Starting phenix.real_space_refine
on Thu Jul 24 09:26:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ef2_47968/07_2025/9ef2_47968.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ef2_47968/07_2025/9ef2_47968.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ef2_47968/07_2025/9ef2_47968.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ef2_47968/07_2025/9ef2_47968.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ef2_47968/07_2025/9ef2_47968.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ef2_47968/07_2025/9ef2_47968.cif"
  }
  resolution = 3.36
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.022
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: 6
    Type Number    sf(0)   Gaussians
     Ca      3      9.91       5
     Mn      3      7.51       5
     S      20      5.16       5
     C    3658      2.51       5
     N     932      2.21       5
     O    1140      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5756
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 3227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 443, 3227
          Classifications: {'peptide': 443}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 31, 'TRANS': 411}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 115
          Unresolved non-hydrogen angles: 144
          Unresolved non-hydrogen dihedrals: 90
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'HIS:plan': 2, 'ARG:plan': 2, 'ASP:plan': 9}
          Unresolved non-hydrogen planarities: 91
    Chain: "B"
      Number of atoms: 1861
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 240, 1861
          Classifications: {'peptide': 240}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 10, 'TRANS': 229}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "C"
      Number of atoms: 426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 426
          Classifications: {'peptide': 61}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 1, 'TRANS': 59}
          Unresolved non-hydrogen bonds: 64
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 53
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 46
    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: "G"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 72
          Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "H"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 45
          Unusual residues: {' MN': 3, 'NAG': 3}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 5.02, per 1000 atoms: 0.87
  Number of scatterers: 5756
  At special positions: 0
  Unit cell: (70.686, 92.004, 93.126, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      3     24.99
     Ca      3     19.99
     S      20     16.00
     O    1140      8.00
     N     932      7.00
     C    3658      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  58 " - pdb=" SG  CYS A  67 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 115 " - pdb=" SG  CYS A 135 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 151 " - pdb=" SG  CYS A 164 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 187 " - pdb=" SG  CYS B 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 241 " - pdb=" SG  CYS B 281 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA G   3 " - " MAN G   6 "
      " MAN G   4 " - " MAN G   5 "
    ALPHA1-6
      " BMA G   3 " - " MAN G   4 "
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG H   1 " - " NAG H   2 "
    BETA1-6
      " NAG H   1 " - " FUC H   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG B 801 " - " ASN B 192 "
      " NAG B 802 " - " ASN B 249 "
      " NAG B 803 " - " ASN B 343 "
      " NAG D   1 " - " ASN A  43 "
      " NAG E   1 " - " ASN A 256 "
      " NAG F   1 " - " ASN A 266 "
      " NAG G   1 " - " ASN A 275 "
      " NAG H   1 " - " ASN A 141 "
  Time building additional restraints: 1.95
  Conformation dependent library (CDL) restraints added in 909.3 milliseconds
  

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1322

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 11 sheets defined
      20.7% alpha, 22.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 184 through 189
    Processing helix  chain 'A' and resid 196 through 204
    Processing helix  chain 'A' and resid 223 through 227
    Processing helix  chain 'B' and resid 132 through 136
    Processing helix  chain 'B' and resid 138 through 157
      removed outlier: 3.800A  pdb=" N   ASN B 151 " --> pdb=" O   THR B 147 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   ARG B 155 " --> pdb=" O   ASN B 151 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ILE B 156 " --> pdb=" O   GLU B 152 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   THR B 157 " --> pdb=" O   MET B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 185
      removed outlier: 4.012A  pdb=" N   ARG B 184 " --> pdb=" O   PRO B 180 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ASN B 185 " --> pdb=" O   ALA B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 217
      removed outlier: 3.683A  pdb=" N   PHE B 212 " --> pdb=" O   LYS B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 241
      removed outlier: 4.387A  pdb=" N   ALA B 234 " --> pdb=" O   GLY B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 246
      removed outlier: 3.800A  pdb=" N   ILE B 245 " --> pdb=" O   CYS B 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 272
    Processing helix  chain 'B' and resid 298 through 310
    Processing helix  chain 'B' and resid 321 through 332
      removed outlier: 3.594A  pdb=" N   LEU B 331 " --> pdb=" O   GLU B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 357
    Processing helix  chain 'C' and resid 12 through 26
      removed outlier: 3.925A  pdb=" N   LEU C  16 " --> pdb=" O   PRO C  12 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LEU C  18 " --> pdb=" O   SER C  14 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 57
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 12
      removed outlier: 8.953A  pdb=" N   ALA A   7 " --> pdb=" O   ARG A 447 " (cutoff:3.500A)
      removed outlier: 7.525A  pdb=" N   ARG A 447 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   ARG A 423 " --> pdb=" O   ASP A 432 " (cutoff:3.500A)
      removed outlier: 7.554A  pdb=" N   ILE A 434 " --> pdb=" O   GLY A 421 " (cutoff:3.500A)
      removed outlier: 5.742A  pdb=" N   GLY A 421 " --> pdb=" O   ILE A 434 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   GLY A 436 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   LEU A 419 " --> pdb=" O   GLY A 436 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26
      removed outlier: 3.879A  pdb=" N   THR A  68 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95
      removed outlier: 3.730A  pdb=" N   SER A 120 " --> pdb=" O   TYR A  95 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 108
      removed outlier: 3.646A  pdb=" N   ARG A 144 " --> pdb=" O   THR A 139 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 172
      removed outlier: 3.688A  pdb=" N   SER A 169 " --> pdb=" O   GLY A 181 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 238
      removed outlier: 4.264A  pdb=" N   PHE A 248 " --> pdb=" O   LEU A 265 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   VAL A 262 " --> pdb=" O   ASN A 275 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ASN A 275 " --> pdb=" O   VAL A 262 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   ILE A 264 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 289 through 292
    Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 312
    Processing sheet with id=AA9, first strand: chain 'A' and resid 355 through 359
      removed outlier: 5.823A  pdb=" N   ASP A 368 " --> pdb=" O   LEU A 358 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 200 through 206
      removed outlier: 6.836A  pdb=" N   VAL B 202 " --> pdb=" O   SER B 166 " (cutoff:3.500A)
      removed outlier: 8.623A  pdb=" N   SER B 166 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
      removed outlier: 5.301A  pdb=" N   SER B 204 " --> pdb=" O   PHE B 164 " (cutoff:3.500A)
      removed outlier: 5.434A  pdb=" N   PHE B 164 " --> pdb=" O   SER B 204 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ARG B 161 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY B 163 " --> pdb=" O   LEU B 125 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   ARG B 252 " --> pdb=" O   GLN B 312 " (cutoff:3.500A)
      removed outlier: 8.068A  pdb=" N   ILE B 314 " --> pdb=" O   ARG B 252 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   LEU B 254 " --> pdb=" O   ILE B 314 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   ALA B 316 " --> pdb=" O   LEU B 254 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   PHE B 256 " --> pdb=" O   ALA B 316 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   VAL B 317 " --> pdb=" O   GLY B 338 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 5

    200 hydrogen bonds defined for protein.
