M 379 "
      ideal   model   delta    sigma   weight residual
     114.40  120.41   -6.01 2.30e+00 1.89e-01 6.82e+00
  ... (remaining 9369 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 3727
       17.19 -    34.39: 327
       34.39 -    51.58: 56
       51.58 -    68.77: 8
       68.77 -    85.96: 3
  Dihedral angle restraints: 4121
    sinusoidal: 1683
      harmonic: 2438
  Sorted by residual:
  dihedral pdb=" CB  CYS M 379 "
           pdb=" SG  CYS M 379 "
           pdb=" SG  CYS M 432 "
           pdb=" CB  CYS M 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   31.66   61.34     1      1.00e+01 1.00e-02 5.00e+01
  dihedral pdb=" CA  ALA M 520 "
           pdb=" C   ALA M 520 "
           pdb=" N   PRO M 521 "
           pdb=" CA  PRO M 521 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.66   28.34     0      5.00e+00 4.00e-02 3.21e+01
  dihedral pdb=" CB  CYS E 480 "
           pdb=" SG  CYS E 480 "
           pdb=" SG  CYS E 488 "
           pdb=" CB  CYS E 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -129.46   43.46     1      1.00e+01 1.00e-02 2.63e+01
  ... (remaining 4118 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 630
       0.032 -    0.064: 249
       0.064 -    0.097: 80
       0.097 -    0.129: 54
       0.129 -    0.161: 6
  Chirality restraints: 1019
  Sorted by residual:
  chirality pdb=" CA  PRO D  81 "
            pdb=" N   PRO D  81 "
            pdb=" C   PRO D  81 "
            pdb=" CB  PRO D  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.48e-01
  chirality pdb=" C1  NAG G   1 "
            pdb=" ND2 ASN E 343 "
            pdb=" C2  NAG G   1 "
            pdb=" O5  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.26   -0.14 2.00e-01 2.50e+01 4.92e-01
  chirality pdb=" CA  ILE B  76 "
            pdb=" N   ILE B  76 "
            pdb=" C   ILE B  76 "
            pdb=" CB  ILE B  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.65e-01
  ... (remaining 1016 not shown)

  Planarity restraints: 1205
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D  80 "    0.046 5.00e-02 4.00e+02   6.76e-02 7.32e+00
        pdb=" N   PRO D  81 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO D  81 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO D  81 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR E 385 "   -0.009 2.00e-02 2.50e+03   1.89e-02 3.56e+00
        pdb=" C   THR E 385 "    0.033 2.00e-02 2.50e+03
        pdb=" O   THR E 385 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   LYS E 386 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA M 520 "    0.024 5.00e-02 4.00e+02   3.70e-02 2.19e+00
        pdb=" N   PRO M 521 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO M 521 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO M 521 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1202 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 230
        2.71 -     3.26: 6147
        3.26 -     3.81: 9889
        3.81 -     4.35: 12177
        4.35 -     4.90: 21925
  Nonbonded interactions: 50368
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP E 442 "
            pdb=" OH  TYR E 451 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" OH  TYR M 369 "
            pdb=" O   PRO M 384 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" NH2 ARG E 457 "
            pdb=" OD1 ASN E 460 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" O   ASN M 439 "
            pdb=" OG  SER M 443 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OG  SER B  12 "
            pdb=" OE2 GLU B 105 "
     model   vdw
     2.254 3.040
  ... (remaining 50363 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'C' and resid 1 through 124)
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'D' and resid 1 through 105)
}
ncs_group {
  reference = chain 'E'
  selection = (chain 'M' and resid 332 through 516)
}
ncs_group {
  reference = chain 'F'
  selection = chain 'G'
}

