Starting phenix.real_space_refine
on Sun Apr 27 11:14:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yi7_39311/04_2025/8yi7_39311_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yi7_39311/04_2025/8yi7_39311.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yi7_39311/04_2025/8yi7_39311.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yi7_39311/04_2025/8yi7_39311.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yi7_39311/04_2025/8yi7_39311_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yi7_39311/04_2025/8yi7_39311_neut.cif"
  }
  resolution = 3.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.049
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      43      5.16       5
     C    3514      2.51       5
     N     943      2.21       5
     O    1086      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 5586
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1485
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 1485
          Classifications: {'peptide': 185}
          Link IDs: {'PTRANS': 6, 'TRANS': 178}
    Chain: "B"
      Number of atoms: 2413
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2413
          Classifications: {'peptide': 303}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 288}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 764
          Classifications: {'peptide': 98}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 94}
    Chain: "D"
      Number of atoms: 871
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 871
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 6, 'TRANS': 104}
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 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: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.46, per 1000 atoms: 0.80
  Number of scatterers: 5586
  At special positions: 0
  Unit cell: (117.41, 97.4064, 101.755, 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      43     16.00
     O    1086      8.00
     N     943      7.00
     C    3514      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  37 " - pdb=" SG  CYS A 110 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  64 " - pdb=" SG  CYS A 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  85 " - pdb=" SG  CYS A 123 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  96 " - pdb=" SG  CYS B 199 " distance=2.25
    Simple disulfide: pdb=" SG  CYS B  50 " - pdb=" SG  CYS B  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 142 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 170 " - pdb=" SG  CYS B 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 300 " - pdb=" SG  CYS B 327 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  28 " - pdb=" SG  CYS C 114 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  51 " - pdb=" SG  CYS C 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  59 " - pdb=" SG  CYS C 105 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  29 " - pdb=" SG  CYS D  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  52 " - pdb=" SG  CYS D  62 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  80 " - pdb=" SG  CYS D  86 " distance=2.05

  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 E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG C 401 " - " ASN C  48 "
      " NAG E   1 " - " ASN B 222 "
  Time building additional restraints: 1.46
  Conformation dependent library (CDL) restraints added in 688.2 milliseconds
  

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1332

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 13 sheets defined
      17.4% alpha, 31.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 59
    Processing helix  chain 'A' and resid 80 through 85
    Processing helix  chain 'A' and resid 117 through 147
      removed outlier: 4.010A  pdb=" N   MET A 147 " --> pdb=" O   ALA A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 171
    Processing helix  chain 'A' and resid 187 through 218
      removed outlier: 3.937A  pdb=" N   THR A 191 " --> pdb=" O   ASP A 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 85
    Processing helix  chain 'B' and resid 228 through 233
    Processing sheet with id=AA1, first strand: chain 'B' and resid 23 through 27
      removed outlier: 6.270A  pdb=" N   ILE B  23 " --> pdb=" O   GLU B  34 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   GLU B  34 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   GLU B  25 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   VAL B  32 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LYS B  27 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   TYR B  31 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   HIS B 105 " --> pdb=" O   TYR B  31 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   VAL B  33 " --> pdb=" O   HIS B 105 " (cutoff:3.500A)
      removed outlier: 7.181A  pdb=" N   LYS B 107 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   LEU B  35 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   VAL B  96 " --> pdb=" O   LYS B  92 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   LYS B  92 " --> pdb=" O   VAL B  96 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   HIS B  91 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY B  70 " --> pdb=" O   TRP B  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 27
      removed outlier: 6.270A  pdb=" N   ILE B  23 " --> pdb=" O   GLU B  34 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   GLU B  34 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   GLU B  25 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   VAL B  32 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LYS B  27 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   TYR B  31 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   HIS B 105 " --> pdb=" O   TYR B  31 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   VAL B  33 " --> pdb=" O   HIS B 105 " (cutoff:3.500A)
      removed outlier: 7.181A  pdb=" N   LYS B 107 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   LEU B  35 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 49
    Processing sheet with id=AA4, first strand: chain 'B' and resid 130 through 133
      removed outlier: 6.526A  pdb=" N   GLU B 188 " --> pdb=" O   SER B 176 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 153
    Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 160
    Processing sheet with id=AA7, first strand: chain 'B' and resid 239 through 245
      removed outlier: 5.333A  pdb=" N   ASN B 240 " --> pdb=" O   GLU B 257 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   GLU B 257 " --> pdb=" O   ASN B 240 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 289 through 291
      removed outlier: 4.262A  pdb=" N   ALA B 304 " --> pdb=" O   CYS B 327 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   CYS B 327 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE B 306 " --> pdb=" O   VAL B 325 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 31 through 34
    Processing sheet with id=AB1, first strand: chain 'C' and resid 40 through 42
      removed outlier: 5.755A  pdb=" N   ILE C  41 " --> pdb=" O   GLY C 121 " (cutoff:3.500A)
      removed outlier: 5.551A  pdb=" N   GLN C 112 " --> pdb=" O   LEU C 103 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   LEU C 103 " --> pdb=" O   GLN C 112 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   CYS C 114 " --> pdb=" O   CYS C 101 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLY C  95 " --> pdb=" O   VAL C 120 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   LEU C  68 " --> pdb=" O   PHE C  79 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   PHE C  79 " --> pdb=" O   LEU C  68 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   LEU C  70 " --> pdb=" O   ILE C  77 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 47 through 56
      removed outlier: 4.035A  pdb=" N   LEU D  50 " --> pdb=" O   SER D  63 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   SER D  63 " --> pdb=" O   LEU D  50 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   CYS D  52 " --> pdb=" O   GLU D  61 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   GLU D  61 " --> pdb=" O   CYS D  52 " (cutoff:3.500A)
      removed outlier: 5.197A  pdb=" N   ARG D  54 " --> pdb=" O   ARG D  59 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   ARG D  59 " --> pdb=" O   ARG D  54 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 87 through 88
    Processing sheet with id=AB4, first strand: chain 'D' and resid 87 through 88
      removed outlier: 3.765A  pdb=" N   VAL D 111 " --> pdb=" O   LEU D 131 " (cutoff:3.500A)

