Starting phenix.real_space_refine
on Thu Jul 24 16:11:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jna_22403/07_2025/7jna_22403.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jna_22403/07_2025/7jna_22403.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jna_22403/07_2025/7jna_22403.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jna_22403/07_2025/7jna_22403.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jna_22403/07_2025/7jna_22403.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jna_22403/07_2025/7jna_22403.cif"
  }
  resolution = 3.6
  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=   0.004
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      24      5.16       5
     C    4176      2.51       5
     N    1071      2.21       5
     O    1161      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6432
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2074
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2074
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 59}
          Link IDs: {'PTRANS': 13, 'TRANS': 264}
          Unresolved non-hydrogen bonds: 194
          Unresolved non-hydrogen angles: 237
          Unresolved non-hydrogen dihedrals: 160
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 97
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Restraints were copied for chains:
    J, O, C, B
  Time building chain proxies: 3.61, per 1000 atoms: 0.56
  Number of scatterers: 6432
  At special positions: 0
  Unit cell: (83.106, 82.08, 127.224, 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      24     16.00
     O    1161      8.00
     N    1071      7.00
     C    4176      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 128 " - pdb=" SG  CYS A 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 128 " - pdb=" SG  CYS C 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 128 " - pdb=" SG  CYS B 149 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG J   1 " - " NAG J   2 "
      " NAG O   1 " - " NAG O   2 "
    NAG-ASN
      " NAG A 401 " - " ASN A 148 "
      " NAG A 402 " - " ASN A 162 "
      " NAG A 403 " - " ASN A 190 "
      " NAG B 401 " - " ASN B 148 "
      " NAG B 402 " - " ASN B 162 "
      " NAG B 403 " - " ASN B 190 "
      " NAG C 401 " - " ASN C 148 "
      " NAG C 402 " - " ASN C 162 "
      " NAG C 403 " - " ASN C 190 "
      " NAG E   1 " - " ASN A 155 "
      " NAG J   1 " - " ASN B 155 "
      " NAG O   1 " - " ASN C 155 "
  Time building additional restraints: 1.51
  Conformation dependent library (CDL) restraints added in 948.3 milliseconds
  

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1608

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 15 sheets defined
      32.7% alpha, 15.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 98
      removed outlier: 3.535A  pdb=" N   PHE A  66 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ILE A  73 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   TYR A  74 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 213
      removed outlier: 3.523A  pdb=" N   PHE A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 227
      removed outlier: 3.984A  pdb=" N   GLN A 221 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 338
    Processing helix  chain 'B' and resid 62 through 98
      removed outlier: 3.535A  pdb=" N   PHE B  66 " --> pdb=" O   LEU B  62 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ILE B  73 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   TYR B  74 " --> pdb=" O   LEU B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 213
      removed outlier: 3.523A  pdb=" N   PHE B 210 " --> pdb=" O   SER B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 227
      removed outlier: 3.984A  pdb=" N   GLN B 221 " --> pdb=" O   VAL B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 338
    Processing helix  chain 'C' and resid 62 through 98
      removed outlier: 3.535A  pdb=" N   PHE C  66 " --> pdb=" O   LEU C  62 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ILE C  73 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   TYR C  74 " --> pdb=" O   LEU C  70 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 206 through 213
      removed outlier: 3.524A  pdb=" N   PHE C 210 " --> pdb=" O   SER C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 215 through 227
      removed outlier: 3.984A  pdb=" N   GLN C 221 " --> pdb=" O   VAL C 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 306 through 338
    Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 105
    Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 172
    Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 130