    522 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: 1.84

  Time building geometry restraints manager: 2.24 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1704
        1.33 -     1.45: 1026
        1.45 -     1.57: 3123
        1.57 -     1.69: 0
        1.69 -     1.81: 30
  Bond restraints: 5883
  Sorted by residual:
  bond pdb=" N   ASN A 266 "
       pdb=" CA  ASN A 266 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.034 1.33e-02 5.65e+03 6.41e+00
  bond pdb=" N   LYS C  40 "
       pdb=" CA  LYS C  40 "
    ideal  model  delta    sigma   weight residual
    1.456  1.483 -0.027 1.23e-02 6.61e+03 4.73e+00
  bond pdb=" N   SER B 344 "
       pdb=" CA  SER B 344 "
    ideal  model  delta    sigma   weight residual
    1.456  1.484 -0.028 1.32e-02 5.74e+03 4.47e+00
  bond pdb=" N   GLU A  81 "
       pdb=" CA  GLU A  81 "
    ideal  model  delta    sigma   weight residual
    1.456  1.481 -0.025 1.22e-02 6.72e+03 4.27e+00
  bond pdb=" N   ASN B 343 "
       pdb=" CA  ASN B 343 "
    ideal  model  delta    sigma   weight residual
    1.462  1.485 -0.024 1.27e-02 6.20e+03 3.54e+00
  ... (remaining 5878 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 7742
        1.44 -     2.89: 218
        2.89 -     4.33: 47
        4.33 -     5.77: 9
        5.77 -     7.21: 1
  Bond angle restraints: 8017
  Sorted by residual:
  angle pdb=" CA  ASN A 266 "
        pdb=" CB  ASN A 266 "
        pdb=" CG  ASN A 266 "
      ideal   model   delta    sigma   weight residual
     112.60  119.81   -7.21 1.00e+00 1.00e+00 5.20e+01
  angle pdb=" C   ASN A 141 "
        pdb=" CA  ASN A 141 "
        pdb=" CB  ASN A 141 "
      ideal   model   delta    sigma   weight residual
     116.54  111.56    4.98 1.15e+00 7.56e-01 1.88e+01
  angle pdb=" CA  ARG C  35 "
        pdb=" C   ARG C  35 "
        pdb=" O   ARG C  35 "
      ideal   model   delta    sigma   weight residual
     121.54  117.28    4.26 1.16e+00 7.43e-01 1.35e+01
  angle pdb=" N   ASN A 266 "
        pdb=" CA  ASN A 266 "
        pdb=" C   ASN A 266 "
      ideal   model   delta    sigma   weight residual
     112.89  108.48    4.41 1.24e+00 6.50e-01 1.27e+01
  angle pdb=" N   SER B 344 "
        pdb=" CA  SER B 344 "
        pdb=" C   SER B 344 "
      ideal   model   delta    sigma   weight residual
     113.02  109.53    3.49 1.20e+00 6.94e-01 8.46e+00
  ... (remaining 8012 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.37: 3507
       24.37 -    48.74: 122
       48.74 -    73.11: 20
       73.11 -    97.48: 4
       97.48 -   121.85: 6
  Dihedral angle restraints: 3659
    sinusoidal: 1562
      harmonic: 2097
  Sorted by residual:
  dihedral pdb=" CA  LYS C  40 "
           pdb=" C   LYS C  40 "
           pdb=" N   GLY C  41 "
           pdb=" CA  GLY C  41 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.28   21.72     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" C2  MAN G   6 "
           pdb=" C1  MAN G   6 "
           pdb=" O5  MAN G   6 "
           pdb=" C5  MAN G   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.62   64.23 -121.85     1      3.00e+01 1.11e-03 1.63e+01
  dihedral pdb=" C2  MAN G   5 "
           pdb=" C1  MAN G   5 "
           pdb=" O5  MAN G   5 "
           pdb=" C5  MAN G   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.62   60.66 -118.28     1      3.00e+01 1.11e-03 1.57e+01
  ... (remaining 3656 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 715
       0.047 -    0.094: 167
       0.094 -    0.141: 59
       0.141 -    0.188: 5
       0.188 -    0.235: 1
  Chirality restraints: 947
  Sorted by residual:
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.30   -0.10 2.00e-02 2.50e+03 2.58e+01
  chirality pdb=" C1  NAG B 802 "
            pdb=" ND2 ASN B 249 "
            pdb=" C2  NAG B 802 "
            pdb=" O5  NAG B 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.16   -0.24 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN A 266 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-01 2.50e+01 8.51e-01
  ... (remaining 944 not shown)

  Planarity restraints: 1028
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 803 "   -0.256 2.00e-02 2.50e+03   2.15e-01 5.78e+02
        pdb=" C7  NAG B 803 "    0.067 2.00e-02 2.50e+03
        pdb=" C8  NAG B 803 "   -0.171 2.00e-02 2.50e+03
        pdb=" N2  NAG B 803 "    0.363 2.00e-02 2.50e+03
        pdb=" O7  NAG B 803 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F   1 "    0.135 2.00e-02 2.50e+03   1.15e-01 1.65e+02
        pdb=" C7  NAG F   1 "   -0.024 2.00e-02 2.50e+03
        pdb=" C8  NAG F   1 "   -0.031 2.00e-02 2.50e+03
        pdb=" N2  NAG F   1 "   -0.186 2.00e-02 2.50e+03
        pdb=" O7  NAG F   1 "    0.107 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F   2 "   -0.121 2.00e-02 2.50e+03   9.88e-02 1.22e+02
        pdb=" C7  NAG F   2 "    0.034 2.00e-02 2.50e+03
        pdb=" C8  NAG F   2 "   -0.091 2.00e-02 2.50e+03
        pdb=" N2  NAG F   2 "    0.156 2.00e-02 2.50e+03
        pdb=" O7  NAG F   2 "    0.022 2.00e-02 2.50e+03
  ... (remaining 1025 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 32
        2.57 -     3.15: 4725
        3.15 -     3.73: 8489
        3.73 -     4.32: 11728
        4.32 -     4.90: 20443
  Nonbonded interactions: 45417
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 224 "
            pdb="MN    MN B 806 "
     model   vdw
     1.985 2.320
  nonbonded pdb=" O   PRO B 228 "
            pdb="MN    MN B 806 "
     model   vdw
     2.015 2.320
  nonbonded pdb=" OD1 ASP B 226 "
            pdb="MN    MN B 806 "
     model   vdw
     2.061 2.320
  nonbonded pdb=" OD2 ASP B 259 "