    204 hydrogen bonds defined for protein.
    543 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: 1.46

  Time building geometry restraints manager: 1.73 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1072
        1.32 -     1.45: 1396
        1.45 -     1.57: 3181
        1.57 -     1.69: 0
        1.69 -     1.82: 55
  Bond restraints: 5704
  Sorted by residual:
  bond pdb=" CA  VAL D 107 "
       pdb=" CB  VAL D 107 "
    ideal  model  delta    sigma   weight residual
    1.537  1.479  0.058 1.24e-02 6.50e+03 2.20e+01
  bond pdb=" CA  VAL D 105 "
       pdb=" CB  VAL D 105 "
    ideal  model  delta    sigma   weight residual
    1.541  1.488  0.053 1.30e-02 5.92e+03 1.65e+01
  bond pdb=" CA  PRO B 237 "
       pdb=" C   PRO B 237 "
    ideal  model  delta    sigma   weight residual
    1.514  1.536 -0.022 5.50e-03 3.31e+04 1.60e+01
  bond pdb=" N   VAL B 325 "
       pdb=" CA  VAL B 325 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.035 9.00e-03 1.23e+04 1.54e+01
  bond pdb=" N   THR B  52 "
       pdb=" CA  THR B  52 "
    ideal  model  delta    sigma   weight residual
    1.453  1.489 -0.035 9.20e-03 1.18e+04 1.49e+01
  ... (remaining 5699 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 6213
        2.13 -     4.26: 1422
        4.26 -     6.38: 77
        6.38 -     8.51: 7
        8.51 -    10.64: 2
  Bond angle restraints: 7721
  Sorted by residual:
  angle pdb=" N   ARG C  65 "
        pdb=" CA  ARG C  65 "
        pdb=" C   ARG C  65 "
      ideal   model   delta    sigma   weight residual
     114.62  106.84    7.78 1.14e+00 7.69e-01 4.65e+01
  angle pdb=" C   THR D 123 "
        pdb=" CA  THR D 123 "
        pdb=" CB  THR D 123 "
      ideal   model   delta    sigma   weight residual
     110.78  100.14   10.64 1.60e+00 3.91e-01 4.42e+01
  angle pdb=" CA  GLY B  72 "
        pdb=" C   GLY B  72 "
        pdb=" O   GLY B  72 "
      ideal   model   delta    sigma   weight residual
     122.23  117.93    4.30 6.90e-01 2.10e+00 3.89e+01
  angle pdb=" CA  THR D 112 "
        pdb=" C   THR D 112 "
        pdb=" O   THR D 112 "
      ideal   model   delta    sigma   weight residual
     121.81  115.62    6.19 1.18e+00 7.18e-01 2.75e+01
  angle pdb=" N   SER D 106 "
        pdb=" CA  SER D 106 "
        pdb=" C   SER D 106 "
      ideal   model   delta    sigma   weight residual
     109.59  117.10   -7.51 1.47e+00 4.63e-01 2.61e+01
  ... (remaining 7716 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.20: 3301
       20.20 -    40.40: 196
       40.40 -    60.60: 37
       60.60 -    80.80: 8
       80.80 -   101.00: 6
  Dihedral angle restraints: 3548
    sinusoidal: 1498
      harmonic: 2050
  Sorted by residual:
  dihedral pdb=" CB  CYS C  59 "
           pdb=" SG  CYS C  59 "
           pdb=" SG  CYS C 105 "
           pdb=" CB  CYS C 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.24  -73.24     1      1.00e+01 1.00e-02 6.83e+01
  dihedral pdb=" CB  CYS B 300 "
           pdb=" SG  CYS B 300 "
           pdb=" SG  CYS B 327 "
           pdb=" CB  CYS B 327 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -147.42   61.42     1      1.00e+01 1.00e-02 5.01e+01
  dihedral pdb=" CB  CYS B  50 "
           pdb=" SG  CYS B  50 "
           pdb=" SG  CYS B  90 "
           pdb=" CB  CYS B  90 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.54  -60.54     1      1.00e+01 1.00e-02 4.88e+01
  ... (remaining 3545 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 396
       0.076 -    0.151: 318
       0.151 -    0.227: 119
       0.227 -    0.302: 38
       0.302 -    0.378: 3
  Chirality restraints: 874
  Sorted by residual:
  chirality pdb=" CA  THR D 123 "
            pdb=" N   THR D 123 "
            pdb=" C   THR D 123 "
            pdb=" CB  THR D 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.90   -0.38 2.00e-01 2.50e+01 3.57e+00
  chirality pdb=" CA  ASN B 184 "
            pdb=" N   ASN B 184 "
            pdb=" C   ASN B 184 "
            pdb=" CB  ASN B 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.32e+00
  chirality pdb=" CB  VAL B 180 "
            pdb=" CA  VAL B 180 "
            pdb=" CG1 VAL B 180 "
            pdb=" CG2 VAL B 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.29   -0.34 2.00e-01 2.50e+01 2.96e+00
  ... (remaining 871 not shown)

