Starting phenix.real_space_refine
on Mon May 12 09:18:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g5b_29738/05_2025/8g5b_29738.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g5b_29738/05_2025/8g5b_29738.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g5b_29738/05_2025/8g5b_29738.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g5b_29738/05_2025/8g5b_29738.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g5b_29738/05_2025/8g5b_29738.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g5b_29738/05_2025/8g5b_29738.cif"
  }
  resolution = 3.1
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     C    5682      2.51       5
     N    1503      2.21       5
     O    1783      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9009
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2100
          Classifications: {'peptide': 270}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 252}
    Chain: "H"
      Number of atoms: 947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 947
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 3, 'TRANS': 117}
    Chain: "I"
      Number of atoms: 1639
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1639
          Classifications: {'peptide': 221}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208}
    Chain: "J"
      Number of atoms: 1012
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 1012
          Classifications: {'peptide': 131}
          Link IDs: {'PTRANS': 4, 'TRANS': 126}
    Chain: "L"
      Number of atoms: 861
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 861
          Classifications: {'peptide': 112}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 106}
    Chain: "M"
      Number of atoms: 1647
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1647
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201}
    Chain: "N"
      Number of atoms: 775
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 775
          Classifications: {'peptide': 103}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 97}
    Chain: "A"
      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
  Residues with excluded nonbonded symmetry interactions: 8
    residue:
      pdb=" N   VAL A  78 " occ=0.43
      ... (5 atoms not shown)
      pdb=" CG2 VAL A  78 " occ=0.43
    residue:
      pdb=" N   ARG A 207 " occ=0.48
      ... (9 atoms not shown)
      pdb=" NH2 ARG A 207 " occ=0.48
    residue:
      pdb=" N   SER A 227 " occ=0.54
      ... (4 atoms not shown)
      pdb=" OG  SER A 227 " occ=0.54
    residue:
      pdb=" N   SER A 228 " occ=0.54
      ... (4 atoms not shown)
      pdb=" OG  SER A 228 " occ=0.54
    residue:
      pdb=" N   TRP A 234 " occ=0.52
      ... (12 atoms not shown)
      pdb=" CH2 TRP A 234 " occ=0.52
    residue:
      pdb=" N   MET A 260 " occ=0.50
      ... (6 atoms not shown)
      pdb=" CE  MET A 260 " occ=0.50
    residue:
      pdb=" N   ILE A 274 " occ=0.62
      ... (6 atoms not shown)
      pdb=" CD1 ILE A 274 " occ=0.62
    residue:
      pdb=" N   ASP A 275 " occ=0.62
      ... (6 atoms not shown)
      pdb=" OD2 ASP A 275 " occ=0.62
  Time building chain proxies: 5.39, per 1000 atoms: 0.60
  Number of scatterers: 9009
  At special positions: 0
  Unit cell: (94.875, 123.75, 136.95, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      41     16.00
     O    1783      8.00
     N    1503      7.00
     C    5682      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  52 " - pdb=" SG  CYS A 277 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  64 " - pdb=" SG  CYS A  76 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  97 " - pdb=" SG  CYS A 139 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 281 " - pdb=" SG  CYS A 305 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  22 " - pdb=" SG  CYS I  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 144 " - pdb=" SG  CYS I 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  22 " - pdb=" SG  CYS J  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  23 " - pdb=" SG  CYS M  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS M 134 " - pdb=" SG  CYS M 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  23 " - pdb=" SG  CYS N  88 " 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
    NAG-ASN
      " NAG A 401 " - " ASN A 165 "
      " NAG A 402 " - " ASN A 285 "
  Time building additional restraints: 2.14
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2134

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 32 sheets defined
      9.7% alpha, 46.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 72
    Processing helix  chain 'A' and resid 73 through 77
      removed outlier: 3.735A  pdb=" N   ASP A  77 " --> pdb=" O   PRO A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 116
    Processing helix  chain 'A' and resid 187 through 195
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 62 through 65
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'I' and resid 28 through 32
      removed outlier: 3.711A  pdb=" N   TYR I  32 " --> pdb=" O   PHE I  29 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 62 through 65
    Processing helix  chain 'I' and resid 84 through 88
    Processing helix  chain 'I' and resid 97 through 101
    Processing helix  chain 'I' and resid 160 through 162
      No H-bonds generated for 'chain 'I' and resid 160 through 162'
    Processing helix  chain 'I' and resid 191 through 196
      removed outlier: 3.983A  pdb=" N   THR I 195 " --> pdb=" O   SER I 191 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 205 through 208
    Processing helix  chain 'J' and resid 88 through 92
    Processing helix  chain 'L' and resid 84 through 88
      removed outlier: 3.877A  pdb=" N   VAL L  88 " --> pdb=" O   ALA L  85 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 79 through 83
      removed outlier: 3.970A  pdb=" N   PHE M  83 " --> pdb=" O   PRO M  80 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 121 through 127
      removed outlier: 3.636A  pdb=" N   SER M 127 " --> pdb=" O   GLU M 123 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 183 through 188
    Processing helix  chain 'N' and resid 79 through 83
      removed outlier: 3.680A  pdb=" N   PHE N  83 " --> pdb=" O   PRO N  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 44
    Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 54
      removed outlier: 7.081A  pdb=" N   CYS A 277 " --> pdb=" O   ASN A  53 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 61
    Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 101
      removed outlier: 4.785A  pdb=" N   ILE A 179 " --> pdb=" O   GLY A 256 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   GLY A 256 " --> pdb=" O   ILE A 179 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 100 through 101
      removed outlier: 7.722A  pdb=" N   ILE A 179 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 130 through 131
    Processing sheet with id=AA7, first strand: chain 'A' and resid 164 through 169
      removed outlier: 5.109A  pdb=" N   ARG A 201 " --> pdb=" O   ASN A 248 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 286 through 287
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.287A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 117 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   MET H  34 " --> pdb=" O   GLU H  50 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   GLU H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.287A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 117 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   CYS H  96 " --> pdb=" O   TRP H 110 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   TRP H 110 " --> pdb=" O   CYS H  96 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   ARG H  98 " --> pdb=" O   ASP H 108 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'I' and resid 3 through 6