            pdb="MN    MN B 805 "
     model   vdw
     2.074 2.320
  nonbonded pdb=" OD1 ASP B 137 "
            pdb="MN    MN B 805 "
     model   vdw
     2.085 2.320
  ... (remaining 45412 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain '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:             2.690
  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:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.010
  Find NCS groups from input model:        0.070
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
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   0.034   5906  Z= 0.193
  Angle     :  0.635   7.578   8081  Z= 0.353
  Chirality :  0.046   0.235    947
  Planarity :  0.009   0.215   1020
  Dihedral  : 13.747 121.847   2322
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  :  7.05 %
    Favored  : 90.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.31), residues: 734
  helix:  0.53 (0.48), residues: 116
  sheet: -0.95 (0.36), residues: 202
  loop : -1.08 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 121 
 HIS   0.003   0.001   HIS B 282 
 PHE   0.011   0.001   PHE B 264 
 TYR   0.009   0.001   TYR A 327 
 ARG   0.002   0.000   ARG B 220 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00539 (    8)
  link_NAG-ASN         : angle       1.74502 (   24)
  link_ALPHA1-6        : bond        0.00185 (    1)
  link_ALPHA1-6        : angle       1.51632 (    3)
  link_BETA1-4         : bond        0.00839 (    6)
  link_BETA1-4         : angle       2.15080 (   18)
  link_ALPHA1-3        : bond        0.00250 (    2)
  link_ALPHA1-3        : angle       1.69429 (    6)
  hydrogen bonds       : bond        0.15703 (  200)
  hydrogen bonds       : angle       7.58652 (  522)
  link_BETA1-6         : bond        0.00703 (    1)
  link_BETA1-6         : angle       1.51352 (    3)
  SS BOND              : bond        0.00327 (    5)
  SS BOND              : angle       1.08930 (   10)
  covalent geometry    : bond        0.00394 ( 5883)
  covalent geometry    : angle       0.61799 ( 8017)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 ASN cc_start: 0.8401 (t0) cc_final: 0.7930 (t0)
REVERT: A  284 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.7984 (m-80)
REVERT: B  152 GLU cc_start: 0.8632 (tp30) cc_final: 0.8416 (tp30)
REVERT: B  153 MET cc_start: 0.8185 (ttp) cc_final: 0.7742 (ttm)
REVERT: B  183 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7958 (mm)
REVERT: B  287 MET cc_start: 0.8382 (ttt) cc_final: 0.8148 (ttm)
REVERT: C   49 GLU cc_start: 0.8969 (tp30) cc_final: 0.8683 (tp30)
REVERT: C   50 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8937 (mm)
  outliers start: 13
  outliers final: 7
  residues processed: 61
  average time/residue: 0.2013
  time to fit residues: 16.1551
Evaluate side-chains
  53 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   61 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B 286 ASN
B 301 HIS
B 312 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.081208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.066929 restraints weight = 12936.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 3.13
r_work: 0.2773 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.0641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5906  Z= 0.176
  Angle     :  0.599   8.023   8081  Z= 0.295
  Chirality :  0.046   0.220    947
  Planarity :  0.004   0.030   1020
  Dihedral  : 10.342 108.139   1181
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 10.93 %
    Favored  : 86.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.31), residues: 734
  helix:  1.04 (0.48), residues: 122
  sheet: -0.88 (0.36), residues: 203
  loop : -1.04 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 121 
 HIS   0.005   0.001   HIS C  34 
 PHE   0.014   0.002   PHE B 164 
 TYR   0.012   0.001   TYR B 325 
 ARG   0.006   0.000   ARG C  35 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00438 (    8)
  link_NAG-ASN         : angle       1.31058 (   24)
  link_ALPHA1-6        : bond        0.00222 (    1)
  link_ALPHA1-6        : angle       1.83022 (    3)
  link_BETA1-4         : bond        0.00848 (    6)
  link_BETA1-4         : angle       2.16796 (   18)
  link_ALPHA1-3        : bond        0.00579 (    2)
  link_ALPHA1-3        : angle       2.71305 (    6)
  hydrogen bonds       : bond        0.04300 (  200)
  hydrogen bonds       : angle       6.03088 (  522)
  link_BETA1-6         : bond        0.00662 (    1)
  link_BETA1-6         : angle       1.54324 (    3)
  SS BOND              : bond        0.00348 (    5)
  SS BOND              : angle       0.71422 (   10)
  covalent geometry    : bond        0.00413 ( 5883)
  covalent geometry    : angle       0.58117 ( 8017)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 46
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7987 (mtm180)
REVERT: A  211 ASN cc_start: 0.8345 (t0) cc_final: 0.7878 (t0)
REVERT: A  284 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8029 (m-80)
REVERT: B  183 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7985 (mm)
REVERT: B  287 MET cc_start: 0.8428 (ttt) cc_final: 0.8197 (ttm)
  outliers start: 15
  outliers final: 5
  residues processed: 57
  average time/residue: 0.1888
  time to fit residues: 14.3615
Evaluate side-chains
  52 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   61 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0570
   chunk 23 optimal weight:    0.0770
   chunk 52 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.6260

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