  Planarity restraints: 979
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER D 100 "   -0.015 2.00e-02 2.50e+03   3.04e-02 9.22e+00
        pdb=" C   SER D 100 "    0.053 2.00e-02 2.50e+03
        pdb=" O   SER D 100 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ASP D 101 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 196 "   -0.014 2.00e-02 2.50e+03   2.96e-02 8.76e+00
        pdb=" C   ASP B 196 "    0.051 2.00e-02 2.50e+03
        pdb=" O   ASP B 196 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   SER B 197 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 265 "    0.014 2.00e-02 2.50e+03   2.80e-02 7.83e+00
        pdb=" C   PRO B 265 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   PRO B 265 "    0.018 2.00e-02 2.50e+03
        pdb=" N   HIS B 266 "    0.016 2.00e-02 2.50e+03
  ... (remaining 976 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 138
        2.68 -     3.23: 4878
        3.23 -     3.79: 8010
        3.79 -     4.34: 11305
        4.34 -     4.90: 17923
  Nonbonded interactions: 42254
  Sorted by model distance:
  nonbonded pdb=" CD2 LEU B 117 "
            pdb=" CG2 THR B 146 "
     model   vdw
     2.122 3.880
  nonbonded pdb=" CG2 THR B 141 "
            pdb=" OE1 GLU B 192 "
     model   vdw
     2.338 3.460
  nonbonded pdb=" O   ASP A 187 "
            pdb=" OD1 ASP A 187 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" NZ  LYS B 157 "
            pdb=" OD2 ASP B 213 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" O5  NAG C 401 "
            pdb=" O6  NAG C 401 "
     model   vdw
     2.447 2.432
  ... (remaining 42249 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.280
  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:             0.020
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     17.980
  Find NCS groups from input model:        0.060
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
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      :  0.013   0.216   5722  Z= 1.002
  Angle     :  1.644  29.628   7761  Z= 1.216
  Chirality :  0.114   0.378    874
  Planarity :  0.005   0.030    977
  Dihedral  : 13.654 100.996   2174
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 10.81 %
    Favored  : 87.44 %
  Cbeta Deviations :  0.60 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.32), residues: 687
  helix:  3.02 (0.48), residues: 119
  sheet:  0.51 (0.35), residues: 230
  loop : -0.76 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP B  60 
 HIS   0.004   0.001   HIS A  71 
 PHE   0.026   0.002   PHE D  99 
 TYR   0.025   0.002   TYR B 268 
 ARG   0.004   0.001   ARG A 205 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01318 (    2)
  link_NAG-ASN         : angle       5.06095 (    6)
  link_BETA1-4         : bond        0.01249 (    2)
  link_BETA1-4         : angle       2.26960 (    6)
  hydrogen bonds       : bond        0.20263 (  195)
  hydrogen bonds       : angle       8.79343 (  543)
  SS BOND              : bond        0.05808 (   14)
  SS BOND              : angle       5.92036 (   28)
  covalent geometry    : bond        0.01306 ( 5704)
  covalent geometry    : angle       1.60222 ( 7721)