    Processing sheet with id=AB4, first strand: chain 'I' and resid 10 through 12
      removed outlier: 6.280A  pdb=" N   ILE I  34 " --> pdb=" O   GLU I  50 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLU I  50 " --> pdb=" O   ILE I  34 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   TRP I  36 " --> pdb=" O   ILE I  48 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ARG I  40 " --> pdb=" O   GLY I  44 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLY I  44 " --> pdb=" O   ARG I  40 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   SER I  57 " --> pdb=" O   LEU I  52 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'I' and resid 10 through 12
      removed outlier: 3.845A  pdb=" N   TYR I 106 " --> pdb=" O   ARG I  95 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'I' and resid 124 through 128
      removed outlier: 6.016A  pdb=" N   TYR I 180 " --> pdb=" O   ASP I 148 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'I' and resid 124 through 128
      removed outlier: 6.016A  pdb=" N   TYR I 180 " --> pdb=" O   ASP I 148 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'I' and resid 155 through 158
      removed outlier: 3.923A  pdb=" N   TYR I 198 " --> pdb=" O   VAL I 215 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'J' and resid 3 through 7
    Processing sheet with id=AC1, first strand: chain 'J' and resid 11 through 12
      removed outlier: 6.209A  pdb=" N   TRP J  36 " --> pdb=" O   TYR J  52 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   TYR J  52 " --> pdb=" O   TRP J  36 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   TRP J  38 " --> pdb=" O   LEU J  50 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   THR J  42 " --> pdb=" O   GLY J  46 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'J' and resid 11 through 12
      removed outlier: 6.686A  pdb=" N   CYS J  97 " --> pdb=" O   TRP J 120 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   TRP J 120 " --> pdb=" O   CYS J  97 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ARG J  99 " --> pdb=" O   ASP J 118 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 5
    Processing sheet with id=AC4, first strand: chain 'L' and resid 11 through 12
      removed outlier: 5.429A  pdb=" N   ASN L  11 " --> pdb=" O   GLU L 110 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   LEU L  42 " --> pdb=" O   LEU L  51 " (cutoff:3.500A)
      removed outlier: 5.531A  pdb=" N   LEU L  51 " --> pdb=" O   LEU L  42 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'L' and resid 11 through 12
      removed outlier: 5.429A  pdb=" N   ASN L  11 " --> pdb=" O   GLU L 110 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'M' and resid 4 through 7
      removed outlier: 3.841A  pdb=" N   ASP M  70 " --> pdb=" O   SER M  67 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'M' and resid 10 through 13
      removed outlier: 6.147A  pdb=" N   LEU M  33 " --> pdb=" O   TYR M  49 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   TYR M  49 " --> pdb=" O   LEU M  33 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   TRP M  35 " --> pdb=" O   LEU M  47 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'M' and resid 10 through 13
      removed outlier: 4.004A  pdb=" N   THR M  97 " --> pdb=" O   GLN M  90 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'M' and resid 114 through 118
      removed outlier: 5.661A  pdb=" N   TYR M 173 " --> pdb=" O   ASN M 138 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'M' and resid 153 through 155
      removed outlier: 4.323A  pdb=" N   TRP M 148 " --> pdb=" O   GLN M 155 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'N' and resid 4 through 7
      removed outlier: 3.828A  pdb=" N   ASP N  70 " --> pdb=" O   SER N  67 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'N' and resid 12 through 13
    Processing sheet with id=AD4, first strand: chain 'N' and resid 53 through 54
      removed outlier: 6.425A  pdb=" N   TRP N  35 " --> pdb=" O   LEU N  47 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'N' and resid 53 through 54
      removed outlier: 6.425A  pdb=" N   TRP N  35 " --> pdb=" O   LEU N  47 " (cutoff:3.500A)

    416 hydrogen bonds defined for protein.
    993 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.85

  Time building geometry restraints manager: 2.51 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2842
        1.34 -     1.46: 2359
        1.46 -     1.59: 3964
        1.59 -     1.71: 0
        1.71 -     1.84: 58
  Bond restraints: 9223
  Sorted by residual:
  bond pdb=" N   VAL L  13 "
       pdb=" CA  VAL L  13 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.77e+00
  bond pdb=" N   ILE A 182 "
       pdb=" CA  ILE A 182 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.035 1.29e-02 6.01e+03 7.52e+00
  bond pdb=" N   ILE M  21 "
       pdb=" CA  ILE M  21 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.24e-02 6.50e+03 7.45e+00
  bond pdb=" N   THR L   5 "
       pdb=" CA  THR L   5 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.21e-02 6.83e+03 6.79e+00
  bond pdb=" N   GLU J 103 "
       pdb=" CA  GLU J 103 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.032 1.27e-02 6.20e+03 6.39e+00
  ... (remaining 9218 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 12275
        1.89 -     3.79: 232
        3.79 -     5.68: 23
        5.68 -     7.58: 1
        7.58 -     9.47: 1
  Bond angle restraints: 12532
  Sorted by residual:
  angle pdb=" C   GLU M  93 "
        pdb=" CA  GLU M  93 "
        pdb=" CB  GLU M  93 "
      ideal   model   delta    sigma   weight residual
     112.99  103.52    9.47 2.10e+00 2.27e-01 2.03e+01
  angle pdb=" C   ASP M 151 "
        pdb=" CA  ASP M 151 "
        pdb=" CB  ASP M 151 "
      ideal   model   delta    sigma   weight residual
     115.79  111.19    4.60 1.19e+00 7.06e-01 1.50e+01
  angle pdb=" N   PRO M  95 "
        pdb=" CA  PRO M  95 "
        pdb=" CB  PRO M  95 "
      ideal   model   delta    sigma   weight residual
     103.25  107.09   -3.84 1.05e+00 9.07e-01 1.34e+01
  angle pdb=" CA  PRO M  95 "
        pdb=" N   PRO M  95 "
        pdb=" CD  PRO M  95 "
      ideal   model   delta    sigma   weight residual
     112.00  107.29    4.71 1.40e+00 5.10e-01 1.13e+01
  angle pdb=" CA  GLU M  93 "
        pdb=" C   GLU M  93 "
        pdb=" O   GLU M  93 "
      ideal   model   delta    sigma   weight residual
     121.98  118.40    3.58 1.13e+00 7.83e-01 1.00e+01
  ... (remaining 12527 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 5063
       17.66 -    35.33: 313
       35.33 -    52.99: 89
       52.99 -    70.65: 16
       70.65 -    88.31: 16
  Dihedral angle restraints: 5497
    sinusoidal: 2139
      harmonic: 3358
  Sorted by residual:
  dihedral pdb=" CB  CYS A 281 "
           pdb=" SG  CYS A 281 "
           pdb=" SG  CYS A 305 "
           pdb=" CB  CYS A 305 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   25.88   67.12     1      1.00e+01 1.00e-02 5.87e+01
  dihedral pdb=" CB  CYS J  22 "
           pdb=" SG  CYS J  22 "
           pdb=" SG  CYS J  97 "
           pdb=" CB  CYS J  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   46.98   46.02     1      1.00e+01 1.00e-02 2.93e+01
  dihedral pdb=" CB  CYS M 134 "
           pdb=" SG  CYS M 134 "
           pdb=" SG  CYS M 194 "