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 individual isotropic
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:             5.910
  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:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.890
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6900  Z= 0.231
  Angle     :  0.555   7.971   9374  Z= 0.293
  Chirality :  0.044   0.161   1019
  Planarity :  0.004   0.068   1203
  Dihedral  : 12.506  85.964   2549
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.55 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -1.22 (0.28), residues: 836
  helix: -3.96 (0.55), residues: 33
  sheet:  0.49 (0.32), residues: 281
  loop : -1.40 (0.25), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  50 
 HIS   0.004   0.002   HIS B  92 
 PHE   0.011   0.001   PHE E 347 
 TYR   0.016   0.001   TYR C 100 
 ARG   0.003   0.000   ARG M 403 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   81 MET cc_start: 0.6596 (tmm) cc_final: 0.6215 (tmm)
REVERT: D   71 ASP cc_start: 0.7084 (t70) cc_final: 0.6857 (t0)
REVERT: D   82 GLU cc_start: 0.7055 (pm20) cc_final: 0.6744 (pm20)
REVERT: E  386 LYS cc_start: 0.8775 (mmpt) cc_final: 0.8549 (mmpt)
REVERT: E  438 SER cc_start: 0.8339 (p) cc_final: 0.8122 (p)
REVERT: E  439 ASN cc_start: 0.7959 (t0) cc_final: 0.7691 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.8362
  time to fit residues: 131.7774
Evaluate side-chains
  137 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 64 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
B  92 HIS
M 439 ASN
M 450 ASN
D   6 GLN
** D  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  43 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.149300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.126546 restraints weight = 10249.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3809 rms_B_bonded: 2.44
r_work: 0.3690 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3537 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.1077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   6900  Z= 0.334
  Angle     :  0.581   6.265   9374  Z= 0.309
  Chirality :  0.046   0.185   1019
  Planarity :  0.005   0.045   1203
  Dihedral  :  5.235  35.576   1063
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.74 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 10.04 %
    Favored  : 88.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    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: -1.21 (0.28), residues: 836
  helix: -4.33 (0.37), residues: 47
  sheet:  0.80 (0.32), residues: 274
  loop : -1.44 (0.25), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  50 
 HIS   0.006   0.002   HIS B  92 
 PHE   0.011   0.001   PHE E 392 
 TYR   0.021   0.002   TYR M 501 
 ARG   0.005   0.001   ARG M 408 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 120
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   81 MET cc_start: 0.7349 (tmm) cc_final: 0.6883 (tmm)
REVERT: D   82 GLU cc_start: 0.7474 (pm20) cc_final: 0.6939 (pm20)
REVERT: E  439 ASN cc_start: 0.8325 (t0) cc_final: 0.8072 (t0)
REVERT: E  501 TYR cc_start: 0.7725 (m-10) cc_final: 0.7442 (m-10)
  outliers start: 7
  outliers final: 2
  residues processed: 123
  average time/residue: 0.8403
  time to fit residues: 111.1863
Evaluate side-chains
  128 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 126
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain E residue  434 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 74 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   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  59 ASN
M 439 ASN
M 450 ASN
** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  39 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 = 0.4089 r_free = 0.4089 target = 0.151060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.128558 restraints weight = 10521.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.3794 rms_B_bonded: 2.49
r_work: 0.3672 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   6900  Z= 0.381
  Angle     :  0.588   6.308   9374  Z= 0.312
  Chirality :  0.047   0.193   1019
  Planarity :  0.005   0.051   1203
  Dihedral  :  5.335  35.285   1063
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.10 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.13 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    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: -1.35 (0.27), residues: 836
  helix: -4.75 (0.32), residues: 40
  sheet:  0.77 (0.32), residues: 273
  loop : -1.60 (0.24), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  50 
 HIS   0.005   0.002   HIS D  92 
 PHE   0.009   0.001   PHE M 377 
 TYR   0.017   0.002   TYR C  27 
 ARG   0.004   0.000   ARG B  78 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   81 MET cc_start: 0.7035 (tmm) cc_final: 0.6656 (tmm)
REVERT: D   82 GLU cc_start: 0.7386 (pm20) cc_final: 0.6875 (pm20)
REVERT: E  439 ASN cc_start: 0.8170 (t0) cc_final: 0.7894 (t0)
REVERT: E  501 TYR cc_start: 0.7596 (m-10) cc_final: 0.7311 (m-10)
  outliers start: 12
  outliers final: 4
  residues processed: 129
  average time/residue: 0.6896
  time to fit residues: 97.2583
Evaluate side-chains
  127 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 123
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 VAL
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   53 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 27 optimal weight:    0.3980
   chunk 0 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 1 optimal weight:    0.2980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
B  43 GLN
** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 439 ASN
** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  39 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 = 0.4089 r_free = 0.4089 target = 0.148517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.126033 restraints weight = 10441.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3805 rms_B_bonded: 2.44
r_work: 0.3685 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3527 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.1524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6900  Z= 0.307
  Angle     :  0.554   6.744   9374  Z= 0.292
  Chirality :  0.045   0.155   1019
  Planarity :  0.004   0.054   1203
  Dihedral  :  5.220  34.814   1063
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.86 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 14.23 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    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: -1.34 (0.27), residues: 836
  helix: -4.77 (0.31), residues: 40
  sheet:  0.81 (0.31), residues: 273
  loop : -1.61 (0.24), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  50 
 HIS   0.004   0.001   HIS D  92 
 PHE   0.007   0.001   PHE M 338 
 TYR   0.020   0.002   TYR M 501 
 ARG   0.003   0.000   ARG M 408 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 126
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   81 MET cc_start: 0.7423 (tmm) cc_final: 0.6999 (tmm)
REVERT: D   82 GLU cc_start: 0.7484 (pm20) cc_final: 0.7010 (pm20)
REVERT: D   95 SER cc_start: 0.8398 (p) cc_final: 0.8125 (t)
REVERT: E  439 ASN cc_start: 0.8352 (t0) cc_final: 0.8052 (t0)
REVERT: E  501 TYR cc_start: 0.7730 (m-10) cc_final: 0.7458 (m-10)
  outliers start: 11
  outliers final: 7
  residues processed: 129
  average time/residue: 0.7594
  time to fit residues: 106.0788
Evaluate side-chains
  131 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 124
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 VAL
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain M residue  385 THR
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain E residue  461 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 67 optimal weight:    0.2980
   chunk 35 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 54 optimal weight:    0.4980
   chunk 47 optimal weight:    0.9980
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 439 ASN
** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.148814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.126461 restraints weight = 10349.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3805 rms_B_bonded: 2.41
r_work: 0.3690 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3537 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6900  Z= 0.279
  Angle     :  0.543   7.433   9374  Z= 0.286
  Chirality :  0.045   0.151   1019
  Planarity :  0.004   0.055   1203
  Dihedral  :  5.142  34.421   1063
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.74 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 14.64 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    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: -1.30 (0.27), residues: 836
  helix: -4.75 (0.32), residues: 38
  sheet:  0.88 (0.31), residues: 273
  loop : -1.62 (0.24), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C  50 
 HIS   0.004   0.001   HIS D  92 
 PHE   0.007   0.001   PHE M 377 
 TYR   0.019   0.001   TYR M 351 
 ARG   0.003   0.000   ARG M 408 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   81 MET cc_start: 0.7454 (tmm) cc_final: 0.7031 (tmm)
REVERT: D   82 GLU cc_start: 0.7513 (pm20) cc_final: 0.7049 (pm20)
REVERT: E  439 ASN cc_start: 0.8356 (t0) cc_final: 0.8049 (t0)
REVERT: E  501 TYR cc_start: 0.7719 (m-10) cc_final: 0.7440 (m-10)
  outliers start: 18
  outliers final: 9
  residues processed: 140
  average time/residue: 0.6464
  time to fit residues: 99.0297
Evaluate side-chains
  137 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  461 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 78 optimal weight:    0.2980
   chunk 70 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0370
   chunk 58 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 63 optimal weight:    0.4980
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.4658