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 176
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 THR cc_start: 0.8516 (p) cc_final: 0.8123 (p)
REVERT: B  114 THR cc_start: 0.8475 (m) cc_final: 0.8270 (p)
REVERT: B  271 LEU cc_start: 0.8973 (mt) cc_final: 0.8768 (mt)
REVERT: B  275 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8017 (m)
REVERT: B  276 GLN cc_start: 0.7301 (tt0) cc_final: 0.7020 (pp30)
REVERT: D   51 ARG cc_start: 0.8152 (ttm170) cc_final: 0.7787 (ptp-110)
REVERT: D   63 SER cc_start: 0.8564 (t) cc_final: 0.8130 (m)
REVERT: D   65 GLN cc_start: 0.7776 (tt0) cc_final: 0.7498 (mt0)
REVERT: D   96 ARG cc_start: 0.7965 (ptp-170) cc_final: 0.7495 (ptp90)
REVERT: D   98 GLN cc_start: 0.8315 (mt0) cc_final: 0.7879 (mt0)
  outliers start: 11
  outliers final: 1
  residues processed: 183
  average time/residue: 0.1945
  time to fit residues: 45.0630
Evaluate side-chains
  113 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 111
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain D residue  107 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 57 optimal weight:    0.3980
   chunk 51 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0470
   chunk 20 optimal weight:    7.9990
   chunk 32 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0670
   chunk 61 optimal weight:    4.9990
   overall best weight:    0.3616

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

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN
B  87 GLN
B  99 HIS
D 102 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.171401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.141536 restraints weight = 6761.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.140768 restraints weight = 6316.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.141493 restraints weight = 5860.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   5722  Z= 0.142
  Angle     :  0.617   8.032   7761  Z= 0.328
  Chirality :  0.042   0.157    874
  Planarity :  0.004   0.040    977
  Dihedral  :  7.781  64.229    836
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.53 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.32), residues: 687
  helix:  3.55 (0.43), residues: 109
  sheet:  0.59 (0.35), residues: 226
  loop : -0.67 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 118 
 HIS   0.008   0.001   HIS B  91 
 PHE   0.012   0.001   PHE A 118 
 TYR   0.024   0.002   TYR B 314 
 ARG   0.005   0.001   ARG C  75 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00426 (    2)
  link_NAG-ASN         : angle       3.72930 (    6)
  link_BETA1-4         : bond        0.01115 (    2)
  link_BETA1-4         : angle       2.16359 (    6)
  hydrogen bonds       : bond        0.06178 (  195)
  hydrogen bonds       : angle       6.06529 (  543)
  SS BOND              : bond        0.00370 (   14)
  SS BOND              : angle       2.32753 (   28)
  covalent geometry    : bond        0.00299 ( 5704)
  covalent geometry    : angle       0.59011 ( 7721)

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 GLN cc_start: 0.6775 (OUTLIER) cc_final: 0.6441 (mp10)
REVERT: B  114 THR cc_start: 0.8430 (m) cc_final: 0.8072 (p)
REVERT: B  271 LEU cc_start: 0.8870 (mt) cc_final: 0.8651 (mt)
REVERT: B  288 ARG cc_start: 0.7346 (ptp-170) cc_final: 0.6691 (mtt180)
REVERT: D   98 GLN cc_start: 0.8429 (mt0) cc_final: 0.8205 (mt0)
REVERT: D  123 THR cc_start: 0.7222 (OUTLIER) cc_final: 0.7020 (m)
  outliers start: 15
  outliers final: 7
  residues processed: 114
  average time/residue: 0.1896
  time to fit residues: 28.0362
Evaluate side-chains
  102 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain B residue   87 GLN
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue  123 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0670
   chunk 6 optimal weight:    0.0970
   chunk 10 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 12 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 32 optimal weight:    0.4980
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.4316