Flipped N/Q/H residues before XYZ refinement:
B 301 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.081965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.067456 restraints weight = 12792.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 3.14
r_work: 0.2791 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.0901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5906  Z= 0.134
  Angle     :  0.564   8.126   8081  Z= 0.272
  Chirality :  0.045   0.214    947
  Planarity :  0.003   0.034   1020
  Dihedral  :  9.320  97.390   1173
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 11.64 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.31), residues: 734
  helix:  1.15 (0.47), residues: 128
  sheet: -1.00 (0.35), residues: 201
  loop : -1.04 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 121 
 HIS   0.003   0.001   HIS C  34 
 PHE   0.010   0.001   PHE B 264 
 TYR   0.014   0.001   TYR B 325 
 ARG   0.003   0.000   ARG C  35 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00417 (    8)
  link_NAG-ASN         : angle       1.19749 (   24)
  link_ALPHA1-6        : bond        0.00192 (    1)
  link_ALPHA1-6        : angle       1.75311 (    3)
  link_BETA1-4         : bond        0.00841 (    6)
  link_BETA1-4         : angle       2.06347 (   18)
  link_ALPHA1-3        : bond        0.00830 (    2)
  link_ALPHA1-3        : angle       2.87793 (    6)
  hydrogen bonds       : bond        0.03612 (  200)
  hydrogen bonds       : angle       5.64912 (  522)
  link_BETA1-6         : bond        0.00693 (    1)
  link_BETA1-6         : angle       1.37040 (    3)
  SS BOND              : bond        0.00291 (    5)
  SS BOND              : angle       0.61481 (   10)
  covalent geometry    : bond        0.00308 ( 5883)
  covalent geometry    : angle       0.54581 ( 8017)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 54
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8009 (mtm180)
REVERT: A  211 ASN cc_start: 0.8316 (t0) cc_final: 0.7887 (t0)
REVERT: A  284 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.7962 (m-80)
REVERT: B  153 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7792 (ttm)
REVERT: B  155 ARG cc_start: 0.8194 (ttm110) cc_final: 0.7980 (ttp80)
REVERT: B  183 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8173 (mt)
REVERT: B  287 MET cc_start: 0.8417 (ttt) cc_final: 0.8192 (ttm)
REVERT: B  290 MET cc_start: 0.8983 (tpp) cc_final: 0.8681 (tpp)
REVERT: B  319 GLU cc_start: 0.8218 (tm-30) cc_final: 0.8011 (tm-30)
REVERT: B  327 GLU cc_start: 0.8597 (tp30) cc_final: 0.8135 (tp30)
REVERT: C   49 GLU cc_start: 0.8959 (tp30) cc_final: 0.8728 (tp30)
REVERT: C   56 LYS cc_start: 0.8572 (tppp) cc_final: 0.8292 (tppt)
  outliers start: 22
  outliers final: 10
  residues processed: 69
  average time/residue: 0.1920
  time to fit residues: 17.2739
Evaluate side-chains
  64 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue   22 VAL
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   43 SER
Chi-restraints excluded: chain C residue   61 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 9 optimal weight:    0.0980
   chunk 42 optimal weight:    0.0470
   chunk 6 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 20 optimal weight:    0.2980
   chunk 23 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
B 301 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.082670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.068196 restraints weight = 13073.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 3.11
r_work: 0.2797 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.1118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5906  Z= 0.114
  Angle     :  0.558   8.746   8081  Z= 0.263
  Chirality :  0.044   0.206    947
  Planarity :  0.003   0.038   1020
  Dihedral  :  8.370  88.933   1172
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 13.05 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.31), residues: 734
  helix:  1.22 (0.47), residues: 129
  sheet: -0.94 (0.35), residues: 199
  loop : -1.01 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 121 
 HIS   0.003   0.001   HIS C  34 
 PHE   0.009   0.001   PHE B 264 
 TYR   0.015   0.001   TYR B 325 
 ARG   0.006   0.000   ARG C  32 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00417 (    8)
  link_NAG-ASN         : angle       1.14096 (   24)
  link_ALPHA1-6        : bond        0.00252 (    1)
  link_ALPHA1-6        : angle       1.73262 (    3)
  link_BETA1-4         : bond        0.00860 (    6)
  link_BETA1-4         : angle       2.03273 (   18)
  link_ALPHA1-3        : bond        0.01120 (    2)
  link_ALPHA1-3        : angle       3.11968 (    6)
  hydrogen bonds       : bond        0.03244 (  200)
  hydrogen bonds       : angle       5.39400 (  522)
  link_BETA1-6         : bond        0.00703 (    1)
  link_BETA1-6         : angle       1.24427 (    3)
  SS BOND              : bond        0.00252 (    5)
  SS BOND              : angle       0.54868 (   10)
  covalent geometry    : bond        0.00256 ( 5883)
  covalent geometry    : angle       0.53941 ( 8017)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 54
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8102 (mtm180)
REVERT: A  211 ASN cc_start: 0.8285 (t0) cc_final: 0.7891 (t0)
REVERT: A  284 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.8020 (m-80)
REVERT: A  342 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8363 (mm)
REVERT: B  153 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7766 (ttm)
REVERT: B  183 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8243 (mt)
REVERT: B  287 MET cc_start: 0.8388 (ttt) cc_final: 0.8173 (ttm)