           pdb=" CB  CYS M 194 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.11   37.89     1      1.00e+01 1.00e-02 2.02e+01
  ... (remaining 5494 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 1249
       0.081 -    0.162: 135
       0.162 -    0.243: 4
       0.243 -    0.324: 0
       0.324 -    0.405: 2
  Chirality restraints: 1390
  Sorted by residual:
  chirality pdb=" CA  GLU M  93 "
            pdb=" N   GLU M  93 "
            pdb=" C   GLU M  93 "
            pdb=" CB  GLU M  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.92   -0.41 2.00e-01 2.50e+01 4.11e+00
  chirality pdb=" CA  TYR M  94 "
            pdb=" N   TYR M  94 "
            pdb=" C   TYR M  94 "
            pdb=" CB  TYR M  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.91e+00
  chirality pdb=" CA  ILE A 182 "
            pdb=" N   ILE A 182 "
            pdb=" C   ILE A 182 "
            pdb=" CB  ILE A 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 1387 not shown)

  Planarity restraints: 1599
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR M  94 "   -0.067 5.00e-02 4.00e+02   9.85e-02 1.55e+01
        pdb=" N   PRO M  95 "    0.170 5.00e-02 4.00e+02
        pdb=" CA  PRO M  95 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO M  95 "   -0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 292 "    0.065 5.00e-02 4.00e+02   9.74e-02 1.52e+01
        pdb=" N   PRO A 293 "   -0.168 5.00e-02 4.00e+02
        pdb=" CA  PRO A 293 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO A 293 "    0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN L  11 "   -0.058 5.00e-02 4.00e+02   8.71e-02 1.21e+01
        pdb=" N   PRO L  12 "    0.151 5.00e-02 4.00e+02
        pdb=" CA  PRO L  12 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO L  12 "   -0.046 5.00e-02 4.00e+02
  ... (remaining 1596 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1074
        2.75 -     3.28: 8684
        3.28 -     3.82: 14851
        3.82 -     4.36: 18597
        4.36 -     4.90: 32730
  Nonbonded interactions: 75936
  Sorted by model distance:
  nonbonded pdb=" O   SER H   7 "
            pdb=" OG1 THR H 114 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OH  TYR A  98 "
            pdb=" OG  SER A 228 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OE2 GLU M 195 "
            pdb=" OG1 THR M 206 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   GLU M 187 "
            pdb=" NH2 ARG M 211 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" O   PRO J  14 "
            pdb=" OG  SER J  15 "
     model   vdw
     2.289 3.040
  ... (remaining 75931 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             0.670
  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:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.120
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
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      :  0.006   0.042   9237  Z= 0.289
  Angle     :  0.630   9.473  12562  Z= 0.365
  Chirality :  0.047   0.405   1390
  Planarity :  0.005   0.098   1597
  Dihedral  : 13.651  88.313   3327
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  0.80 %
    Favored  : 98.50 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 12.28 %
    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:  0.40 (0.25), residues: 1157
  helix:  0.62 (0.79), residues: 42
  sheet:  0.43 (0.23), residues: 506
  loop :  0.23 (0.27), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP I  47 
 HIS   0.004   0.001   HIS M  91 
 PHE   0.017   0.001   PHE N  46 
 TYR   0.020   0.002   TYR J  35 
 ARG   0.005   0.001   ARG M 211 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00147 (    2)
  link_NAG-ASN         : angle       1.28851 (    6)
  hydrogen bonds       : bond        0.21289 (  355)
  hydrogen bonds       : angle       9.34750 (  993)
  SS BOND              : bond        0.00308 (   12)
  SS BOND              : angle       1.16081 (   24)
  covalent geometry    : bond        0.00589 ( 9223)
  covalent geometry    : angle       0.62826 (12532)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 193
  time to evaluate  : 0.934 
Fit side-chains
REVERT: A  110 SER cc_start: 0.8084 (t) cc_final: 0.7518 (m)
REVERT: A  140 LYS cc_start: 0.7826 (mmtm) cc_final: 0.7234 (mmtt)
REVERT: H   23 LYS cc_start: 0.7968 (tptp) cc_final: 0.7725 (tptt)
REVERT: H   34 MET cc_start: 0.8098 (mmm) cc_final: 0.7830 (tpp)
REVERT: H   46 GLU cc_start: 0.8032 (tt0) cc_final: 0.7708 (tt0)
REVERT: H   65 LYS cc_start: 0.8094 (ttpt) cc_final: 0.7742 (ttmt)
REVERT: I    3 GLN cc_start: 0.8187 (pt0) cc_final: 0.7929 (pt0)
REVERT: I    5 GLN cc_start: 0.7847 (tp40) cc_final: 0.7620 (tp40)
REVERT: I   23 LYS cc_start: 0.8014 (ttmt) cc_final: 0.7778 (tttm)
REVERT: I   65 LYS cc_start: 0.8029 (tppt) cc_final: 0.7635 (tptp)
REVERT: I  210 LYS cc_start: 0.7970 (tttp) cc_final: 0.7494 (ttpt)
REVERT: I  213 LYS cc_start: 0.6977 (tptt) cc_final: 0.6695 (tptt)
REVERT: J   25 SER cc_start: 0.7840 (m) cc_final: 0.7482 (p)
REVERT: J   45 LYS cc_start: 0.8383 (mttp) cc_final: 0.7722 (mtpt)
REVERT: J   91 ASP cc_start: 0.8500 (m-30) cc_final: 0.8156 (m-30)
REVERT: L   27 LYS cc_start: 0.7577 (ttmt) cc_final: 0.6781 (tttm)
REVERT: L   75 ASP cc_start: 0.6888 (p0) cc_final: 0.6419 (m-30)
REVERT: M   77 SER cc_start: 0.8093 (p) cc_final: 0.7883 (t)
REVERT: M  165 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6925 (mm-30)
REVERT: M  183 LYS cc_start: 0.7558 (tttm) cc_final: 0.7349 (tttt)
REVERT: N   65 SER cc_start: 0.8367 (t) cc_final: 0.8082 (m)
REVERT: N   96 GLN cc_start: 0.8220 (mp10) cc_final: 0.7819 (mp10)
  outliers start: 7
  outliers final: 2
  residues processed: 198
  average time/residue: 0.2196
  time to fit residues: 58.6851
Evaluate side-chains
  142 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 140
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain M residue   93 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    5.9990
   chunk 87 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 59 optimal weight:    8.9990
   chunk 46 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:    7.9990
   chunk 67 optimal weight:    0.8980
   chunk 105 optimal weight:    7.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
A  80 GLN
A 189 GLN
H  62 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.141439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.103074 restraints weight = 10515.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 2.19
r_work: 0.2736 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2598 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2529
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2529 r_free = 0.2529    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2515 r_free = 0.2515    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2515
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.1375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9237  Z= 0.212
  Angle     :  0.643   8.084  12562  Z= 0.338
  Chirality :  0.047   0.206   1390
  Planarity :  0.005   0.073   1597
  Dihedral  :  5.778  50.469   1308
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  7.49 %
    Favored  : 90.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.28 %
    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:  0.42 (0.25), residues: 1157
  helix:  0.80 (0.76), residues: 43
  sheet:  0.47 (0.22), residues: 515
  loop :  0.20 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP J  36 
 HIS   0.006   0.001   HIS H  35 
 PHE   0.016   0.002   PHE N  46 
 TYR   0.037   0.002   TYR J  35 
 ARG   0.003   0.001   ARG J  99 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00190 (    2)
