Starting phenix.real_space_refine
on Tue Mar  3 17:36:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s05_24784/03_2026/7s05_24784.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s05_24784/03_2026/7s05_24784.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s05_24784/03_2026/7s05_24784.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s05_24784/03_2026/7s05_24784.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s05_24784/03_2026/7s05_24784.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s05_24784/03_2026/7s05_24784.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.077
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
     Ca      2      9.91       5
     S      40      5.16       5
     C    4778      2.51       5
     N    1274      2.21       5
     O    1410      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7504
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 3653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 437, 3653
          Classifications: {'peptide': 437}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 414}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 3653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 437, 3653
          Classifications: {'peptide': 437}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 414}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 43
          Unusual residues: {' CA': 1, 'NAG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 43
          Unusual residues: {' CA': 1, 'NAG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 1.75, per 1000 atoms: 0.23
  Number of scatterers: 7504
  At special positions: 0
  Unit cell: (116.748, 123.372, 72.864, 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)
     Ca      2     19.99
     S      40     16.00
     O    1410      8.00
     N    1274      7.00
     C    4778      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  70 " - pdb=" SG  CYS A  70 " distance=2.04

  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 C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A1301 " - " ASN A1009 "
      " NAG A1302 " - " ASN A1056 "
      " NAG A1303 " - " ASN A 376 "
      " NAG B1301 " - " ASN B1009 "
      " NAG B1302 " - " ASN B1056 "
      " NAG B1303 " - " ASN B 376 "
      " NAG C   1 " - " ASN B  83 "
      " NAG D   1 " - " ASN B1129 "
      " NAG E   1 " - " ASN A  83 "
      " NAG F   1 " - " ASN A1129 "
  Time building additional restraints: 1.03
  Conformation dependent library (CDL) restraints added in 279.6 milliseconds
  

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1704

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 10 sheets defined
      52.3% alpha, 12.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'B' and resid 49 through 55
    Processing helix  chain 'B' and resid 65 through 70
    Processing helix  chain 'B' and resid 85 through 111
    Processing helix  chain 'B' and resid 327 through 340
      removed outlier: 3.589A  pdb=" N   TYR B 331 " --> pdb=" O   GLU B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 374
      removed outlier: 3.606A  pdb=" N   VAL B 373 " --> pdb=" O   THR B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 391
      removed outlier: 4.216A  pdb=" N   HIS B 391 " --> pdb=" O   ALA B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 395
    Processing helix  chain 'B' and resid 416 through 419
    Processing helix  chain 'B' and resid 931 through 947
    Processing helix  chain 'B' and resid 963 through 973
    Processing helix  chain 'B' and resid 973 through 983
    Processing helix  chain 'B' and resid 993 through 1003
    Processing helix  chain 'B' and resid 1009 through 1018
    Processing helix  chain 'B' and resid 1026 through 1038
    Processing helix  chain 'B' and resid 1043 through 1061
      removed outlier: 3.642A  pdb=" N   LEU B1047 " --> pdb=" O   SER B1043 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1087 through 1094
      removed outlier: 3.634A  pdb=" N   VAL B1091 " --> pdb=" O   THR B1087 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1094 through 1105
    Processing helix  chain 'B' and resid 1129 through 1143
    Processing helix  chain 'B' and resid 1161 through 1176
    Processing helix  chain 'B' and resid 1195 through 1204
    Processing helix  chain 'A' and resid 50 through 55
    Processing helix  chain 'A' and resid 65 through 70
    Processing helix  chain 'A' and resid 85 through 111
    Processing helix  chain 'A' and resid 327 through 340
      removed outlier: 3.591A  pdb=" N   TYR A 331 " --> pdb=" O   GLU A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 374
      removed outlier: 3.605A  pdb=" N   VAL A 373 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 391
      removed outlier: 4.216A  pdb=" N   HIS A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 395
    Processing helix  chain 'A' and resid 416 through 419
    Processing helix  chain 'A' and resid 931 through 947
    Processing helix  chain 'A' and resid 963 through 973
    Processing helix  chain 'A' and resid 973 through 983
    Processing helix  chain 'A' and resid 993 through 1003
    Processing helix  chain 'A' and resid 1009 through 1018
    Processing helix  chain 'A' and resid 1026 through 1038
    Processing helix  chain 'A' and resid 1043 through 1061
      removed outlier: 3.641A  pdb=" N   LEU A1047 " --> pdb=" O   SER A1043 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1087 through 1094