REVERT: B  290 MET cc_start: 0.8996 (tpp) cc_final: 0.8773 (tpp)
REVERT: B  319 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8077 (tm-30)
REVERT: C   32 ARG cc_start: 0.8586 (ttt-90) cc_final: 0.8349 (tpt-90)
REVERT: C   49 GLU cc_start: 0.8946 (tp30) cc_final: 0.8690 (tp30)
REVERT: C   56 LYS cc_start: 0.8594 (tppp) cc_final: 0.8328 (tppt)
  outliers start: 22
  outliers final: 9
  residues processed: 69
  average time/residue: 0.2164
  time to fit residues: 19.2638
Evaluate side-chains
  64 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   47 ILE
Chi-restraints excluded: chain C residue   61 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 64 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 23 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
B 301 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.082806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.068734 restraints weight = 12910.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 3.05
r_work: 0.2825 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5906  Z= 0.145
  Angle     :  0.581   8.932   8081  Z= 0.273
  Chirality :  0.044   0.192    947
  Planarity :  0.003   0.031   1020
  Dihedral  :  7.500  80.991   1172
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 12.70 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.31), residues: 734
  helix:  1.30 (0.48), residues: 129
  sheet: -0.88 (0.36), residues: 197
  loop : -0.99 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 121 
 HIS   0.003   0.001   HIS C  34 
 PHE   0.010   0.001   PHE B 264 
 TYR   0.014   0.001   TYR B 325 
 ARG   0.006   0.000   ARG C  35 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00394 (    8)
  link_NAG-ASN         : angle       1.17629 (   24)
  link_ALPHA1-6        : bond        0.00202 (    1)
  link_ALPHA1-6        : angle       1.71611 (    3)
  link_BETA1-4         : bond        0.00846 (    6)
  link_BETA1-4         : angle       2.09707 (   18)
  link_ALPHA1-3        : bond        0.01362 (    2)
  link_ALPHA1-3        : angle       2.97706 (    6)
  hydrogen bonds       : bond        0.03332 (  200)
  hydrogen bonds       : angle       5.35322 (  522)
  link_BETA1-6         : bond        0.00736 (    1)
  link_BETA1-6         : angle       1.33722 (    3)
  SS BOND              : bond        0.00286 (    5)
  SS BOND              : angle       0.58697 (   10)
  covalent geometry    : bond        0.00335 ( 5883)
  covalent geometry    : angle       0.56358 ( 8017)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 53
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8039 (mtm180)
REVERT: A  211 ASN cc_start: 0.8231 (t0) cc_final: 0.7833 (t0)
REVERT: A  284 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.8033 (m-80)
REVERT: A  342 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8382 (mm)
REVERT: B  287 MET cc_start: 0.8462 (ttt) cc_final: 0.8260 (ttm)
REVERT: B  290 MET cc_start: 0.9045 (tpp) cc_final: 0.8836 (tpp)
REVERT: B  319 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8207 (tm-30)
REVERT: C   32 ARG cc_start: 0.8636 (ttt-90) cc_final: 0.7850 (tpt-90)
REVERT: C   49 GLU cc_start: 0.8965 (tp30) cc_final: 0.8709 (tp30)
REVERT: C   56 LYS cc_start: 0.8569 (tppp) cc_final: 0.8329 (tppt)
  outliers start: 24
  outliers final: 13
  residues processed: 70
  average time/residue: 0.1986
  time to fit residues: 18.1123
Evaluate side-chains
  66 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 50
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue   22 VAL
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   47 ILE
Chi-restraints excluded: chain C residue   61 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0870
   chunk 34 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    1.1562

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
B 301 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.080892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.066600 restraints weight = 13157.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.2884 rms_B_bonded: 3.09
r_work: 0.2778 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.1385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   5906  Z= 0.212
  Angle     :  0.635   9.249   8081  Z= 0.302
  Chirality :  0.046   0.184    947
  Planarity :  0.004   0.033   1020
  Dihedral  :  7.012  72.546   1170
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 12.70 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.31), residues: 734
  helix:  1.19 (0.47), residues: 129
  sheet: -1.00 (0.35), residues: 204
  loop : -1.10 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 121 
 HIS   0.004   0.001   HIS B 263 
 PHE   0.014   0.002   PHE B 264 
 TYR   0.014   0.001   TYR B 325 
 ARG   0.008   0.001   ARG C  35 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00422 (    8)
  link_NAG-ASN         : angle       1.36584 (   24)
  link_ALPHA1-6        : bond        0.00127 (    1)
  link_ALPHA1-6        : angle       1.78453 (    3)
  link_BETA1-4         : bond        0.00808 (    6)
  link_BETA1-4         : angle       2.17862 (   18)
  link_ALPHA1-3        : bond        0.01345 (    2)
  link_ALPHA1-3        : angle       2.92672 (    6)
  hydrogen bonds       : bond        0.03808 (  200)
  hydrogen bonds       : angle       5.52180 (  522)
  link_BETA1-6         : bond        0.00764 (    1)
  link_BETA1-6         : angle       1.56544 (    3)
  SS BOND              : bond        0.00367 (    5)
  SS BOND              : angle       0.71911 (   10)
  covalent geometry    : bond        0.00498 ( 5883)