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

Flipped N/Q/H residues before XYZ refinement:
B  87 GLN
C  39 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.167213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.135920 restraints weight = 6897.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.135773 restraints weight = 7180.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.136852 restraints weight = 6539.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.3217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   5722  Z= 0.121
  Angle     :  0.543   6.974   7761  Z= 0.288
  Chirality :  0.040   0.200    874
  Planarity :  0.004   0.040    977
  Dihedral  :  5.674  39.498    834
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 18.92 %
    Favored  : 77.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.31), residues: 687
  helix:  3.36 (0.45), residues: 109
  sheet:  0.60 (0.34), residues: 226
  loop : -0.69 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  60 
 HIS   0.009   0.001   HIS B  91 
 PHE   0.011   0.001   PHE B 140 
 TYR   0.016   0.001   TYR C  71 
 ARG   0.004   0.000   ARG D  48 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00281 (    2)
  link_NAG-ASN         : angle       3.61474 (    6)
  link_BETA1-4         : bond        0.00899 (    2)
  link_BETA1-4         : angle       1.84429 (    6)
  hydrogen bonds       : bond        0.05122 (  195)
  hydrogen bonds       : angle       5.30032 (  543)
  SS BOND              : bond        0.00504 (   14)
  SS BOND              : angle       1.90925 (   28)
  covalent geometry    : bond        0.00271 ( 5704)
  covalent geometry    : angle       0.52000 ( 7721)

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.631 
Fit side-chains
REVERT: A  157 GLN cc_start: 0.6662 (OUTLIER) cc_final: 0.6374 (mp10)
REVERT: B  114 THR cc_start: 0.8506 (m) cc_final: 0.8008 (p)
REVERT: B  275 VAL cc_start: 0.8111 (OUTLIER) cc_final: 0.7825 (m)
REVERT: B  288 ARG cc_start: 0.7461 (ptp-170) cc_final: 0.7087 (mtt180)
REVERT: D  122 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7334 (mp10)
  outliers start: 20
  outliers final: 8
  residues processed: 116
  average time/residue: 0.1680
  time to fit residues: 25.6473
Evaluate side-chains
  105 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain B residue   87 GLN
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  135 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 51 optimal weight:    9.9990
   chunk 21 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0010
   chunk 3 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0970
   chunk 32 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.7588

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

Flipped N/Q/H residues before XYZ refinement:
** B  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.162290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.128262 restraints weight = 7061.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.129655 restraints weight = 5860.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.131037 restraints weight = 5228.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.3693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   5722  Z= 0.131
  Angle     :  0.549   7.889   7761  Z= 0.288
  Chirality :  0.040   0.152    874
  Planarity :  0.004   0.039    977
  Dihedral  :  4.581  28.802    834
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.71 %
    Favored  : 77.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.32), residues: 687
  helix:  3.35 (0.46), residues: 112
  sheet:  0.64 (0.34), residues: 232
  loop : -0.73 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  60 
 HIS   0.011   0.001   HIS B  91 
 PHE   0.012   0.001   PHE B 228 
 TYR   0.014   0.001   TYR C  71 
 ARG   0.003   0.000   ARG B 313 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00244 (    2)
  link_NAG-ASN         : angle       3.59975 (    6)
  link_BETA1-4         : bond        0.00784 (    2)
  link_BETA1-4         : angle       1.75052 (    6)
  hydrogen bonds       : bond        0.04696 (  195)
  hydrogen bonds       : angle       4.91835 (  543)
  SS BOND              : bond        0.00382 (   14)
  SS BOND              : angle       1.80083 (   28)
  covalent geometry    : bond        0.00307 ( 5704)
  covalent geometry    : angle       0.52847 ( 7721)