      removed outlier: 3.634A  pdb=" N   VAL A1091 " --> pdb=" O   THR A1087 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1094 through 1105
    Processing helix  chain 'A' and resid 1129 through 1143
    Processing helix  chain 'A' and resid 1161 through 1176
    Processing helix  chain 'A' and resid 1195 through 1204
    Processing sheet with id=AA1, first strand: chain 'B' and resid 365 through 368
      removed outlier: 6.607A  pdb=" N   ILE B 346 " --> pdb=" O   THR B 366 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   VAL B 368 " --> pdb=" O   ILE B 346 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   ILE B 348 " --> pdb=" O   VAL B 368 " (cutoff:3.500A)
      removed outlier: 8.739A  pdb=" N   PHE B 347 " --> pdb=" O   ILE B  75 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   VAL B  77 " --> pdb=" O   PHE B 347 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   VAL B 349 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   TYR B  79 " --> pdb=" O   VAL B 349 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ASP B  76 " --> pdb=" O   ILE B 403 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   LEU B 405 " --> pdb=" O   ASP B  76 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   VAL B  78 " --> pdb=" O   LEU B 405 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 409 through 411
      removed outlier: 3.533A  pdb=" N   VAL B1148 " --> pdb=" O   MET B 410 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   ALA B1122 " --> pdb=" O   CYS B1149 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   ASN B1151 " --> pdb=" O   ALA B1122 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   LYS B1124 " --> pdb=" O   ASN B1151 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 421 through 422
      removed outlier: 4.142A  pdb=" N   VAL B 953 " --> pdb=" O   THR B 432 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 421 through 422
      removed outlier: 3.632A  pdb=" N   LEU B 431 " --> pdb=" O   MET B1116 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 1005 through 1006
      removed outlier: 3.774A  pdb=" N   GLN B1006 " --> pdb=" O   LYS B1108 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   LYS B1108 " --> pdb=" O   GLN B1006 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 368
      removed outlier: 6.606A  pdb=" N   ILE A 346 " --> pdb=" O   THR A 366 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   VAL A 368 " --> pdb=" O   ILE A 346 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   ILE A 348 " --> pdb=" O   VAL A 368 " (cutoff:3.500A)
      removed outlier: 8.740A  pdb=" N   PHE A 347 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   VAL A  77 " --> pdb=" O   PHE A 347 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   VAL A 349 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   TYR A  79 " --> pdb=" O   VAL A 349 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ASP A  76 " --> pdb=" O   ILE A 403 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   LEU A 405 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   VAL A  78 " --> pdb=" O   LEU A 405 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 409 through 411
      removed outlier: 3.533A  pdb=" N   VAL A1148 " --> pdb=" O   MET A 410 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   ALA A1122 " --> pdb=" O   CYS A1149 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   ASN A1151 " --> pdb=" O   ALA A1122 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   LYS A1124 " --> pdb=" O   ASN A1151 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 421 through 422
      removed outlier: 4.143A  pdb=" N   VAL A 953 " --> pdb=" O   THR A 432 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 421 through 422
      removed outlier: 3.633A  pdb=" N   LEU A 431 " --> pdb=" O   MET A1116 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1005 through 1006
      removed outlier: 3.774A  pdb=" N   GLN A1006 " --> pdb=" O   LYS A1108 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   LYS A1108 " --> pdb=" O   GLN A1006 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    317 hydrogen bonds defined for protein.
    921 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: 1.30

  Time building geometry restraints manager: 1.26 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2421
        1.34 -     1.46: 1682
        1.46 -     1.58: 3513
        1.58 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 7688
  Sorted by residual:
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.06e+00
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.01e+00
  bond pdb=" C1  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.440 -0.034 2.00e-02 2.50e+03 2.95e+00
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.440 -0.034 2.00e-02 2.50e+03 2.93e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.48e+00
  ... (remaining 7683 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 9845
        1.40 -     2.80: 463
        2.80 -     4.21: 70
        4.21 -     5.61: 14
        5.61 -     7.01: 6
  Bond angle restraints: 10398
  Sorted by residual:
  angle pdb=" C   GLU A1118 "
        pdb=" CA  GLU A1118 "
        pdb=" CB  GLU A1118 "
      ideal   model   delta    sigma   weight residual
     111.22  106.92    4.30 1.24e+00 6.50e-01 1.21e+01