  covalent geometry    : angle       0.61741 ( 8017)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 51
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8000 (mtm180)
REVERT: A  211 ASN cc_start: 0.8170 (t0) cc_final: 0.7778 (t0)
REVERT: A  284 TYR cc_start: 0.8978 (OUTLIER) cc_final: 0.8140 (m-80)
REVERT: A  342 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8436 (mm)
REVERT: B  154 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7695 (ttm110)
REVERT: B  287 MET cc_start: 0.8482 (ttt) cc_final: 0.8276 (ttm)
REVERT: B  290 MET cc_start: 0.9039 (tpp) cc_final: 0.8813 (tpp)
REVERT: B  327 GLU cc_start: 0.8657 (tp30) cc_final: 0.8124 (tp30)
REVERT: C   32 ARG cc_start: 0.8636 (ttt-90) cc_final: 0.7851 (tpt-90)
REVERT: C   35 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7707 (ttp-110)
REVERT: C   49 GLU cc_start: 0.8990 (tp30) cc_final: 0.8723 (tp30)
REVERT: C   56 LYS cc_start: 0.8656 (tppp) cc_final: 0.8422 (tppt)
  outliers start: 27
  outliers final: 17
  residues processed: 71
  average time/residue: 0.2396
  time to fit residues: 21.7305
Evaluate side-chains
  70 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 49
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   46 GLN
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain B residue  154 ARG
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue   22 VAL
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   40 LYS
Chi-restraints excluded: chain C residue   47 ILE
Chi-restraints excluded: chain C residue   61 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 20 optimal weight:    0.2980
   chunk 1 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0670
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.5320

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

Flipped N/Q/H residues before XYZ refinement:
B 301 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.081852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.067096 restraints weight = 12991.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 3.19
r_work: 0.2773 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5906  Z= 0.123
  Angle     :  0.570   9.499   8081  Z= 0.272
  Chirality :  0.044   0.193    947
  Planarity :  0.003   0.032   1020
  Dihedral  :  6.256  58.560   1170
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 13.93 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.31), residues: 734
  helix:  1.29 (0.47), residues: 129
  sheet: -0.98 (0.35), residues: 199
  loop : -1.00 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 121 
 HIS   0.002   0.001   HIS B 263 
 PHE   0.010   0.001   PHE B 264 
 TYR   0.015   0.001   TYR B 325 
 ARG   0.005   0.000   ARG C  35 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00387 (    8)
  link_NAG-ASN         : angle       1.13069 (   24)
  link_ALPHA1-6        : bond        0.00250 (    1)
  link_ALPHA1-6        : angle       1.59369 (    3)
  link_BETA1-4         : bond        0.00884 (    6)
  link_BETA1-4         : angle       2.02935 (   18)
  link_ALPHA1-3        : bond        0.01425 (    2)
  link_ALPHA1-3        : angle       2.76607 (    6)
  hydrogen bonds       : bond        0.03252 (  200)
  hydrogen bonds       : angle       5.37806 (  522)
  link_BETA1-6         : bond        0.00755 (    1)
  link_BETA1-6         : angle       1.30523 (    3)
  SS BOND              : bond        0.00259 (    5)
  SS BOND              : angle       0.52405 (   10)
  covalent geometry    : bond        0.00278 ( 5883)
  covalent geometry    : angle       0.55423 ( 8017)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 54
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7944 (mtm180)
REVERT: A  211 ASN cc_start: 0.8228 (t0) cc_final: 0.7844 (t0)
REVERT: A  284 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.8056 (m-80)
REVERT: A  342 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8357 (mm)
REVERT: B  173 MET cc_start: 0.8455 (tpp) cc_final: 0.8130 (tpp)
REVERT: B  287 MET cc_start: 0.8435 (ttt) cc_final: 0.8224 (ttm)
REVERT: B  290 MET cc_start: 0.8982 (tpp) cc_final: 0.8742 (tpp)
REVERT: B  327 GLU cc_start: 0.8707 (tp30) cc_final: 0.8132 (tp30)
REVERT: C   32 ARG cc_start: 0.8654 (ttt-90) cc_final: 0.7887 (tpt-90)
REVERT: C   35 ARG cc_start: 0.7908 (ttm110) cc_final: 0.7569 (ttp-110)
REVERT: C   49 GLU cc_start: 0.8962 (tp30) cc_final: 0.8693 (tp30)
REVERT: C   56 LYS cc_start: 0.8634 (tppp) cc_final: 0.8402 (tppt)
  outliers start: 20
  outliers final: 12
  residues processed: 68
  average time/residue: 0.2308
  time to fit residues: 20.0395
Evaluate side-chains
  68 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 53
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 GLN
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   40 LYS
Chi-restraints excluded: chain C residue   61 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 63 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B 301 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.081688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.067658 restraints weight = 12864.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.2909 rms_B_bonded: 2.99
r_work: 0.2807 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.1539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5906  Z= 0.163
  Angle     :  0.594   9.008   8081  Z= 0.283
  Chirality :  0.045   0.176    947
  Planarity :  0.003   0.032   1020
  Dihedral  :  5.432  58.602   1170
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 13.76 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.31), residues: 734
  helix:  1.26 (0.47), residues: 129