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 GLN cc_start: 0.6836 (OUTLIER) cc_final: 0.6525 (mp10)
REVERT: B  114 THR cc_start: 0.8365 (m) cc_final: 0.8010 (p)
REVERT: B  118 LYS cc_start: 0.8235 (ptmt) cc_final: 0.7896 (ptmt)
REVERT: B  288 ARG cc_start: 0.7530 (ptp-170) cc_final: 0.7183 (mtt180)
REVERT: D   48 ARG cc_start: 0.7023 (mpt180) cc_final: 0.6745 (mmt180)
  outliers start: 15
  outliers final: 10
  residues processed: 106
  average time/residue: 0.1668
  time to fit residues: 23.2239
Evaluate side-chains
  107 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  135 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 21 optimal weight:    0.3980
   chunk 2 optimal weight:    3.9990
   chunk 48 optimal weight:    0.4980
   chunk 18 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 49 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** B  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS
B 166 GLN
** D  98 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 = 0.3758 r_free = 0.3758 target = 0.159689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.128751 restraints weight = 6846.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.127136 restraints weight = 6794.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.127875 restraints weight = 6574.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.4183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   5722  Z= 0.169
  Angle     :  0.572   6.424   7761  Z= 0.298
  Chirality :  0.040   0.188    874
  Planarity :  0.004   0.040    977
  Dihedral  :  4.234  16.922    834
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 20.51 %
    Favored  : 76.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.32), residues: 687
  helix:  3.24 (0.46), residues: 112
  sheet:  0.73 (0.35), residues: 219
  loop : -0.83 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  60 
 HIS   0.011   0.002   HIS B  91 
 PHE   0.018   0.002   PHE B 228 
 TYR   0.014   0.002   TYR C  71 
 ARG   0.003   0.000   ARG A 205 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00306 (    2)
  link_NAG-ASN         : angle       3.63201 (    6)
  link_BETA1-4         : bond        0.00756 (    2)
  link_BETA1-4         : angle       1.72154 (    6)
  hydrogen bonds       : bond        0.04665 (  195)
  hydrogen bonds       : angle       4.75642 (  543)
  SS BOND              : bond        0.00354 (   14)
  SS BOND              : angle       1.81729 (   28)
  covalent geometry    : bond        0.00414 ( 5704)
  covalent geometry    : angle       0.55159 ( 7721)

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
REVERT: B  114 THR cc_start: 0.8428 (m) cc_final: 0.8059 (p)
REVERT: B  288 ARG cc_start: 0.7729 (ptp-170) cc_final: 0.7444 (mtt180)
REVERT: D  122 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7338 (mp10)
  outliers start: 16
  outliers final: 11
  residues processed: 108
  average time/residue: 0.1815
  time to fit residues: 26.1564
Evaluate side-chains
  100 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  135 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 19 optimal weight:    0.2980
   chunk 10 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 59 optimal weight:    4.9990
   chunk 11 optimal weight:    0.3980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN
B  91 HIS
B 166 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.159249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.126828 restraints weight = 6864.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.126048 restraints weight = 5914.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.126284 restraints weight = 6171.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.4378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   5722  Z= 0.118
  Angle     :  0.534   6.286   7761  Z= 0.279
  Chirality :  0.039   0.186    874
  Planarity :  0.004   0.041    977
  Dihedral  :  4.179  18.718    834
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 19.87 %
    Favored  : 76.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.32), residues: 687
  helix:  2.85 (0.47), residues: 118
  sheet:  0.82 (0.36), residues: 219
  loop : -0.84 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  60 
 HIS   0.012   0.001   HIS B  91 
 PHE   0.015   0.001   PHE A 172 
 TYR   0.012   0.001   TYR C  71 
 ARG   0.008   0.000   ARG D  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00208 (    2)
  link_NAG-ASN         : angle       3.33650 (    6)
  link_BETA1-4         : bond        0.00856 (    2)
  link_BETA1-4         : angle       1.63624 (    6)
  hydrogen bonds       : bond        0.04174 (  195)
  hydrogen bonds       : angle       4.50351 (  543)
  SS BOND              : bond        0.00533 (   14)
  SS BOND              : angle       1.80715 (   28)
  covalent geometry    : bond        0.00281 ( 5704)
  covalent geometry    : angle       0.51435 ( 7721)

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 0.678 
Fit side-chains
REVERT: A  157 GLN cc_start: 0.6794 (OUTLIER) cc_final: 0.6529 (mp10)
REVERT: B  114 THR cc_start: 0.8197 (m) cc_final: 0.7808 (p)
REVERT: B  288 ARG cc_start: 0.7712 (ptp-170) cc_final: 0.7475 (mtt180)
  outliers start: 20
  outliers final: 11
  residues processed: 101
  average time/residue: 0.1883
  time to fit residues: 24.7412
Evaluate side-chains
  97 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  107 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0170
   chunk 0 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    0.2980
   chunk 57 optimal weight:    0.0370
   chunk 41 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.3896