  angle pdb=" C   GLU B1118 "
        pdb=" CA  GLU B1118 "
        pdb=" CB  GLU B1118 "
      ideal   model   delta    sigma   weight residual
     111.22  106.96    4.26 1.24e+00 6.50e-01 1.18e+01
  angle pdb=" N   THR B1128 "
        pdb=" CA  THR B1128 "
        pdb=" CB  THR B1128 "
      ideal   model   delta    sigma   weight residual
     112.28  107.19    5.09 1.49e+00 4.50e-01 1.17e+01
  angle pdb=" N   THR A1128 "
        pdb=" CA  THR A1128 "
        pdb=" CB  THR A1128 "
      ideal   model   delta    sigma   weight residual
     112.28  107.24    5.04 1.49e+00 4.50e-01 1.14e+01
  angle pdb=" N   LEU B 380 "
        pdb=" CA  LEU B 380 "
        pdb=" C   LEU B 380 "
      ideal   model   delta    sigma   weight residual
     109.81  115.90   -6.09 2.21e+00 2.05e-01 7.58e+00
  ... (remaining 10393 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.33: 4336
       20.33 -    40.65: 419
       40.65 -    60.98: 40
       60.98 -    81.31: 20
       81.31 -   101.63: 10
  Dihedral angle restraints: 4825
    sinusoidal: 2219
      harmonic: 2606
  Sorted by residual:
  dihedral pdb=" CA  ARG A1127 "
           pdb=" C   ARG A1127 "
           pdb=" N   THR A1128 "
           pdb=" CA  THR A1128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.03   29.97     0      5.00e+00 4.00e-02 3.59e+01
  dihedral pdb=" CA  ARG B1127 "
           pdb=" C   ARG B1127 "
           pdb=" N   THR B1128 "
           pdb=" CA  THR B1128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.07   29.93     0      5.00e+00 4.00e-02 3.58e+01
  dihedral pdb=" CA  PRO B 381 "
           pdb=" C   PRO B 381 "
           pdb=" N   THR B 382 "
           pdb=" CA  THR B 382 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.57  -23.43     0      5.00e+00 4.00e-02 2.20e+01
  ... (remaining 4822 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 1078
       0.093 -    0.186: 68
       0.186 -    0.279: 0
       0.279 -    0.372: 2
       0.372 -    0.465: 4
  Chirality restraints: 1152
  Sorted by residual:
  chirality pdb=" C1  NAG A1303 "
            pdb=" ND2 ASN A 376 "
            pdb=" C2  NAG A1303 "
            pdb=" O5  NAG A1303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.93   -0.47 2.00e-01 2.50e+01 5.41e+00
  chirality pdb=" C1  NAG B1303 "
            pdb=" ND2 ASN B 376 "
            pdb=" C2  NAG B1303 "
            pdb=" O5  NAG B1303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.94   -0.46 2.00e-01 2.50e+01 5.34e+00
  chirality pdb=" C1  NAG A1302 "
            pdb=" ND2 ASN A1056 "
            pdb=" C2  NAG A1302 "
            pdb=" O5  NAG A1302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.02   -0.38 2.00e-01 2.50e+01 3.57e+00
  ... (remaining 1149 not shown)

  Planarity restraints: 1336
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 376 "   -0.027 2.00e-02 2.50e+03   2.58e-02 8.33e+00
        pdb=" CG  ASN B 376 "    0.026 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 376 "   -0.003 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 376 "    0.033 2.00e-02 2.50e+03
        pdb=" C1  NAG B1303 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 376 "    0.027 2.00e-02 2.50e+03   2.58e-02 8.32e+00
        pdb=" CG  ASN A 376 "   -0.026 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 376 "    0.003 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 376 "   -0.033 2.00e-02 2.50e+03
        pdb=" C1  NAG A1303 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B1178 "    0.028 5.00e-02 4.00e+02   4.31e-02 2.97e+00
        pdb=" N   PRO B1179 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B1179 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B1179 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1333 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 797
        2.75 -     3.29: 7235
        3.29 -     3.82: 12351
        3.82 -     4.36: 14719
        4.36 -     4.90: 25433
  Nonbonded interactions: 60535
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  79 "
            pdb=" OG  SER B 332 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OH  TYR A  79 "
            pdb=" OG  SER A 332 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   SER B 356 "
            pdb=" NH2 ARG B1186 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" O   SER A 356 "
            pdb=" NH2 ARG A1186 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" OH  TYR A 937 "
            pdb=" OE1 GLU A 976 "
     model   vdw
     2.344 3.040
  ... (remaining 60530 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             3.500
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.640
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
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      :  0.004   0.053   7703  Z= 0.181
  Angle     :  0.721  10.314  10442  Z= 0.381
  Chirality :  0.052   0.465   1152
  Planarity :  0.004   0.043   1326
  Dihedral  : 16.047 101.632   3118
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.29), residues: 858
  helix:  1.27 (0.26), residues: 394
  sheet:  0.37 (0.55), residues: 98
  loop : -1.39 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1127 
 TYR   0.016   0.001   TYR A 999 
 PHE   0.010   0.001   PHE B1176 
 TRP   0.007   0.001   TRP A1201 
 HIS   0.013   0.001   HIS A 987 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 7688)
  covalent geometry    : angle       0.67856 (10398)