  sheet: -0.97 (0.36), residues: 197
  loop : -1.01 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 121 
 HIS   0.003   0.001   HIS B 263 
 PHE   0.012   0.001   PHE B 264 
 TYR   0.015   0.001   TYR B 325 
 ARG   0.005   0.000   ARG C  35 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00368 (    8)
  link_NAG-ASN         : angle       1.27297 (   24)
  link_ALPHA1-6        : bond        0.00164 (    1)
  link_ALPHA1-6        : angle       1.96393 (    3)
  link_BETA1-4         : bond        0.00849 (    6)
  link_BETA1-4         : angle       2.12247 (   18)
  link_ALPHA1-3        : bond        0.01358 (    2)
  link_ALPHA1-3        : angle       2.89270 (    6)
  hydrogen bonds       : bond        0.03471 (  200)
  hydrogen bonds       : angle       5.39926 (  522)
  link_BETA1-6         : bond        0.00751 (    1)
  link_BETA1-6         : angle       1.40504 (    3)
  SS BOND              : bond        0.00313 (    5)
  SS BOND              : angle       0.59735 (   10)
  covalent geometry    : bond        0.00380 ( 5883)
  covalent geometry    : angle       0.57601 ( 8017)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 54
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8016 (mtm180)
REVERT: A  211 ASN cc_start: 0.8118 (t0) cc_final: 0.7729 (t0)
REVERT: A  284 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.8204 (m-80)
REVERT: A  342 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8381 (mm)
REVERT: B  154 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7703 (ttm110)
REVERT: B  173 MET cc_start: 0.8496 (tpp) cc_final: 0.8206 (tpp)
REVERT: B  327 GLU cc_start: 0.8647 (tp30) cc_final: 0.8114 (tp30)
REVERT: C   32 ARG cc_start: 0.8611 (ttt-90) cc_final: 0.7884 (tpt-90)
REVERT: C   35 ARG cc_start: 0.8114 (ttm110) cc_final: 0.7819 (ttp-110)
REVERT: C   49 GLU cc_start: 0.8967 (tp30) cc_final: 0.8642 (tp30)
REVERT: C   56 LYS cc_start: 0.8693 (tppp) cc_final: 0.8489 (tppt)
  outliers start: 24
  outliers final: 16
  residues processed: 71
  average time/residue: 0.2188
  time to fit residues: 19.6987
Evaluate side-chains
  73 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 GLN
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain B residue  154 ARG
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   40 LYS
Chi-restraints excluded: chain C residue   47 ILE
Chi-restraints excluded: chain C residue   61 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 13 optimal weight:    0.0970
   chunk 64 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 73 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 301 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.082164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.068041 restraints weight = 12926.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.2916 rms_B_bonded: 3.06
r_work: 0.2812 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.1600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5906  Z= 0.140
  Angle     :  0.575   8.803   8081  Z= 0.276
  Chirality :  0.044   0.181    947
  Planarity :  0.003   0.032   1020
  Dihedral  :  5.249  58.750   1170
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 14.11 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.31), residues: 734
  helix:  1.32 (0.47), residues: 129
  sheet: -0.95 (0.36), residues: 197
  loop : -0.96 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 121 
 HIS   0.002   0.001   HIS B 263 
 PHE   0.010   0.001   PHE B 264 
 TYR   0.015   0.001   TYR B 325 
 ARG   0.004   0.000   ARG C  35 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00350 (    8)
  link_NAG-ASN         : angle       1.15657 (   24)
  link_ALPHA1-6        : bond        0.00099 (    1)
  link_ALPHA1-6        : angle       1.88704 (    3)
  link_BETA1-4         : bond        0.00836 (    6)
  link_BETA1-4         : angle       2.04960 (   18)
  link_ALPHA1-3        : bond        0.01087 (    2)
  link_ALPHA1-3        : angle       2.51435 (    6)
  hydrogen bonds       : bond        0.03293 (  200)
  hydrogen bonds       : angle       5.38059 (  522)
  link_BETA1-6         : bond        0.00764 (    1)
  link_BETA1-6         : angle       1.33159 (    3)
  SS BOND              : bond        0.00273 (    5)
  SS BOND              : angle       0.52668 (   10)
  covalent geometry    : bond        0.00327 ( 5883)
  covalent geometry    : angle       0.55941 ( 8017)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 52
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8001 (mtm180)
REVERT: A  122 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8092 (ttt90)
REVERT: A  211 ASN cc_start: 0.8159 (t0) cc_final: 0.7781 (t0)
REVERT: A  284 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.8136 (m-80)
REVERT: A  342 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8306 (mm)
REVERT: B  121 TYR cc_start: 0.7859 (m-10) cc_final: 0.7622 (m-10)
REVERT: B  173 MET cc_start: 0.8454 (tpp) cc_final: 0.8155 (tpp)
REVERT: B  327 GLU cc_start: 0.8702 (tp30) cc_final: 0.8133 (tp30)
REVERT: C   17 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8021 (mp0)
REVERT: C   32 ARG cc_start: 0.8630 (ttt-90) cc_final: 0.7860 (tpt-90)
REVERT: C   34 HIS cc_start: 0.7397 (t-170) cc_final: 0.7056 (t-170)
REVERT: C   35 ARG cc_start: 0.7980 (ttm110) cc_final: 0.7483 (ttp-110)
REVERT: C   49 GLU cc_start: 0.9020 (tp30) cc_final: 0.8708 (tp30)
REVERT: C   56 LYS cc_start: 0.8673 (tppp) cc_final: 0.8471 (tppt)
  outliers start: 22
  outliers final: 16
  residues processed: 68
  average time/residue: 0.2221
  time to fit residues: 19.3393
Evaluate side-chains
  71 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 51