      removed outlier: 6.450A  pdb=" N   GLN A 186 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   CYS A 128 " --> pdb=" O   PHE A 184 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   PHE A 184 " --> pdb=" O   CYS A 128 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   HIS A 130 " --> pdb=" O   LEU A 182 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   LEU A 182 " --> pdb=" O   HIS A 130 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL A 283 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   PHE A 236 " --> pdb=" O   PHE A 282 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   VAL A 284 " --> pdb=" O   PHE A 236 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   THR A 238 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   GLU A 286 " --> pdb=" O   THR A 238 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL A 240 " --> pdb=" O   GLU A 286 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 200
    Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 247
    Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 105
    Processing sheet with id=AA7, first strand: chain 'B' and resid 169 through 172
    Processing sheet with id=AA8, first strand: chain 'B' and resid 125 through 130
      removed outlier: 6.450A  pdb=" N   GLN B 186 " --> pdb=" O   LEU B 126 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   CYS B 128 " --> pdb=" O   PHE B 184 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   PHE B 184 " --> pdb=" O   CYS B 128 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   HIS B 130 " --> pdb=" O   LEU B 182 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   LEU B 182 " --> pdb=" O   HIS B 130 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   VAL B 283 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   PHE B 236 " --> pdb=" O   PHE B 282 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   VAL B 284 " --> pdb=" O   PHE B 236 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   THR B 238 " --> pdb=" O   VAL B 284 " (cutoff:3.500A)
      removed outlier: 7.429A  pdb=" N   GLU B 286 " --> pdb=" O   THR B 238 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   VAL B 240 " --> pdb=" O   GLU B 286 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 200
    Processing sheet with id=AB1, first strand: chain 'B' and resid 244 through 247
    Processing sheet with id=AB2, first strand: chain 'C' and resid 103 through 105
    Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 172
    Processing sheet with id=AB4, first strand: chain 'C' and resid 125 through 130
      removed outlier: 6.450A  pdb=" N   GLN C 186 " --> pdb=" O   LEU C 126 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   CYS C 128 " --> pdb=" O   PHE C 184 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   PHE C 184 " --> pdb=" O   CYS C 128 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   HIS C 130 " --> pdb=" O   LEU C 182 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   LEU C 182 " --> pdb=" O   HIS C 130 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL C 283 " --> pdb=" O   LEU C 185 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   PHE C 236 " --> pdb=" O   PHE C 282 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   VAL C 284 " --> pdb=" O   PHE C 236 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   THR C 238 " --> pdb=" O   VAL C 284 " (cutoff:3.500A)
      removed outlier: 7.429A  pdb=" N   GLU C 286 " --> pdb=" O   THR C 238 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL C 240 " --> pdb=" O   GLU C 286 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 198 through 200
    Processing sheet with id=AB6, first strand: chain 'C' and resid 244 through 247

    270 hydrogen bonds defined for protein.
    783 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.52

  Time building geometry restraints manager: 1.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1990
        1.34 -     1.45: 1037
        1.45 -     1.57: 3531
        1.57 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 6594
  Sorted by residual:
  bond pdb=" N   ILE B  89 "
       pdb=" CA  ILE B  89 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.033 1.17e-02 7.31e+03 8.16e+00
  bond pdb=" N   ILE A  89 "
       pdb=" CA  ILE A  89 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.17e-02 7.31e+03 7.78e+00
  bond pdb=" N   ILE C  89 "
       pdb=" CA  ILE C  89 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.032 1.17e-02 7.31e+03 7.64e+00
  bond pdb=" N   LYS A 319 "
       pdb=" CA  LYS A 319 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.21e-02 6.83e+03 5.19e+00
  bond pdb=" N   LYS B 319 "
       pdb=" CA  LYS B 319 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.21e-02 6.83e+03 5.10e+00
  ... (remaining 6589 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.01: 7951
        1.01 -     2.02: 805
        2.02 -     3.03: 164
        3.03 -     4.04: 50
        4.04 -     5.05: 24
  Bond angle restraints: 8994
  Sorted by residual:
  angle pdb=" C   SER B 206 "
        pdb=" N   PHE B 207 "
        pdb=" CA  PHE B 207 "
      ideal   model   delta    sigma   weight residual
     120.29  124.94   -4.65 1.42e+00 4.96e-01 1.07e+01
  angle pdb=" C   SER C 206 "
        pdb=" N   PHE C 207 "
        pdb=" CA  PHE C 207 "
      ideal   model   delta    sigma   weight residual
     120.29  124.89   -4.60 1.42e+00 4.96e-01 1.05e+01
  angle pdb=" C   SER A 206 "
        pdb=" N   PHE A 207 "