  SS BOND              : bond        0.00430 (    1)
  SS BOND              : angle       2.44459 (    2)
  hydrogen bonds       : bond        0.16026 (  313)
  hydrogen bonds       : angle       6.74831 (  921)
  link_BETA1-4         : bond        0.00799 (    4)
  link_BETA1-4         : angle       1.63571 (   12)
  link_NAG-ASN         : bond        0.00890 (   10)
  link_NAG-ASN         : angle       4.45648 (   30)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.322 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.0868
  time to fit residues: 14.1894
Evaluate side-chains
  85 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0010
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
B 987 HIS
B1012 GLN
A 987 HIS
A1012 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.177822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.134175 restraints weight = 8123.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.17
r_work: 0.3298 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3135 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.1030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7703  Z= 0.143
  Angle     :  0.640   7.273  10442  Z= 0.316
  Chirality :  0.050   0.362   1152
  Planarity :  0.004   0.033   1326
  Dihedral  : 10.670  79.240   1250
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  6.80 %
    Favored  : 91.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.44 (0.29), residues: 858
  helix:  1.61 (0.25), residues: 394
  sheet:  0.34 (0.54), residues: 102
  loop : -1.24 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1127 
 TYR   0.024   0.002   TYR B 999 
 PHE   0.008   0.001   PHE B 931 
 TRP   0.007   0.001   TRP B1201 
 HIS   0.003   0.001   HIS B 423 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 7688)
  covalent geometry    : angle       0.61214 (10398)
  SS BOND              : bond        0.00279 (    1)
  SS BOND              : angle       0.20411 (    2)
  hydrogen bonds       : bond        0.03998 (  313)
  hydrogen bonds       : angle       5.07194 (  921)
  link_BETA1-4         : bond        0.00510 (    4)
  link_BETA1-4         : angle       1.56106 (   12)
  link_NAG-ASN         : bond        0.00941 (   10)
  link_NAG-ASN         : angle       3.43234 (   30)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.225 
Fit side-chains
REVERT: B  975 GLU cc_start: 0.6972 (tm-30) cc_final: 0.6687 (pm20)
REVERT: B 1116 MET cc_start: 0.7899 (mpp) cc_final: 0.7433 (mpp)
REVERT: A  975 GLU cc_start: 0.6926 (tm-30) cc_final: 0.6603 (pm20)
REVERT: A 1127 ARG cc_start: 0.8287 (mtt-85) cc_final: 0.8081 (mtt-85)
  outliers start: 13
  outliers final: 10
  residues processed: 117
  average time/residue: 0.1018
  time to fit residues: 15.9097
Evaluate side-chains
  101 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 ASN
Chi-restraints excluded: chain B residue  326 ASN
Chi-restraints excluded: chain B residue  351 ASN
Chi-restraints excluded: chain B residue  372 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue 1178 ILE
Chi-restraints excluded: chain A residue  326 ASN
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  372 ASP
Chi-restraints excluded: chain A residue  373 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 50 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0980
   chunk 68 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   chunk 60 optimal weight:    4.9990
   chunk 78 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 326 ASN
B 987 HIS
A 326 ASN
A 987 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.175119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.131709 restraints weight = 8120.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 2.16
r_work: 0.3307 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.1514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7703  Z= 0.138
  Angle     :  0.618   7.206  10442  Z= 0.302
  Chirality :  0.049   0.324   1152
  Planarity :  0.004   0.032   1326
  Dihedral  :  9.176  67.896   1250
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  9.47 %
    Favored  : 89.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.29), residues: 858
  helix:  1.80 (0.26), residues: 394
  sheet:  0.46 (0.53), residues: 98
  loop : -1.25 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B1127 
 TYR   0.020   0.002   TYR B 999 
 PHE   0.008   0.001   PHE B 931 
 TRP   0.007   0.001   TRP B1201 
 HIS   0.003   0.001   HIS A 423 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 7688)
  covalent geometry    : angle       0.59227 (10398)
  SS BOND              : bond        0.00044 (    1)
  SS BOND              : angle       0.09355 (    2)
  hydrogen bonds       : bond        0.03519 (  313)
  hydrogen bonds       : angle       4.66569 (  921)
  link_BETA1-4         : bond        0.00461 (    4)
  link_BETA1-4         : angle       1.84337 (   12)
  link_NAG-ASN         : bond        0.00948 (   10)
  link_NAG-ASN         : angle       3.12922 (   30)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.308 
Fit side-chains
REVERT: B  392 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8368 (mp)
REVERT: B  975 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6757 (pm20)
REVERT: B 1158 HIS cc_start: 0.8091 (t-90) cc_final: 0.7885 (t-90)
REVERT: A  392 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8375 (mp)