  link_NAG-ASN         : angle       1.30348 (    6)
  hydrogen bonds       : bond        0.03942 (  355)
  hydrogen bonds       : angle       6.51890 (  993)
  SS BOND              : bond        0.00525 (   12)
  SS BOND              : angle       1.49087 (   24)
  covalent geometry    : bond        0.00496 ( 9223)
  covalent geometry    : angle       0.64018 (12532)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 146
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
REVERT: A  104 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7514 (m-30)
REVERT: A  241 ASP cc_start: 0.8311 (t0) cc_final: 0.7885 (t70)
REVERT: H   23 LYS cc_start: 0.8334 (tptp) cc_final: 0.8104 (tptt)
REVERT: H   31 ARG cc_start: 0.8183 (mtm180) cc_final: 0.7848 (mtt180)
REVERT: H   34 MET cc_start: 0.8637 (mmm) cc_final: 0.8427 (tpp)
REVERT: H   46 GLU cc_start: 0.8580 (tt0) cc_final: 0.8369 (tt0)
REVERT: H   65 LYS cc_start: 0.8354 (ttpt) cc_final: 0.8118 (tttt)
REVERT: H   80 TYR cc_start: 0.8338 (m-80) cc_final: 0.7978 (m-80)
REVERT: I   65 LYS cc_start: 0.8151 (tppt) cc_final: 0.7750 (tptp)
REVERT: L   27 LYS cc_start: 0.7902 (ttmt) cc_final: 0.7306 (tttm)
REVERT: L   55 GLN cc_start: 0.7963 (mt0) cc_final: 0.7704 (mt0)
REVERT: L   65 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.6823 (m-30)
REVERT: L   66 ARG cc_start: 0.7065 (mtm-85) cc_final: 0.6789 (mtm110)
REVERT: M   77 SER cc_start: 0.8405 (p) cc_final: 0.8187 (t)
REVERT: M  133 VAL cc_start: 0.7993 (OUTLIER) cc_final: 0.7764 (t)
REVERT: M  160 GLN cc_start: 0.7049 (mm-40) cc_final: 0.6741 (mm-40)
REVERT: M  165 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7210 (mm-30)
REVERT: N   65 SER cc_start: 0.8515 (t) cc_final: 0.8193 (m)
  outliers start: 16
  outliers final: 7
  residues processed: 154
  average time/residue: 0.2020
  time to fit residues: 44.0491
Evaluate side-chains
  146 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 136
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue   65 ASP
Chi-restraints excluded: chain M residue  133 VAL
Chi-restraints excluded: chain N residue    5 THR
Chi-restraints excluded: chain N residue   19 VAL
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   74 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 105 optimal weight:    0.1980
   chunk 47 optimal weight:    5.9990
   chunk 101 optimal weight:    0.9980
   chunk 80 optimal weight:    9.9990
   chunk 88 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 74 optimal weight:   10.0000
   chunk 65 optimal weight:    5.9990
   chunk 59 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    2.1984

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

Flipped N/Q/H residues before XYZ refinement:
A  80 GLN
I 109 GLN
** I 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  50 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.136134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.097985 restraints weight = 10690.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.2957 rms_B_bonded: 2.85
r_work: 0.2655 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2515 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2515
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2506
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2506 r_free = 0.2506    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2505 r_free = 0.2505    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2505
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9237  Z= 0.196
  Angle     :  0.597   7.049  12562  Z= 0.312
  Chirality :  0.045   0.177   1390
  Planarity :  0.005   0.062   1597
  Dihedral  :  5.192  49.738   1305
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  :  9.69 %
    Favored  : 87.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.25), residues: 1157
  helix:  0.93 (0.78), residues: 44
  sheet:  0.55 (0.22), residues: 509
  loop :  0.12 (0.26), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP J  36 
 HIS   0.005   0.001   HIS M  91 
 PHE   0.012   0.002   PHE N  46 
 TYR   0.026   0.002   TYR J  35 
 ARG   0.003   0.000   ARG H  40 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00188 (    2)
  link_NAG-ASN         : angle       1.08165 (    6)
  hydrogen bonds       : bond        0.03639 (  355)
  hydrogen bonds       : angle       6.04118 (  993)
  SS BOND              : bond        0.00553 (   12)
  SS BOND              : angle       1.35437 (   24)
  covalent geometry    : bond        0.00457 ( 9223)
  covalent geometry    : angle       0.59383 (12532)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 130
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
REVERT: A  123 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8563 (mt-10)
REVERT: A  168 MET cc_start: 0.8166 (mmp) cc_final: 0.7615 (mmt)
REVERT: H   31 ARG cc_start: 0.8114 (mtm180) cc_final: 0.7758 (mtt180)
REVERT: I   65 LYS cc_start: 0.8092 (tppt) cc_final: 0.7651 (tptp)
REVERT: L   27 LYS cc_start: 0.7859 (ttmt) cc_final: 0.7247 (tttm)
REVERT: L   55 GLN cc_start: 0.7999 (mt0) cc_final: 0.7732 (mt0)
REVERT: L   65 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.6688 (m-30)
REVERT: L   66 ARG cc_start: 0.7014 (mtm-85) cc_final: 0.6797 (mtm110)
REVERT: M  133 VAL cc_start: 0.7879 (OUTLIER) cc_final: 0.7625 (t)
REVERT: M  160 GLN cc_start: 0.6965 (mm-40) cc_final: 0.6649 (mm-40)
REVERT: M  195 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7032 (mm-30)
REVERT: N   65 SER cc_start: 0.8497 (t) cc_final: 0.8162 (m)
  outliers start: 30
  outliers final: 24
  residues processed: 149
  average time/residue: 0.2014
  time to fit residues: 42.1617
Evaluate side-chains
  157 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  210 GLN
Chi-restraints excluded: chain A residue  270 SER
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain I residue  109 GLN
Chi-restraints excluded: chain J residue    7 SER
Chi-restraints excluded: chain J residue   42 THR
Chi-restraints excluded: chain J residue  110 VAL
Chi-restraints excluded: chain J residue  111 ILE
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   65 ASP
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain M residue   20 THR
Chi-restraints excluded: chain M residue   97 THR
Chi-restraints excluded: chain M residue  133 VAL
Chi-restraints excluded: chain M residue  135 LEU
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue    5 THR
Chi-restraints excluded: chain N residue   19 VAL
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain N residue   93 THR
Chi-restraints excluded: chain N residue  100 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 73 optimal weight:    0.5980
   chunk 98 optimal weight:    0.9990
   chunk 1 optimal weight:    6.9990
   chunk 2 optimal weight:    8.9990
   chunk 113 optimal weight:    5.9990
   chunk 81 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
A  80 GLN
I 109 GLN
** I 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  50 GLN
M 137 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.138372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.099164 restraints weight = 10571.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 2.65
r_work: 0.2686 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2540 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2540
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2508
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2508 r_free = 0.2508    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2508 r_free = 0.2508    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2508
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9237  Z= 0.151