        pdb=" CA  PHE A 207 "
      ideal   model   delta    sigma   weight residual
     120.29  124.88   -4.59 1.42e+00 4.96e-01 1.05e+01
  angle pdb=" CA  ILE B  89 "
        pdb=" C   ILE B  89 "
        pdb=" O   ILE B  89 "
      ideal   model   delta    sigma   weight residual
     121.17  117.90    3.27 1.06e+00 8.90e-01 9.53e+00
  angle pdb=" CA  ILE A  89 "
        pdb=" C   ILE A  89 "
        pdb=" O   ILE A  89 "
      ideal   model   delta    sigma   weight residual
     121.17  117.91    3.26 1.06e+00 8.90e-01 9.48e+00
  ... (remaining 8989 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.44: 3581
       15.44 -    30.87: 430
       30.87 -    46.31: 57
       46.31 -    61.74: 12
       61.74 -    77.18: 6
  Dihedral angle restraints: 4086
    sinusoidal: 1617
      harmonic: 2469
  Sorted by residual:
  dihedral pdb=" CA  ASN B 190 "
           pdb=" C   ASN B 190 "
           pdb=" N   LYS B 191 "
           pdb=" CA  LYS B 191 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.58  -24.42     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CA  ASN A 190 "
           pdb=" C   ASN A 190 "
           pdb=" N   LYS A 191 "
           pdb=" CA  LYS A 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.64  -24.36     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" CA  ASN C 190 "
           pdb=" C   ASN C 190 "
           pdb=" N   LYS C 191 "
           pdb=" CA  LYS C 191 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.66  -24.34     0      5.00e+00 4.00e-02 2.37e+01
  ... (remaining 4083 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 722
       0.039 -    0.079: 228
       0.079 -    0.118: 97
       0.118 -    0.158: 9
       0.158 -    0.197: 6
  Chirality restraints: 1062
  Sorted by residual:
  chirality pdb=" C1  NAG B 402 "
            pdb=" ND2 ASN B 162 "
            pdb=" C2  NAG B 402 "
            pdb=" O5  NAG B 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.20   -0.20 2.00e-01 2.50e+01 9.72e-01
  chirality pdb=" C1  NAG C 402 "
            pdb=" ND2 ASN C 162 "
            pdb=" C2  NAG C 402 "
            pdb=" O5  NAG C 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.20   -0.20 2.00e-01 2.50e+01 9.71e-01
  chirality pdb=" C1  NAG A 402 "
            pdb=" ND2 ASN A 162 "
            pdb=" C2  NAG A 402 "
            pdb=" O5  NAG A 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.20   -0.20 2.00e-01 2.50e+01 9.65e-01
  ... (remaining 1059 not shown)

  Planarity restraints: 1143
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   2 "    0.341 2.00e-02 2.50e+03   2.95e-01 1.09e+03
        pdb=" C7  NAG E   2 "   -0.079 2.00e-02 2.50e+03
        pdb=" C8  NAG E   2 "    0.114 2.00e-02 2.50e+03
        pdb=" N2  NAG E   2 "   -0.527 2.00e-02 2.50e+03
        pdb=" O7  NAG E   2 "    0.151 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG J   2 "    0.341 2.00e-02 2.50e+03   2.95e-01 1.09e+03
        pdb=" C7  NAG J   2 "   -0.079 2.00e-02 2.50e+03
        pdb=" C8  NAG J   2 "    0.114 2.00e-02 2.50e+03
        pdb=" N2  NAG J   2 "   -0.527 2.00e-02 2.50e+03
        pdb=" O7  NAG J   2 "    0.151 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG O   2 "   -0.340 2.00e-02 2.50e+03   2.95e-01 1.09e+03
        pdb=" C7  NAG O   2 "    0.079 2.00e-02 2.50e+03
        pdb=" C8  NAG O   2 "   -0.114 2.00e-02 2.50e+03
        pdb=" N2  NAG O   2 "    0.527 2.00e-02 2.50e+03
        pdb=" O7  NAG O   2 "   -0.151 2.00e-02 2.50e+03
  ... (remaining 1140 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 841
        2.75 -     3.29: 6563
        3.29 -     3.83: 10337
        3.83 -     4.36: 11863
        4.36 -     4.90: 20118
  Nonbonded interactions: 49722
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 156 "
            pdb=" OE1 GLU B 224 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OH  TYR A 156 "
            pdb=" OE1 GLU A 224 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OH  TYR C 156 "
            pdb=" OE1 GLU C 224 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" ND1 HIS C 130 "
            pdb=" OE2 GLU C 181 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" ND1 HIS A 130 "
            pdb=" OE2 GLU A 181 "
     model   vdw
     2.262 3.120
  ... (remaining 49717 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'E'
  selection = chain 'J'
  selection = chain 'O'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.550
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.330
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
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      :  0.005   0.036   6612  Z= 0.252
  Angle     :  0.766  10.453   9045  Z= 0.416
  Chirality :  0.045   0.197   1062
  Planarity :  0.025   0.295   1131
  Dihedral  : 12.954  77.175   2469
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.83 (0.24), residues: 828
  helix: -0.91 (0.27), residues: 267
  sheet: -3.40 (0.25), residues: 255
  loop : -3.02 (0.29), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 330 
 HIS   0.003   0.001   HIS A 131 
 PHE   0.015   0.002   PHE C 204 