REVERT: A  975 GLU cc_start: 0.7000 (tm-30) cc_final: 0.6691 (pm20)
REVERT: A 1127 ARG cc_start: 0.8358 (mtt-85) cc_final: 0.8095 (mtt-85)
  outliers start: 11
  outliers final: 9
  residues processed: 114
  average time/residue: 0.0966
  time to fit residues: 14.8675
Evaluate side-chains
  103 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 ASN
Chi-restraints excluded: chain B residue  372 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue 1178 ILE
Chi-restraints excluded: chain A residue  326 ASN
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  372 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue 1178 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0070
   chunk 78 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
B 987 HIS
A 987 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.175375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.131131 restraints weight = 8209.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 2.22
r_work: 0.3284 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078   7703  Z= 0.139
  Angle     :  0.610   7.339  10442  Z= 0.298
  Chirality :  0.049   0.316   1152
  Planarity :  0.004   0.042   1326
  Dihedral  :  8.211  59.892   1250
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 10.80 %
    Favored  : 87.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.29), residues: 858
  helix:  1.91 (0.25), residues: 394
  sheet:  0.40 (0.54), residues: 98
  loop : -1.18 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B1127 
 TYR   0.023   0.002   TYR A 999 
 PHE   0.011   0.001   PHE B 946 
 TRP   0.006   0.001   TRP B1201 
 HIS   0.002   0.001   HIS B 423 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 7688)
  covalent geometry    : angle       0.58694 (10398)
  SS BOND              : bond        0.00042 (    1)
  SS BOND              : angle       0.14728 (    2)
  hydrogen bonds       : bond        0.03359 (  313)
  hydrogen bonds       : angle       4.58034 (  921)
  link_BETA1-4         : bond        0.00424 (    4)
  link_BETA1-4         : angle       1.91782 (   12)
  link_NAG-ASN         : bond        0.00856 (   10)
  link_NAG-ASN         : angle       2.94614 (   30)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.301 
Fit side-chains
REVERT: B  975 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6805 (pm20)
REVERT: A  107 MET cc_start: 0.5300 (mmp) cc_final: 0.4836 (mtt)
REVERT: A  392 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8457 (mp)
REVERT: A  975 GLU cc_start: 0.6983 (tm-30) cc_final: 0.6689 (pm20)
  outliers start: 13
  outliers final: 9
  residues processed: 106
  average time/residue: 0.0869
  time to fit residues: 12.7450
Evaluate side-chains
  99 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 ASN
Chi-restraints excluded: chain B residue  372 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  985 VAL
Chi-restraints excluded: chain B residue 1178 ILE
Chi-restraints excluded: chain A residue  372 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  985 VAL
Chi-restraints excluded: chain A residue 1178 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 74 optimal weight:    0.0020
   chunk 43 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 48 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
B 326 ASN
B 987 HIS
B1151 ASN
A 326 ASN
A 987 HIS
A1151 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.176035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.130444 restraints weight = 8141.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 2.29
r_work: 0.3271 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   7703  Z= 0.142
  Angle     :  0.612   7.432  10442  Z= 0.300
  Chirality :  0.048   0.306   1152
  Planarity :  0.004   0.035   1326
  Dihedral  :  7.396  52.176   1250
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 11.17 %
    Favored  : 86.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.29), residues: 858
  helix:  2.02 (0.25), residues: 394
  sheet:  0.41 (0.54), residues: 98
  loop : -1.10 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B1127 
 TYR   0.021   0.002   TYR B 999 
 PHE   0.010   0.001   PHE B 998 
 TRP   0.008   0.001   TRP B 357 
 HIS   0.004   0.001   HIS A1158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 7688)
  covalent geometry    : angle       0.59046 (10398)
  SS BOND              : bond        0.00054 (    1)
  SS BOND              : angle       0.13691 (    2)
  hydrogen bonds       : bond        0.03321 (  313)
  hydrogen bonds       : angle       4.52628 (  921)
  link_BETA1-4         : bond        0.00480 (    4)
  link_BETA1-4         : angle       1.91806 (   12)
  link_NAG-ASN         : bond        0.00835 (   10)
  link_NAG-ASN         : angle       2.80969 (   30)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.318 
Fit side-chains
REVERT: B  107 MET cc_start: 0.5061 (mmp) cc_final: 0.4601 (mtt)
REVERT: B  975 GLU cc_start: 0.6995 (tm-30) cc_final: 0.6758 (pm20)
REVERT: A  107 MET cc_start: 0.5344 (mmp) cc_final: 0.4850 (mtt)
REVERT: A  975 GLU cc_start: 0.6860 (tm-30) cc_final: 0.6629 (pm20)
  outliers start: 19
  outliers final: 11
  residues processed: 108
  average time/residue: 0.0949
  time to fit residues: 13.9494
Evaluate side-chains
  99 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  372 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  985 VAL