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
A  59 ASN
** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 439 ASN
** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  39 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 = 0.4102 r_free = 0.4102 target = 0.149536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.127192 restraints weight = 10369.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3821 rms_B_bonded: 2.41
r_work: 0.3704 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3549 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6900  Z= 0.216
  Angle     :  0.532   8.016   9374  Z= 0.280
  Chirality :  0.044   0.157   1019
  Planarity :  0.004   0.055   1203
  Dihedral  :  4.991  34.281   1063
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.62 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 16.18 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    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: -1.22 (0.28), residues: 836
  helix: -4.75 (0.31), residues: 38
  sheet:  0.93 (0.32), residues: 273
  loop : -1.57 (0.25), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  50 
 HIS   0.003   0.001   HIS D  92 
 PHE   0.007   0.001   PHE B  72 
 TYR   0.021   0.001   TYR M 351 
 ARG   0.002   0.000   ARG M 408 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   82 GLU cc_start: 0.7493 (pm20) cc_final: 0.7036 (pm20)
REVERT: E  439 ASN cc_start: 0.8330 (t0) cc_final: 0.8012 (t0)
REVERT: E  501 TYR cc_start: 0.7719 (m-10) cc_final: 0.7439 (m-10)
  outliers start: 15
  outliers final: 8
  residues processed: 143
  average time/residue: 0.6720
  time to fit residues: 105.0472
Evaluate side-chains
  143 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 135
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain E residue  367 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0770
   chunk 26 optimal weight:    0.9980
   chunk 80 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0980
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.149606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.127327 restraints weight = 10328.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3823 rms_B_bonded: 2.40
r_work: 0.3707 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3555 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6900  Z= 0.204
  Angle     :  0.539   7.751   9374  Z= 0.280
  Chirality :  0.045   0.154   1019
  Planarity :  0.004   0.055   1203
  Dihedral  :  4.934  34.395   1063
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.50 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 16.46 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    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: -1.19 (0.28), residues: 836
  helix: -4.75 (0.31), residues: 38
  sheet:  0.96 (0.32), residues: 273
  loop : -1.55 (0.25), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C  50 
 HIS   0.003   0.001   HIS D  92 
 PHE   0.008   0.001   PHE E 377 
 TYR   0.021   0.001   TYR M 351 
 ARG   0.002   0.000   ARG M 408 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   81 MET cc_start: 0.7324 (tmm) cc_final: 0.6763 (tmm)
REVERT: D   82 GLU cc_start: 0.7415 (pm20) cc_final: 0.6994 (pm20)
REVERT: E  439 ASN cc_start: 0.8304 (t0) cc_final: 0.7988 (t0)
REVERT: E  501 TYR cc_start: 0.7702 (m-10) cc_final: 0.7460 (m-10)
  outliers start: 18
  outliers final: 11
  residues processed: 145
  average time/residue: 0.6650
  time to fit residues: 105.3060
Evaluate side-chains
  149 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 138
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain M residue  441 LEU
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  461 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0970
   chunk 28 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 52 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.7778