  Angle     :  0.558   7.009  12562  Z= 0.291
  Chirality :  0.044   0.161   1390
  Planarity :  0.004   0.058   1597
  Dihedral  :  5.018  50.107   1303
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 11.49 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.25), residues: 1157
  helix:  0.96 (0.76), residues: 45
  sheet:  0.57 (0.22), residues: 511
  loop :  0.15 (0.26), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP J  36 
 HIS   0.004   0.001   HIS M  91 
 PHE   0.011   0.001   PHE J  80 
 TYR   0.021   0.001   TYR J  35 
 ARG   0.002   0.000   ARG H  40 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00117 (    2)
  link_NAG-ASN         : angle       0.99576 (    6)
  hydrogen bonds       : bond        0.03185 (  355)
  hydrogen bonds       : angle       5.76379 (  993)
  SS BOND              : bond        0.00378 (   12)
  SS BOND              : angle       1.21365 (   24)
  covalent geometry    : bond        0.00349 ( 9223)
  covalent geometry    : angle       0.55567 (12532)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
REVERT: A  123 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8573 (mt-10)
REVERT: A  168 MET cc_start: 0.8132 (mmp) cc_final: 0.7617 (mmt)
REVERT: A  195 TYR cc_start: 0.8942 (OUTLIER) cc_final: 0.8418 (m-80)
REVERT: A  241 ASP cc_start: 0.8320 (t0) cc_final: 0.7887 (t0)
REVERT: H   34 MET cc_start: 0.8706 (mmm) cc_final: 0.8502 (tpp)
REVERT: H   80 TYR cc_start: 0.8250 (m-80) cc_final: 0.7859 (m-80)
REVERT: I   65 LYS cc_start: 0.8089 (tppt) cc_final: 0.7676 (tptp)
REVERT: L   27 LYS cc_start: 0.7827 (ttmt) cc_final: 0.7336 (tttm)
REVERT: L   55 GLN cc_start: 0.7948 (mt0) cc_final: 0.7660 (mt0)
REVERT: L   65 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.6700 (m-30)
REVERT: M  133 VAL cc_start: 0.7912 (OUTLIER) cc_final: 0.7691 (t)
REVERT: M  160 GLN cc_start: 0.7089 (mm-40) cc_final: 0.6786 (mm-40)
REVERT: M  195 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7183 (mm-30)
REVERT: N   65 SER cc_start: 0.8458 (t) cc_final: 0.8154 (m)
  outliers start: 28
  outliers final: 16
  residues processed: 150
  average time/residue: 0.2045
  time to fit residues: 42.6847
Evaluate side-chains
  144 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  195 TYR
Chi-restraints excluded: chain A residue  210 GLN
Chi-restraints excluded: chain A residue  270 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain I residue  113 VAL
Chi-restraints excluded: chain J residue    7 SER
Chi-restraints excluded: chain J residue   87 VAL
Chi-restraints excluded: chain J residue  110 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   65 ASP
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain M residue   97 THR
Chi-restraints excluded: chain M residue  133 VAL
Chi-restraints excluded: chain M residue  135 LEU
Chi-restraints excluded: chain N residue   19 VAL
Chi-restraints excluded: chain N residue   63 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 69 optimal weight:    8.9990
   chunk 100 optimal weight:   20.0000
   chunk 115 optimal weight:    8.9990
   chunk 88 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 102 optimal weight:    0.8980
   chunk 80 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   chunk 27 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A  80 GLN
L  50 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.137215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.098033 restraints weight = 10580.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 2.38
r_work: 0.2632 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2495 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2495
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2480
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2480 r_free = 0.2480    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2480 r_free = 0.2480    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2480
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8672
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   9237  Z= 0.233
  Angle     :  0.613   7.559  12562  Z= 0.319
  Chirality :  0.046   0.184   1390
  Planarity :  0.005   0.056   1597
  Dihedral  :  5.195  50.206   1303
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 11.39 %
    Favored  : 84.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.28 %
    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:  0.35 (0.24), residues: 1157
  helix:  0.81 (0.76), residues: 45
  sheet:  0.50 (0.22), residues: 511
  loop :  0.05 (0.26), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP J  36 
 HIS   0.006   0.001   HIS M  91 
 PHE   0.012   0.002   PHE I 102 
 TYR   0.025   0.002   TYR J  35 
 ARG   0.003   0.000   ARG A 201 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00264 (    2)
  link_NAG-ASN         : angle       1.22343 (    6)
  hydrogen bonds       : bond        0.03515 (  355)
  hydrogen bonds       : angle       5.87441 (  993)
  SS BOND              : bond        0.00475 (   12)
  SS BOND              : angle       1.40554 (   24)
  covalent geometry    : bond        0.00548 ( 9223)
  covalent geometry    : angle       0.60977 (12532)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 133
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.8555 (m-80)
REVERT: H  109 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8648 (m)
REVERT: I    5 GLN cc_start: 0.8596 (tp40) cc_final: 0.8373 (tp40)
REVERT: I   65 LYS cc_start: 0.8145 (tppt) cc_final: 0.7656 (tptp)
REVERT: L   23 CYS cc_start: 0.8461 (t) cc_final: 0.7922 (t)
REVERT: L   27 LYS cc_start: 0.7978 (ttmt) cc_final: 0.7389 (tttm)
REVERT: L   55 GLN cc_start: 0.8033 (mt0) cc_final: 0.7796 (mt0)
REVERT: L   65 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.6521 (m-30)
REVERT: M  133 VAL cc_start: 0.7903 (OUTLIER) cc_final: 0.7671 (t)
REVERT: M  160 GLN cc_start: 0.7240 (mm-40) cc_final: 0.6948 (mm-40)
REVERT: M  195 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7073 (mm-30)
REVERT: N   65 SER cc_start: 0.8558 (t) cc_final: 0.8231 (m)
  outliers start: 37
  outliers final: 26
  residues processed: 158
  average time/residue: 0.2094
  time to fit residues: 45.9403
Evaluate side-chains
  157 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  195 TYR
Chi-restraints excluded: chain A residue  210 GLN
Chi-restraints excluded: chain A residue  270 SER
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  109 VAL
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain I residue   75 SER
Chi-restraints excluded: chain I residue  113 VAL
Chi-restraints excluded: chain J residue    7 SER
Chi-restraints excluded: chain J residue   42 THR
Chi-restraints excluded: chain J residue   87 VAL
Chi-restraints excluded: chain J residue  110 VAL
Chi-restraints excluded: chain J residue  111 ILE
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   65 ASP
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain M residue   97 THR
Chi-restraints excluded: chain M residue  133 VAL
Chi-restraints excluded: chain M residue  135 LEU
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue    5 THR
Chi-restraints excluded: chain N residue   19 VAL
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain N residue   93 THR
Chi-restraints excluded: chain N residue  100 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 79 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 86 optimal weight:    6.9990
   chunk 77 optimal weight:    0.0000
   chunk 99 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.6584

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

Flipped N/Q/H residues before XYZ refinement:
A  80 GLN