Chi-restraints excluded: chain B residue 1118 GLU
Chi-restraints excluded: chain B residue 1178 ILE
Chi-restraints excluded: chain A residue  372 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  985 VAL
Chi-restraints excluded: chain A residue 1116 MET
Chi-restraints excluded: chain A residue 1118 GLU
Chi-restraints excluded: chain A residue 1178 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 28 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 58 optimal weight:    0.5980
   chunk 76 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 987 HIS
** B1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 987 HIS
A 992 GLN
** A1158 HIS ** 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 = 0.4007 r_free = 0.4007 target = 0.175004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.129849 restraints weight = 8159.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 2.31
r_work: 0.3259 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7703  Z= 0.152
  Angle     :  0.628   7.716  10442  Z= 0.309
  Chirality :  0.048   0.304   1152
  Planarity :  0.004   0.038   1326
  Dihedral  :  6.768  44.070   1250
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 11.29 %
    Favored  : 86.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.29), residues: 858
  helix:  2.05 (0.25), residues: 394
  sheet:  0.33 (0.54), residues: 98
  loop : -1.02 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1127 
 TYR   0.019   0.002   TYR A 999 
 PHE   0.014   0.001   PHE A 998 
 TRP   0.009   0.001   TRP B 357 
 HIS   0.003   0.001   HIS B 423 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 7688)
  covalent geometry    : angle       0.60853 (10398)
  SS BOND              : bond        0.00083 (    1)
  SS BOND              : angle       0.10534 (    2)
  hydrogen bonds       : bond        0.03309 (  313)
  hydrogen bonds       : angle       4.45186 (  921)
  link_BETA1-4         : bond        0.00366 (    4)
  link_BETA1-4         : angle       1.91962 (   12)
  link_NAG-ASN         : bond        0.00808 (   10)
  link_NAG-ASN         : angle       2.74987 (   30)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.309 
Fit side-chains
REVERT: B  107 MET cc_start: 0.5091 (mmp) cc_final: 0.4621 (mtt)
REVERT: B  975 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6817 (pm20)
REVERT: A  107 MET cc_start: 0.5266 (mmp) cc_final: 0.4739 (mtt)
REVERT: A  975 GLU cc_start: 0.6969 (tm-30) cc_final: 0.6754 (pm20)
  outliers start: 18
  outliers final: 11
  residues processed: 109
  average time/residue: 0.0923
  time to fit residues: 13.8527
Evaluate side-chains
  96 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  372 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  418 ASP
Chi-restraints excluded: chain B residue  985 VAL
Chi-restraints excluded: chain B residue 1116 MET
Chi-restraints excluded: chain B residue 1178 ILE
Chi-restraints excluded: chain A residue  372 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue 1116 MET
Chi-restraints excluded: chain A residue 1118 GLU
Chi-restraints excluded: chain A residue 1178 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 73 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 69 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 987 HIS
B 992 GLN
** B1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 987 HIS
A 992 GLN
A1151 ASN
** A1158 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 = 0.4000 r_free = 0.4000 target = 0.174567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.129498 restraints weight = 8240.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 2.29
r_work: 0.3241 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   7703  Z= 0.148
  Angle     :  0.636   8.907  10442  Z= 0.312
  Chirality :  0.048   0.299   1152
  Planarity :  0.004   0.038   1326
  Dihedral  :  6.468  38.964   1250
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 12.50 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.29), residues: 858
  helix:  2.13 (0.25), residues: 392
  sheet:  0.56 (0.63), residues: 74
  loop : -0.90 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B1127 
 TYR   0.021   0.002   TYR B 999 
 PHE   0.012   0.001   PHE B 998 
 TRP   0.009   0.001   TRP B 357 
 HIS   0.007   0.001   HIS B1158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 7688)
  covalent geometry    : angle       0.61732 (10398)
  SS BOND              : bond        0.00056 (    1)
  SS BOND              : angle       0.14030 (    2)
  hydrogen bonds       : bond        0.03328 (  313)
  hydrogen bonds       : angle       4.48175 (  921)
  link_BETA1-4         : bond        0.00483 (    4)
  link_BETA1-4         : angle       1.85792 (   12)
  link_NAG-ASN         : bond        0.00781 (   10)
  link_NAG-ASN         : angle       2.70750 (   30)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.291 
Fit side-chains
REVERT: B  107 MET cc_start: 0.5158 (mmp) cc_final: 0.4685 (mtt)
REVERT: B  410 MET cc_start: 0.8525 (mtm) cc_final: 0.8313 (mtp)
REVERT: B  975 GLU cc_start: 0.6995 (tm-30) cc_final: 0.6771 (pm20)
REVERT: A  107 MET cc_start: 0.5311 (mmp) cc_final: 0.4781 (mtt)
REVERT: A  975 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6758 (pm20)
  outliers start: 17
  outliers final: 11
  residues processed: 103
  average time/residue: 0.0955
  time to fit residues: 13.3743
Evaluate side-chains