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

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN
B  91 HIS
C  78 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.159508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.127583 restraints weight = 6796.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.126947 restraints weight = 8369.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.128079 restraints weight = 7851.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.4562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   5722  Z= 0.108
  Angle     :  0.528   6.671   7761  Z= 0.275
  Chirality :  0.039   0.201    874
  Planarity :  0.004   0.043    977
  Dihedral  :  4.020  17.272    834
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 21.30 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.32), residues: 687
  helix:  2.95 (0.47), residues: 118
  sheet:  0.89 (0.36), residues: 213
  loop : -0.85 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  60 
 HIS   0.013   0.001   HIS B  91 
 PHE   0.012   0.001   PHE B 140 
 TYR   0.010   0.001   TYR C  71 
 ARG   0.008   0.000   ARG D  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00207 (    2)
  link_NAG-ASN         : angle       3.06763 (    6)
  link_BETA1-4         : bond        0.00838 (    2)
  link_BETA1-4         : angle       1.57766 (    6)
  hydrogen bonds       : bond        0.03881 (  195)
  hydrogen bonds       : angle       4.35080 (  543)
  SS BOND              : bond        0.00494 (   14)
  SS BOND              : angle       1.83047 (   28)
  covalent geometry    : bond        0.00255 ( 5704)
  covalent geometry    : angle       0.50829 ( 7721)

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
REVERT: B  114 THR cc_start: 0.8247 (m) cc_final: 0.7850 (p)
REVERT: D  128 GLU cc_start: 0.7666 (pp20) cc_final: 0.6977 (pp20)
  outliers start: 13
  outliers final: 10
  residues processed: 91
  average time/residue: 0.1864
  time to fit residues: 22.2230
Evaluate side-chains
  91 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  107 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0030
   chunk 19 optimal weight:    0.0050
   chunk 24 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.4404

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

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN
B  91 HIS
D  98 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.158473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.122509 restraints weight = 6846.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.123926 restraints weight = 5529.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.123926 restraints weight = 4890.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.4631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   5722  Z= 0.112
  Angle     :  0.548  10.816   7761  Z= 0.279
  Chirality :  0.039   0.227    874
  Planarity :  0.004   0.047    977
  Dihedral  :  3.951  17.662    834
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 20.83 %
    Favored  : 76.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.32), residues: 687
  helix:  2.97 (0.47), residues: 118
  sheet:  0.86 (0.36), residues: 215
  loop : -0.85 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  60 
 HIS   0.012   0.001   HIS B  91 
 PHE   0.010   0.001   PHE B 140 
 TYR   0.010   0.001   TYR C  71 
 ARG   0.006   0.000   ARG D  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00199 (    2)
  link_NAG-ASN         : angle       2.96212 (    6)
  link_BETA1-4         : bond        0.00808 (    2)
  link_BETA1-4         : angle       1.54747 (    6)
  hydrogen bonds       : bond        0.03803 (  195)
  hydrogen bonds       : angle       4.28166 (  543)
  SS BOND              : bond        0.00619 (   14)
  SS BOND              : angle       2.05759 (   28)
  covalent geometry    : bond        0.00272 ( 5704)
  covalent geometry    : angle       0.52674 ( 7721)

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 GLN cc_start: 0.6867 (OUTLIER) cc_final: 0.6594 (mp10)
REVERT: B  114 THR cc_start: 0.8224 (m) cc_final: 0.7825 (p)
  outliers start: 18
  outliers final: 12
  residues processed: 96
  average time/residue: 0.1860
  time to fit residues: 23.6222
Evaluate side-chains
  97 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   86 CYS
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  107 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0010
   chunk 27 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 22 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 66 optimal weight:    4.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    1.1590

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

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN
B  91 HIS
C  78 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.152577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.116733 restraints weight = 6946.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.118339 restraints weight = 5693.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.119487 restraints weight = 5048.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.4900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   5722  Z= 0.165
  Angle     :  0.594   8.124   7761  Z= 0.304
  Chirality :  0.041   0.241    874
  Planarity :  0.004   0.047    977
  Dihedral  :  4.164  18.540    834
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 21.14 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.32), residues: 687
  helix:  2.71 (0.47), residues: 118
  sheet:  0.78 (0.36), residues: 210
  loop : -0.99 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 256 
 HIS   0.011   0.001   HIS B  91 
 PHE   0.020   0.002   PHE B 228 
 TYR   0.012   0.001   TYR C  71 
 ARG   0.004   0.001   ARG B 230 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00145 (    2)
  link_NAG-ASN         : angle       3.22521 (    6)
  link_BETA1-4         : bond        0.00741 (    2)
  link_BETA1-4         : angle       1.65218 (    6)
  hydrogen bonds       : bond        0.04361 (  195)
  hydrogen bonds       : angle       4.45002 (  543)
  SS BOND              : bond        0.00619 (   14)
  SS BOND              : angle       2.16210 (   28)
  covalent geometry    : bond        0.00406 ( 5704)
  covalent geometry    : angle       0.57197 ( 7721)