I  59 ASN
L  50 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.140804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.102106 restraints weight = 10473.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 2.66
r_work: 0.2743 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2604 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2604
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2567
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2567 r_free = 0.2567    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2567 r_free = 0.2567    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2567
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9237  Z= 0.101
  Angle     :  0.524   8.909  12562  Z= 0.272
  Chirality :  0.042   0.180   1390
  Planarity :  0.004   0.053   1597
  Dihedral  :  4.790  49.724   1303
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.59 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.28 %
    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:  0.51 (0.25), residues: 1157
  helix:  1.38 (0.78), residues: 45
  sheet:  0.57 (0.22), residues: 520
  loop :  0.16 (0.26), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP J  36 
 HIS   0.003   0.001   HIS J  55 
 PHE   0.012   0.001   PHE J  80 
 TYR   0.016   0.001   TYR J  35 
 ARG   0.006   0.000   ARG A 207 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00024 (    2)
  link_NAG-ASN         : angle       0.76898 (    6)
  hydrogen bonds       : bond        0.02780 (  355)
  hydrogen bonds       : angle       5.40965 (  993)
  SS BOND              : bond        0.00286 (   12)
  SS BOND              : angle       1.09267 (   24)
  covalent geometry    : bond        0.00224 ( 9223)
  covalent geometry    : angle       0.52199 (12532)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 LYS cc_start: 0.8122 (mmtm) cc_final: 0.7592 (mmtt)
REVERT: A  168 MET cc_start: 0.7911 (mmt) cc_final: 0.7577 (mmt)
REVERT: A  195 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.8309 (m-80)
REVERT: H   38 LYS cc_start: 0.8749 (tttt) cc_final: 0.8440 (tttp)
REVERT: H   80 TYR cc_start: 0.8255 (m-80) cc_final: 0.7804 (m-80)
REVERT: H  109 VAL cc_start: 0.8870 (p) cc_final: 0.8632 (m)
REVERT: I    3 GLN cc_start: 0.8548 (pt0) cc_final: 0.8314 (pt0)
REVERT: I    5 GLN cc_start: 0.8581 (tp40) cc_final: 0.8320 (tp40)
REVERT: J   45 LYS cc_start: 0.8423 (mttp) cc_final: 0.7878 (mtpt)
REVERT: J  108 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8197 (m)
REVERT: L   27 LYS cc_start: 0.7895 (ttmt) cc_final: 0.7333 (tttm)
REVERT: L   55 GLN cc_start: 0.7862 (mt0) cc_final: 0.7613 (mt0)
REVERT: L   65 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6416 (m-30)
REVERT: M  160 GLN cc_start: 0.7241 (mm-40) cc_final: 0.6911 (mm-40)
REVERT: M  195 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7205 (mm-30)
REVERT: N   65 SER cc_start: 0.8368 (t) cc_final: 0.8059 (m)
  outliers start: 20
  outliers final: 11
  residues processed: 165
  average time/residue: 0.2144
  time to fit residues: 48.6265
Evaluate side-chains
  148 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 134
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  195 TYR
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain J residue    7 SER
Chi-restraints excluded: chain J residue   42 THR
Chi-restraints excluded: chain J residue   87 VAL
Chi-restraints excluded: chain J residue  108 VAL
Chi-restraints excluded: chain J residue  110 VAL
Chi-restraints excluded: chain L residue   65 ASP
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   19 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 93 optimal weight:    0.8980
   chunk 48 optimal weight:    6.9990
   chunk 104 optimal weight:    9.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 111 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
H   5 GLN
I  59 ASN
L  50 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.139294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.100982 restraints weight = 10654.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 2.61
r_work: 0.2652 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2512 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2512
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2503
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2503 r_free = 0.2503    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2503 r_free = 0.2503    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2503
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9237  Z= 0.177
  Angle     :  0.572   8.062  12562  Z= 0.298
  Chirality :  0.044   0.183   1390
  Planarity :  0.004   0.053   1597
  Dihedral  :  4.961  50.342   1303
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 12.99 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.25), residues: 1157
  helix:  1.23 (0.77), residues: 45
  sheet:  0.56 (0.22), residues: 513
  loop :  0.13 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP L 101 
 HIS   0.005   0.001   HIS M  91 
 PHE   0.012   0.001   PHE J  80 
 TYR   0.021   0.002   TYR J  35 
 ARG   0.006   0.000   ARG A 207 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00137 (    2)
  link_NAG-ASN         : angle       1.04486 (    6)
  hydrogen bonds       : bond        0.03148 (  355)
  hydrogen bonds       : angle       5.49501 (  993)
  SS BOND              : bond        0.00394 (   12)
  SS BOND              : angle       1.77781 (   24)
  covalent geometry    : bond        0.00414 ( 9223)
  covalent geometry    : angle       0.56723 (12532)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 138
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 LYS cc_start: 0.8221 (mmtm) cc_final: 0.7662 (mmtt)
REVERT: A  168 MET cc_start: 0.8090 (mmt) cc_final: 0.7633 (mmt)
REVERT: A  195 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.8359 (m-80)
REVERT: H  109 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8651 (m)
REVERT: J  108 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8295 (m)
REVERT: L   27 LYS cc_start: 0.7922 (ttmt) cc_final: 0.7343 (tttm)
REVERT: L   55 GLN cc_start: 0.7899 (mt0) cc_final: 0.7595 (mt0)
REVERT: L   65 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6363 (m-30)
REVERT: M  160 GLN cc_start: 0.7263 (mm-40) cc_final: 0.6960 (mm-40)
REVERT: M  195 GLU cc_start: 0.7687 (mm-30) cc_final: 0.6931 (mm-30)
REVERT: N   65 SER cc_start: 0.8480 (t) cc_final: 0.8189 (m)
  outliers start: 34
  outliers final: 27
  residues processed: 162
  average time/residue: 0.2122
  time to fit residues: 47.5846
Evaluate side-chains
  163 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 132
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  195 TYR
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  270 SER
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  109 VAL
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain I residue   75 SER
Chi-restraints excluded: chain I residue  113 VAL
Chi-restraints excluded: chain J residue    7 SER
Chi-restraints excluded: chain J residue   30 SER
Chi-restraints excluded: chain J residue   42 THR
Chi-restraints excluded: chain J residue   87 VAL
Chi-restraints excluded: chain J residue  108 VAL
Chi-restraints excluded: chain J residue  110 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue    6 GLN
Chi-restraints excluded: chain L residue   65 ASP
Chi-restraints excluded: chain M residue   20 THR
Chi-restraints excluded: chain M residue   97 THR
Chi-restraints excluded: chain M residue  132 VAL
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue    4 MET
Chi-restraints excluded: chain N residue   19 VAL