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
M 439 ASN
** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.147809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.125651 restraints weight = 10384.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3808 rms_B_bonded: 2.39
r_work: 0.3689 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3533 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6900  Z= 0.321
  Angle     :  0.579   7.335   9374  Z= 0.302
  Chirality :  0.046   0.186   1019
  Planarity :  0.004   0.055   1203
  Dihedral  :  5.136  35.266   1063
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.70 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 17.15 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    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: -1.23 (0.28), residues: 836
  helix: -4.75 (0.32), residues: 38
  sheet:  0.98 (0.32), residues: 273
  loop : -1.61 (0.25), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C  50 
 HIS   0.006   0.002   HIS D  92 
 PHE   0.010   0.001   PHE M 377 
 TYR   0.023   0.002   TYR M 351 
 ARG   0.002   0.000   ARG D  55 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 140
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   81 MET cc_start: 0.7324 (tmm) cc_final: 0.6797 (tmm)
REVERT: D   82 GLU cc_start: 0.7485 (pm20) cc_final: 0.7026 (pm20)
REVERT: E  439 ASN cc_start: 0.8359 (t0) cc_final: 0.8120 (t0)
REVERT: E  501 TYR cc_start: 0.7750 (m-10) cc_final: 0.7477 (m-10)
  outliers start: 13
  outliers final: 10
  residues processed: 144
  average time/residue: 0.6882
  time to fit residues: 108.4021
Evaluate side-chains
  150 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  461 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 16 optimal weight:    0.4980
   chunk 2 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0770
   chunk 74 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0970
   chunk 31 optimal weight:    0.1980
   chunk 0 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.3336