  96 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  372 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  418 ASP
Chi-restraints excluded: chain B residue  985 VAL
Chi-restraints excluded: chain B residue 1116 MET
Chi-restraints excluded: chain B residue 1178 ILE
Chi-restraints excluded: chain A residue  372 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue 1116 MET
Chi-restraints excluded: chain A residue 1118 GLU
Chi-restraints excluded: chain A residue 1178 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 55 optimal weight:    0.2980
   chunk 11 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   chunk 68 optimal weight:    0.0470
   chunk 19 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
B 987 HIS
** B1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 987 HIS
** A1158 HIS ** 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 = 0.4017 r_free = 0.4017 target = 0.176223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.130153 restraints weight = 8216.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 2.23
r_work: 0.3265 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7703  Z= 0.122
  Angle     :  0.609   9.088  10442  Z= 0.298
  Chirality :  0.047   0.288   1152
  Planarity :  0.004   0.061   1326
  Dihedral  :  6.097  37.868   1250
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 12.99 %
    Favored  : 85.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.30), residues: 858
  helix:  2.18 (0.25), residues: 394
  sheet:  0.55 (0.64), residues: 74
  loop : -0.76 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.000   ARG B1127 
 TYR   0.018   0.001   TYR A 999 
 PHE   0.010   0.001   PHE A 998 
 TRP   0.008   0.001   TRP A 357 
 HIS   0.011   0.001   HIS A1158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 7688)
  covalent geometry    : angle       0.59090 (10398)
  SS BOND              : bond        0.00034 (    1)
  SS BOND              : angle       0.17692 (    2)
  hydrogen bonds       : bond        0.03196 (  313)
  hydrogen bonds       : angle       4.46032 (  921)
  link_BETA1-4         : bond        0.00418 (    4)
  link_BETA1-4         : angle       1.84892 (   12)
  link_NAG-ASN         : bond        0.00778 (   10)
  link_NAG-ASN         : angle       2.61009 (   30)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.308 
Fit side-chains
REVERT: B   92 GLU cc_start: 0.5920 (mt-10) cc_final: 0.5595 (mm-30)
REVERT: B  107 MET cc_start: 0.5049 (mmp) cc_final: 0.4565 (mtt)
REVERT: B  410 MET cc_start: 0.8557 (mtm) cc_final: 0.8319 (mtp)
REVERT: B  975 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6768 (pm20)
REVERT: B 1127 ARG cc_start: 0.7932 (mtt-85) cc_final: 0.7548 (mpt-90)
REVERT: A  107 MET cc_start: 0.5273 (mmp) cc_final: 0.4734 (mtt)
REVERT: A  975 GLU cc_start: 0.6967 (tm-30) cc_final: 0.6763 (pm20)
  outliers start: 14
  outliers final: 11
  residues processed: 103
  average time/residue: 0.0856
  time to fit residues: 12.1564
Evaluate side-chains
  97 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  372 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  418 ASP
Chi-restraints excluded: chain B residue  985 VAL
Chi-restraints excluded: chain B residue 1116 MET
Chi-restraints excluded: chain B residue 1178 ILE
Chi-restraints excluded: chain A residue  372 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue 1116 MET
Chi-restraints excluded: chain A residue 1118 GLU
Chi-restraints excluded: chain A residue 1178 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 84 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 987 HIS
** B1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 987 HIS
A1151 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.174732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.129188 restraints weight = 8195.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 2.32
r_work: 0.3240 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7703  Z= 0.148
  Angle     :  0.621   7.995  10442  Z= 0.305
  Chirality :  0.048   0.291   1152
  Planarity :  0.004   0.072   1326
  Dihedral  :  5.941  37.021   1250
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.35 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.30), residues: 858
  helix:  2.18 (0.25), residues: 392
  sheet:  0.57 (0.63), residues: 74
  loop : -0.74 (0.33), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG B1127 
 TYR   0.018   0.002   TYR B 999 
 PHE   0.013   0.001   PHE B 998 
 TRP   0.010   0.001   TRP B 357 
 HIS   0.012   0.001   HIS B1158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 7688)
  covalent geometry    : angle       0.60337 (10398)
  SS BOND              : bond        0.00053 (    1)
  SS BOND              : angle       0.11586 (    2)
  hydrogen bonds       : bond        0.03342 (  313)
  hydrogen bonds       : angle       4.45185 (  921)
  link_BETA1-4         : bond        0.00487 (    4)
  link_BETA1-4         : angle       1.77610 (   12)
  link_NAG-ASN         : bond        0.00739 (   10)
  link_NAG-ASN         : angle       2.59308 (   30)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.293 
Fit side-chains
REVERT: B  107 MET cc_start: 0.4990 (mmp) cc_final: 0.4546 (mtt)
REVERT: B  975 GLU cc_start: 0.7037 (tm-30) cc_final: 0.6772 (pm20)
REVERT: A  107 MET cc_start: 0.5259 (mmp) cc_final: 0.4798 (mtt)
REVERT: A  975 GLU cc_start: 0.6996 (tm-30) cc_final: 0.6772 (pm20)
  outliers start: 15
  outliers final: 12