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain N residue  100 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 99 optimal weight:    6.9990
   chunk 108 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 76 optimal weight:    0.8980
   chunk 27 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 52 optimal weight:   30.0000
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
L  50 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.139559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.100724 restraints weight = 10736.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 2.60
r_work: 0.2741 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2602 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2602
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2537
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2537 r_free = 0.2537    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2537 r_free = 0.2537    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2537
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9237  Z= 0.116
  Angle     :  0.535  10.364  12562  Z= 0.277
  Chirality :  0.043   0.202   1390
  Planarity :  0.004   0.051   1597
  Dihedral  :  4.795  50.240   1303
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 13.39 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.28 %
    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:  0.52 (0.25), residues: 1157
  helix:  1.37 (0.76), residues: 45
  sheet:  0.59 (0.22), residues: 521
  loop :  0.15 (0.27), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP J  36 
 HIS   0.004   0.001   HIS M  91 
 PHE   0.011   0.001   PHE J  80 
 TYR   0.016   0.001   TYR J  35 
 ARG   0.006   0.000   ARG A 207 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00087 (    2)
  link_NAG-ASN         : angle       0.79453 (    6)
  hydrogen bonds       : bond        0.02817 (  355)
  hydrogen bonds       : angle       5.25166 (  993)
  SS BOND              : bond        0.00333 (   12)
  SS BOND              : angle       1.40938 (   24)
  covalent geometry    : bond        0.00266 ( 9223)
  covalent geometry    : angle       0.53172 (12532)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 142
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 LYS cc_start: 0.8168 (mmtm) cc_final: 0.7643 (mmtt)
REVERT: A  168 MET cc_start: 0.7921 (mmt) cc_final: 0.7536 (mmt)
REVERT: A  195 TYR cc_start: 0.8925 (OUTLIER) cc_final: 0.8301 (m-80)
REVERT: H  109 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8670 (m)
REVERT: I    3 GLN cc_start: 0.8607 (pt0) cc_final: 0.8379 (pt0)
REVERT: J   45 LYS cc_start: 0.8560 (mttp) cc_final: 0.7986 (mtpt)
REVERT: J  108 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8266 (m)
REVERT: L   27 LYS cc_start: 0.7887 (ttmt) cc_final: 0.7346 (tttm)
REVERT: L   65 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6356 (m-30)
REVERT: M  160 GLN cc_start: 0.7293 (mm-40) cc_final: 0.6986 (mm-40)
REVERT: M  195 GLU cc_start: 0.7674 (mm-30) cc_final: 0.6964 (mm-30)
REVERT: N   65 SER cc_start: 0.8490 (t) cc_final: 0.8200 (m)
  outliers start: 29
  outliers final: 21
  residues processed: 164
  average time/residue: 0.2157
  time to fit residues: 49.1932
Evaluate side-chains
  164 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 139
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  195 TYR
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  109 VAL
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain I residue   75 SER
Chi-restraints excluded: chain I residue  113 VAL
Chi-restraints excluded: chain I residue  173 VAL
Chi-restraints excluded: chain J residue    7 SER
Chi-restraints excluded: chain J residue   42 THR
Chi-restraints excluded: chain J residue   87 VAL
Chi-restraints excluded: chain J residue  108 VAL
Chi-restraints excluded: chain J residue  110 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   65 ASP
Chi-restraints excluded: chain M residue   97 THR
Chi-restraints excluded: chain M residue  132 VAL
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue    4 MET
Chi-restraints excluded: chain N residue   19 VAL
Chi-restraints excluded: chain N residue   74 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 35 optimal weight:    0.8980
   chunk 83 optimal weight:    5.9990
   chunk 44 optimal weight:    0.7980
   chunk 71 optimal weight:    6.9990
   chunk 63 optimal weight:    9.9990
   chunk 45 optimal weight:    0.8980
   chunk 94 optimal weight:    3.9990
   chunk 113 optimal weight:    7.9990
   chunk 58 optimal weight:    8.9990
   chunk 51 optimal weight:    9.9990
   overall best weight:    2.5184

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

Flipped N/Q/H residues before XYZ refinement:
I 109 GLN
J  32 ASN
L  50 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.141948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.103769 restraints weight = 10599.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 2.50
r_work: 0.2653 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2514 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2514
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2502
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2502 r_free = 0.2502    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2502 r_free = 0.2502    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2502
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9237  Z= 0.216
  Angle     :  0.601  10.117  12562  Z= 0.312
  Chirality :  0.045   0.201   1390
  Planarity :  0.005   0.051   1597
  Dihedral  :  5.057  50.514   1303
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 13.69 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.28 %
    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:  0.37 (0.25), residues: 1157
  helix:  1.05 (0.75), residues: 45
  sheet:  0.51 (0.22), residues: 518
  loop :  0.06 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP L 101 
 HIS   0.006   0.001   HIS M  91 
 PHE   0.013   0.002   PHE I 102 
 TYR   0.023   0.002   TYR J  35 
 ARG   0.006   0.000   ARG A 207 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00205 (    2)
  link_NAG-ASN         : angle       1.19548 (    6)
  hydrogen bonds       : bond        0.03309 (  355)
  hydrogen bonds       : angle       5.54191 (  993)
  SS BOND              : bond        0.00448 (   12)
  SS BOND              : angle       1.64776 (   24)
  covalent geometry    : bond        0.00511 ( 9223)
  covalent geometry    : angle       0.59719 (12532)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 1.086 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 LYS cc_start: 0.8234 (mmtm) cc_final: 0.7653 (mmtt)
REVERT: A  168 MET cc_start: 0.8177 (mmt) cc_final: 0.7699 (mmt)
REVERT: A  195 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.8453 (m-80)
REVERT: H  109 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8648 (m)
REVERT: J  108 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8404 (m)
REVERT: L   27 LYS cc_start: 0.7908 (ttmt) cc_final: 0.7305 (tttm)
REVERT: L   65 ASP cc_start: 0.7140 (OUTLIER) cc_final: 0.6345 (m-30)
REVERT: M  160 GLN cc_start: 0.7272 (mm-40) cc_final: 0.6932 (mm-40)
REVERT: M  183 LYS cc_start: 0.7471 (tttt) cc_final: 0.7269 (tttt)
REVERT: M  195 GLU cc_start: 0.7658 (mm-30) cc_final: 0.6915 (mm-30)
REVERT: N   65 SER cc_start: 0.8485 (t) cc_final: 0.8167 (m)
  outliers start: 33
  outliers final: 29
  residues processed: 159
  average time/residue: 0.2180
  time to fit residues: 48.5142
Evaluate side-chains
  165 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 132
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  195 TYR