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 GLN
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   40 LYS
Chi-restraints excluded: chain C residue   47 ILE
Chi-restraints excluded: chain C residue   61 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 53 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 66 optimal weight:    0.5980
   chunk 54 optimal weight:    0.0970
   chunk 10 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 47 optimal weight:    0.2980
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
B 301 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.083450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.069352 restraints weight = 12976.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.2940 rms_B_bonded: 3.07
r_work: 0.2836 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5906  Z= 0.111
  Angle     :  0.551   8.495   8081  Z= 0.265
  Chirality :  0.044   0.249    947
  Planarity :  0.003   0.032   1020
  Dihedral  :  5.068  59.508   1170
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 14.29 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.31), residues: 734
  helix:  1.15 (0.47), residues: 135
  sheet: -0.93 (0.36), residues: 198
  loop : -0.97 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 121 
 HIS   0.002   0.000   HIS B 263 
 PHE   0.009   0.001   PHE B 264 
 TYR   0.015   0.001   TYR B 325 
 ARG   0.004   0.000   ARG C  35 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00347 (    8)
  link_NAG-ASN         : angle       1.09235 (   24)
  link_ALPHA1-6        : bond        0.00161 (    1)
  link_ALPHA1-6        : angle       1.87079 (    3)
  link_BETA1-4         : bond        0.00856 (    6)
  link_BETA1-4         : angle       2.00565 (   18)
  link_ALPHA1-3        : bond        0.00960 (    2)
  link_ALPHA1-3        : angle       2.12497 (    6)
  hydrogen bonds       : bond        0.03043 (  200)
  hydrogen bonds       : angle       5.25374 (  522)
  link_BETA1-6         : bond        0.00750 (    1)
  link_BETA1-6         : angle       1.21127 (    3)
  SS BOND              : bond        0.00230 (    5)
  SS BOND              : angle       0.47647 (   10)
  covalent geometry    : bond        0.00255 ( 5883)
  covalent geometry    : angle       0.53627 ( 8017)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 56
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8069 (mtm180)
REVERT: A  122 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8061 (ttt90)
REVERT: A  211 ASN cc_start: 0.8181 (t0) cc_final: 0.7835 (t0)
REVERT: A  284 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.8115 (m-80)
REVERT: A  342 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8372 (mm)
REVERT: B  121 TYR cc_start: 0.7822 (m-10) cc_final: 0.7584 (m-10)
REVERT: B  173 MET cc_start: 0.8432 (tpp) cc_final: 0.8143 (tpp)
REVERT: C   32 ARG cc_start: 0.8538 (ttt-90) cc_final: 0.7848 (tpt-90)
REVERT: C   34 HIS cc_start: 0.7384 (t-170) cc_final: 0.7051 (t-170)
REVERT: C   35 ARG cc_start: 0.7997 (ttm110) cc_final: 0.7502 (ttp-110)
REVERT: C   49 GLU cc_start: 0.9021 (tp30) cc_final: 0.8710 (tp30)
REVERT: C   56 LYS cc_start: 0.8598 (tppp) cc_final: 0.8396 (tppt)
  outliers start: 22
  outliers final: 14
  residues processed: 71
  average time/residue: 0.2131
  time to fit residues: 19.5431
Evaluate side-chains
  69 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 51
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 GLN
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  284 TYR
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   61 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 63 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
B 301 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.080747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.066729 restraints weight = 13044.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.2885 rms_B_bonded: 3.02
r_work: 0.2781 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.1736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   5906  Z= 0.228
  Angle     :  0.640   9.411   8081  Z= 0.310
  Chirality :  0.046   0.218    947
  Planarity :  0.004   0.038   1020
  Dihedral  :  5.346  58.432   1170
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 14.64 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.31), residues: 734
  helix:  0.97 (0.47), residues: 135
  sheet: -1.05 (0.34), residues: 211
  loop : -1.07 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 188 
 HIS   0.003   0.001   HIS B 263 
 PHE   0.014   0.002   PHE A  19 
 TYR   0.016   0.001   TYR B 325 
 ARG   0.004   0.000   ARG C  35 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00410 (    8)
  link_NAG-ASN         : angle       1.42441 (   24)
  link_ALPHA1-6        : bond        0.00110 (    1)
  link_ALPHA1-6        : angle       2.21909 (    3)
  link_BETA1-4         : bond        0.00750 (    6)
  link_BETA1-4         : angle       2.17512 (   18)
  link_ALPHA1-3        : bond        0.00541 (    2)
  link_ALPHA1-3        : angle       2.35962 (    6)
  hydrogen bonds       : bond        0.03755 (  200)
  hydrogen bonds       : angle       5.52892 (  522)
  link_BETA1-6         : bond        0.00757 (    1)
  link_BETA1-6         : angle       1.54093 (    3)
  SS BOND              : bond        0.00376 (    5)
  SS BOND              : angle       0.66946 (   10)
  covalent geometry    : bond        0.00538 ( 5883)
  covalent geometry    : angle       0.62300 ( 8017)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2903.39 seconds
wall clock time: 51 minutes 25.77 seconds (3085.77 seconds total)