  residues processed: 96
  average time/residue: 0.0926
  time to fit residues: 12.2319
Evaluate side-chains
  95 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  372 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  418 ASP
Chi-restraints excluded: chain B residue  941 ILE
Chi-restraints excluded: chain B residue  985 VAL
Chi-restraints excluded: chain B residue 1116 MET
Chi-restraints excluded: chain B residue 1178 ILE
Chi-restraints excluded: chain A residue  372 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue 1116 MET
Chi-restraints excluded: chain A residue 1118 GLU
Chi-restraints excluded: chain A residue 1178 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 59 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 33 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
B 987 HIS
** B1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 987 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.173907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.128142 restraints weight = 8185.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 2.31
r_work: 0.3226 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7703  Z= 0.171
  Angle     :  0.641   8.303  10442  Z= 0.317
  Chirality :  0.048   0.294   1152
  Planarity :  0.005   0.101   1326
  Dihedral  :  5.893  36.926   1250
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.47 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.30), residues: 858
  helix:  2.14 (0.25), residues: 392
  sheet:  0.25 (0.63), residues: 78
  loop : -0.73 (0.34), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG B1127 
 TYR   0.019   0.002   TYR B 999 
 PHE   0.016   0.001   PHE A 998 
 TRP   0.010   0.001   TRP A 357 
 HIS   0.012   0.001   HIS B1158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 7688)
  covalent geometry    : angle       0.62422 (10398)
  SS BOND              : bond        0.00081 (    1)
  SS BOND              : angle       0.07930 (    2)
  hydrogen bonds       : bond        0.03487 (  313)
  hydrogen bonds       : angle       4.47271 (  921)
  link_BETA1-4         : bond        0.00536 (    4)
  link_BETA1-4         : angle       1.68770 (   12)
  link_NAG-ASN         : bond        0.00731 (   10)
  link_NAG-ASN         : angle       2.61835 (   30)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.282 
Fit side-chains
REVERT: B  107 MET cc_start: 0.4960 (mmp) cc_final: 0.4526 (mtt)
REVERT: B  975 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6817 (pm20)
REVERT: B 1127 ARG cc_start: 0.7957 (mtt-85) cc_final: 0.7554 (mpt-90)
REVERT: A  107 MET cc_start: 0.5246 (mmp) cc_final: 0.4799 (mtt)
REVERT: A  975 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6799 (pm20)
  outliers start: 15
  outliers final: 13
  residues processed: 97
  average time/residue: 0.0953
  time to fit residues: 12.5410
Evaluate side-chains
  97 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  372 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  418 ASP
Chi-restraints excluded: chain B residue  941 ILE
Chi-restraints excluded: chain B residue  985 VAL
Chi-restraints excluded: chain B residue 1116 MET
Chi-restraints excluded: chain B residue 1178 ILE
Chi-restraints excluded: chain A residue  372 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  985 VAL
Chi-restraints excluded: chain A residue 1116 MET
Chi-restraints excluded: chain A residue 1118 GLU
Chi-restraints excluded: chain A residue 1178 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 58 optimal weight:    0.7980
   chunk 74 optimal weight:    4.9990
   chunk 21 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 6 optimal weight:    7.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 987 HIS
** B1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 987 HIS
A 992 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.174339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.128288 restraints weight = 8169.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.30
r_work: 0.3241 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.2603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7703  Z= 0.141
  Angle     :  0.613   7.661  10442  Z= 0.303
  Chirality :  0.047   0.286   1152
  Planarity :  0.004   0.080   1326
  Dihedral  :  5.694  36.805   1250
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 14.08 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.30), residues: 858
  helix:  2.21 (0.25), residues: 392
  sheet:  0.64 (0.64), residues: 74
  loop : -0.74 (0.34), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.000   ARG B1127 
 TYR   0.018   0.002   TYR B 999 
 PHE   0.012   0.001   PHE B 998 
 TRP   0.009   0.001   TRP B 357 
 HIS   0.012   0.001   HIS B1158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 7688)
  covalent geometry    : angle       0.59659 (10398)
  SS BOND              : bond        0.00059 (    1)
  SS BOND              : angle       0.06545 (    2)
  hydrogen bonds       : bond        0.03272 (  313)
  hydrogen bonds       : angle       4.39890 (  921)
  link_BETA1-4         : bond        0.00539 (    4)
  link_BETA1-4         : angle       1.65350 (   12)
  link_NAG-ASN         : bond        0.00739 (   10)
  link_NAG-ASN         : angle       2.54102 (   30)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2201.01 seconds
wall clock time: 38 minutes 18.69 seconds (2298.69 seconds total)