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  270 SER
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  109 VAL
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain I residue   75 SER
Chi-restraints excluded: chain I residue  113 VAL
Chi-restraints excluded: chain I residue  173 VAL
Chi-restraints excluded: chain J residue    7 SER
Chi-restraints excluded: chain J residue   30 SER
Chi-restraints excluded: chain J residue   42 THR
Chi-restraints excluded: chain J residue   87 VAL
Chi-restraints excluded: chain J residue  108 VAL
Chi-restraints excluded: chain J residue  110 VAL
Chi-restraints excluded: chain J residue  111 ILE
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue    6 GLN
Chi-restraints excluded: chain L residue   65 ASP
Chi-restraints excluded: chain M residue   20 THR
Chi-restraints excluded: chain M residue   97 THR
Chi-restraints excluded: chain M residue  132 VAL
Chi-restraints excluded: chain M residue  135 LEU
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue    4 MET
Chi-restraints excluded: chain N residue   19 VAL
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   74 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 55 optimal weight:    9.9990
   chunk 56 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   chunk 63 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 93 optimal weight:    3.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
L  50 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.138866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.100683 restraints weight = 10588.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 2.51
r_work: 0.2642 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2505 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2505
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2499
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2499 r_free = 0.2499    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2499 r_free = 0.2499    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2499
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9237  Z= 0.192
  Angle     :  0.587   9.989  12562  Z= 0.305
  Chirality :  0.045   0.219   1390
  Planarity :  0.004   0.050   1597
  Dihedral  :  5.059  50.074   1303
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 13.79 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.25), residues: 1157
  helix:  1.04 (0.75), residues: 45
  sheet:  0.57 (0.23), residues: 508
  loop : -0.01 (0.26), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP J  36 
 HIS   0.005   0.001   HIS M  91 
 PHE   0.012   0.002   PHE J  80 
 TYR   0.021   0.002   TYR J  35 
 ARG   0.006   0.000   ARG A 207 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00208 (    2)
  link_NAG-ASN         : angle       1.03729 (    6)
  hydrogen bonds       : bond        0.03214 (  355)
  hydrogen bonds       : angle       5.50953 (  993)
  SS BOND              : bond        0.00407 (   12)
  SS BOND              : angle       1.59117 (   24)
  covalent geometry    : bond        0.00450 ( 9223)
  covalent geometry    : angle       0.58347 (12532)

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 136
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 LYS cc_start: 0.8256 (mmtm) cc_final: 0.7682 (mmtt)
REVERT: A  168 MET cc_start: 0.8151 (mmt) cc_final: 0.7682 (mmt)
REVERT: A  195 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.8440 (m-80)
REVERT: H   46 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8235 (tt0)
REVERT: H  109 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8663 (m)
REVERT: J  108 VAL cc_start: 0.8654 (OUTLIER) cc_final: 0.8442 (m)
REVERT: L   27 LYS cc_start: 0.7902 (ttmt) cc_final: 0.7281 (tttm)
REVERT: L   65 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6309 (m-30)
REVERT: M  160 GLN cc_start: 0.7267 (mm-40) cc_final: 0.6933 (mm-40)
REVERT: M  183 LYS cc_start: 0.7489 (tttt) cc_final: 0.7241 (tttt)
REVERT: M  195 GLU cc_start: 0.7670 (mm-30) cc_final: 0.6962 (mm-30)
REVERT: N   65 SER cc_start: 0.8517 (t) cc_final: 0.8198 (m)
  outliers start: 33
  outliers final: 28
  residues processed: 162
  average time/residue: 0.2110
  time to fit residues: 47.2942
Evaluate side-chains
  167 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 134
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  195 TYR
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  270 SER
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  109 VAL
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain I residue   75 SER
Chi-restraints excluded: chain I residue  113 VAL
Chi-restraints excluded: chain I residue  173 VAL
Chi-restraints excluded: chain J residue    7 SER
Chi-restraints excluded: chain J residue   30 SER
Chi-restraints excluded: chain J residue   42 THR
Chi-restraints excluded: chain J residue   87 VAL
Chi-restraints excluded: chain J residue  108 VAL
Chi-restraints excluded: chain J residue  110 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue    6 GLN
Chi-restraints excluded: chain L residue   65 ASP
Chi-restraints excluded: chain M residue   20 THR
Chi-restraints excluded: chain M residue   97 THR
Chi-restraints excluded: chain M residue  132 VAL
Chi-restraints excluded: chain M residue  135 LEU
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue    4 MET
Chi-restraints excluded: chain N residue   19 VAL
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   74 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 86 optimal weight:    0.3980
   chunk 27 optimal weight:    7.9990
   chunk 91 optimal weight:    6.9990
   chunk 43 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 55 optimal weight:    8.9990
   chunk 96 optimal weight:    0.3980
   chunk 38 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
I 203 ASN
L  50 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.141603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.103685 restraints weight = 10629.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 2.40
r_work: 0.2753 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2616 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2576
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2576 r_free = 0.2576    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2576 r_free = 0.2576    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2576
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.2537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9237  Z= 0.108
  Angle     :  0.522   9.547  12562  Z= 0.272
  Chirality :  0.043   0.231   1390
  Planarity :  0.004   0.049   1597
  Dihedral  :  4.731  50.057   1303
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 13.99 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.25), residues: 1157
  helix:  1.41 (0.77), residues: 45
  sheet:  0.64 (0.23), residues: 518
  loop :  0.14 (0.27), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP J  36 
 HIS   0.003   0.001   HIS M  91 
 PHE   0.011   0.001   PHE J  80 
 TYR   0.014   0.001   TYR J  35 
 ARG   0.007   0.000   ARG A 207 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00037 (    2)
  link_NAG-ASN         : angle       0.78234 (    6)
  hydrogen bonds       : bond        0.02715 (  355)
  hydrogen bonds       : angle       5.17282 (  993)
  SS BOND              : bond        0.00307 (   12)
  SS BOND              : angle       1.29028 (   24)
  covalent geometry    : bond        0.00244 ( 9223)
  covalent geometry    : angle       0.51964 (12532)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6030.77 seconds
wall clock time: 104 minutes 52.43 seconds (6292.43 seconds total)