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 MET cc_start: 0.8077 (ttm) cc_final: 0.7779 (ttm)
REVERT: A  157 GLN cc_start: 0.6908 (OUTLIER) cc_final: 0.6642 (mp10)
REVERT: B  174 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8505 (t)
REVERT: B  258 TYR cc_start: 0.8707 (m-80) cc_final: 0.8386 (m-80)
REVERT: C  110 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7236 (mt-10)
REVERT: D  128 GLU cc_start: 0.7722 (pp20) cc_final: 0.7028 (pp20)
  outliers start: 13
  outliers final: 10
  residues processed: 94
  average time/residue: 0.2309
  time to fit residues: 29.0012
Evaluate side-chains
  98 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   86 CYS
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  107 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0170
   chunk 30 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
B  91 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.154934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.119036 restraints weight = 6912.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.120302 restraints weight = 5654.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.120302 restraints weight = 5058.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.4954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   5722  Z= 0.123
  Angle     :  0.562   8.419   7761  Z= 0.287
  Chirality :  0.040   0.229    874
  Planarity :  0.004   0.048    977
  Dihedral  :  4.067  17.742    834
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 22.10 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.32), residues: 687
  helix:  2.84 (0.47), residues: 118
  sheet:  0.77 (0.37), residues: 210
  loop : -0.92 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 143 
 HIS   0.011   0.001   HIS B  91 
 PHE   0.010   0.001   PHE B 228 
 TYR   0.012   0.001   TYR C  71 
 ARG   0.004   0.000   ARG D  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00179 (    2)
  link_NAG-ASN         : angle       3.04849 (    6)
  link_BETA1-4         : bond        0.00763 (    2)
  link_BETA1-4         : angle       1.57076 (    6)
  hydrogen bonds       : bond        0.03970 (  195)
  hydrogen bonds       : angle       4.32350 (  543)
  SS BOND              : bond        0.00564 (   14)
  SS BOND              : angle       2.02948 (   28)
  covalent geometry    : bond        0.00302 ( 5704)
  covalent geometry    : angle       0.54201 ( 7721)

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

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

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 LEU cc_start: 0.7976 (pp) cc_final: 0.7764 (tp)
REVERT: A  141 MET cc_start: 0.8003 (ttm) cc_final: 0.7661 (ttm)
REVERT: A  157 GLN cc_start: 0.6898 (OUTLIER) cc_final: 0.6650 (mp10)
REVERT: B  114 THR cc_start: 0.8280 (m) cc_final: 0.7882 (p)
REVERT: B  258 TYR cc_start: 0.8693 (m-80) cc_final: 0.8384 (m-80)
REVERT: C   67 LYS cc_start: 0.7130 (ptmt) cc_final: 0.6851 (ptmt)
REVERT: D  128 GLU cc_start: 0.7653 (pp20) cc_final: 0.6954 (pp20)
  outliers start: 13
  outliers final: 10
  residues processed: 92
  average time/residue: 0.1896
  time to fit residues: 22.7555
Evaluate side-chains
  95 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   86 CYS
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  107 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 18 optimal weight:    0.4980
   chunk 23 optimal weight:    0.0020
   chunk 63 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 13 optimal weight:    0.4980
   chunk 58 optimal weight:    0.4980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.4588

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

Flipped N/Q/H residues before XYZ refinement:
B  91 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.155636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.119839 restraints weight = 6928.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.121614 restraints weight = 5642.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.122515 restraints weight = 4993.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.5079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   5722  Z= 0.112
  Angle     :  0.550   8.235   7761  Z= 0.280
  Chirality :  0.039   0.221    874
  Planarity :  0.004   0.049    977
  Dihedral  :  3.964  18.336    834
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 21.78 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.32), residues: 687
  helix:  2.91 (0.47), residues: 118
  sheet:  0.77 (0.37), residues: 210
  loop : -0.90 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 143 
 HIS   0.012   0.001   HIS B  91 
 PHE   0.010   0.001   PHE A 172 
 TYR   0.008   0.001   TYR C  71 
 ARG   0.004   0.000   ARG D  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00184 (    2)
  link_NAG-ASN         : angle       2.85799 (    6)
  link_BETA1-4         : bond        0.00812 (    2)
  link_BETA1-4         : angle       1.53028 (    6)
  hydrogen bonds       : bond        0.03702 (  195)
  hydrogen bonds       : angle       4.24466 (  543)
  SS BOND              : bond        0.00540 (   14)
  SS BOND              : angle       1.95965 (   28)
  covalent geometry    : bond        0.00272 ( 5704)
  covalent geometry    : angle       0.53110 ( 7721)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2387.14 seconds
wall clock time: 42 minutes 26.05 seconds (2546.05 seconds total)