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.150087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.127864 restraints weight = 10495.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3833 rms_B_bonded: 2.43
r_work: 0.3716 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3561 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6900  Z= 0.177
  Angle     :  0.534   7.640   9374  Z= 0.278
  Chirality :  0.044   0.157   1019
  Planarity :  0.004   0.057   1203
  Dihedral  :  4.863  34.161   1063
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.90 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.99 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    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: -1.13 (0.28), residues: 836
  helix: -4.75 (0.31), residues: 38
  sheet:  0.92 (0.31), residues: 288
  loop : -1.52 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  50 
 HIS   0.003   0.001   HIS D  92 
 PHE   0.009   0.001   PHE E 377 
 TYR   0.022   0.001   TYR M 351 
 ARG   0.002   0.000   ARG M 408 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 146
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
REVERT: C   81 MET cc_start: 0.7332 (tmm) cc_final: 0.6766 (tmm)
REVERT: D   82 GLU cc_start: 0.7474 (pm20) cc_final: 0.7024 (pm20)
REVERT: E  439 ASN cc_start: 0.8294 (t0) cc_final: 0.7983 (t0)
REVERT: E  501 TYR cc_start: 0.7688 (m-10) cc_final: 0.7426 (m-10)
  outliers start: 14
  outliers final: 9
  residues processed: 149
  average time/residue: 0.6980
  time to fit residues: 113.5750
Evaluate side-chains
  155 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 146
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  461 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 68 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 439 ASN
** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.147786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.125661 restraints weight = 10488.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3803 rms_B_bonded: 2.41
r_work: 0.3684 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3528 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6900  Z= 0.347
  Angle     :  0.602   7.741   9374  Z= 0.313
  Chirality :  0.047   0.184   1019
  Planarity :  0.004   0.055   1203
  Dihedral  :  5.147  35.037   1063
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.46 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.99 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    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: -1.18 (0.28), residues: 836
  helix: -4.75 (0.32), residues: 38
  sheet:  1.04 (0.31), residues: 272
  loop : -1.58 (0.25), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C  50 
 HIS   0.006   0.002   HIS D  92 
 PHE   0.012   0.001   PHE M 377 
 TYR   0.023   0.002   TYR M 351 
 ARG   0.003   0.000   ARG D  46 

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

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

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1672 Ramachandran restraints generated.
    836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 139
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   81 MET cc_start: 0.7313 (tmm) cc_final: 0.6797 (tmm)
REVERT: D   82 GLU cc_start: 0.7528 (pm20) cc_final: 0.7062 (pm20)
REVERT: E  439 ASN cc_start: 0.8361 (t0) cc_final: 0.8111 (t0)
REVERT: E  501 TYR cc_start: 0.7740 (m-10) cc_final: 0.7462 (m-10)
  outliers start: 14
  outliers final: 10
  residues processed: 143
  average time/residue: 0.6428
  time to fit residues: 100.8033
Evaluate side-chains
  148 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 138
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  386 LYS
Chi-restraints excluded: chain E residue  461 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 63 optimal weight:    0.4980
   chunk 22 optimal weight:    0.0270
   chunk 44 optimal weight:    0.1980
   chunk 26 optimal weight:    0.5980
   chunk 32 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.3638

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.149981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.127760 restraints weight = 10474.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3827 rms_B_bonded: 2.42
r_work: 0.3712 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3560 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6900  Z= 0.185
  Angle     :  0.547   7.673   9374  Z= 0.285
  Chirality :  0.044   0.159   1019
  Planarity :  0.004   0.057   1203
  Dihedral  :  4.900  34.458   1063
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.67 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 18.55 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    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: -1.18 (0.28), residues: 836
  helix: -4.75 (0.32), residues: 38
  sheet:  0.92 (0.31), residues: 288
  loop : -1.58 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  50 
 HIS   0.003   0.001   HIS D  92 
 PHE   0.008   0.001   PHE M 374 
 TYR   0.023   0.001   TYR M 351 
 ARG   0.002   0.000   ARG M 408 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6668.53 seconds
wall clock time: 113 minutes 50.14 seconds (6830.14 seconds total)