 TYR   0.007   0.001   TYR C 156 
 ARG   0.002   0.000   ARG A 175 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00757 (   12)
  link_NAG-ASN         : angle       4.05923 (   36)
  link_BETA1-4         : bond        0.00117 (    3)
  link_BETA1-4         : angle       1.09008 (    9)
  hydrogen bonds       : bond        0.13361 (  270)
  hydrogen bonds       : angle       5.99911 (  783)
  SS BOND              : bond        0.00275 (    3)
  SS BOND              : angle       2.77092 (    6)
  covalent geometry    : bond        0.00485 ( 6594)
  covalent geometry    : angle       0.71906 ( 8994)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  156 TYR cc_start: 0.7187 (p90) cc_final: 0.6979 (p90)
REVERT: B  309 LEU cc_start: 0.7550 (tp) cc_final: 0.7307 (tp)
REVERT: C  242 MET cc_start: 0.7600 (mtm) cc_final: 0.7003 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 209
  average time/residue: 0.2304
  time to fit residues: 59.8252
Evaluate side-chains
  130 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 34 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 63 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 172 GLN
B 172 GLN
C 172 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.163627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.133022 restraints weight = 8986.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.134702 restraints weight = 6328.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.137229 restraints weight = 4979.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.3363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   6612  Z= 0.251
  Angle     :  0.868  12.871   9045  Z= 0.399
  Chirality :  0.055   0.292   1062
  Planarity :  0.005   0.043   1131
  Dihedral  :  8.237  51.996   1209
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 22.22 %
    Favored  : 72.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.58 (0.27), residues: 828
  helix:  0.71 (0.30), residues: 267
  sheet: -3.36 (0.25), residues: 249
  loop : -2.28 (0.32), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 230 
 HIS   0.003   0.001   HIS C 131 
 PHE   0.028   0.003   PHE A 236 
 TYR   0.018   0.002   TYR A 201 
 ARG   0.003   0.001   ARG B 259 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01072 (   12)
  link_NAG-ASN         : angle       5.42893 (   36)
  link_BETA1-4         : bond        0.00608 (    3)
  link_BETA1-4         : angle       3.19188 (    9)
  hydrogen bonds       : bond        0.03805 (  270)
  hydrogen bonds       : angle       5.00595 (  783)
  SS BOND              : bond        0.00446 (    3)
  SS BOND              : angle       2.67647 (    6)
  covalent geometry    : bond        0.00573 ( 6594)
  covalent geometry    : angle       0.78994 ( 8994)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 152
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 GLN cc_start: 0.7931 (pm20) cc_final: 0.7305 (pp30)
REVERT: A  259 ARG cc_start: 0.7690 (mtm110) cc_final: 0.7427 (mtm110)
REVERT: A  319 LYS cc_start: 0.7552 (ttpt) cc_final: 0.6974 (mptt)
REVERT: B  260 GLN cc_start: 0.8426 (pp30) cc_final: 0.7701 (pp30)
REVERT: B  309 LEU cc_start: 0.8036 (tp) cc_final: 0.7619 (tp)
REVERT: B  319 LYS cc_start: 0.7574 (ttpt) cc_final: 0.7211 (tppt)
  outliers start: 30
  outliers final: 16
  residues processed: 172
  average time/residue: 0.2523
  time to fit residues: 56.1888
Evaluate side-chains
  131 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  127 SER
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  127 SER
Chi-restraints excluded: chain C residue  225 SER
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain C residue  298 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 78 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 27 optimal weight:   10.0000
   chunk 37 optimal weight:    0.0060
   chunk 70 optimal weight:    0.8980
   chunk 72 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.166363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.134615 restraints weight = 9073.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.137689 restraints weight = 7403.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.139588 restraints weight = 4936.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.3823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6612  Z= 0.140
  Angle     :  0.714  11.919   9045  Z= 0.330
  Chirality :  0.045   0.260   1062
  Planarity :  0.004   0.036   1131
  Dihedral  :  6.978  41.735   1209
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 27.69 %
    Favored  : 69.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.29), residues: 828
  helix:  1.47 (0.31), residues: 267
  sheet: -2.82 (0.27), residues: 261
  loop : -2.00 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 287 
 HIS   0.003   0.001   HIS C 131 
 PHE   0.019   0.002   PHE C 232 
 TYR   0.013   0.002   TYR A 111 
 ARG   0.005   0.001   ARG B 259 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00786 (   12)
  link_NAG-ASN         : angle       5.79244 (   36)
  link_BETA1-4         : bond        0.00294 (    3)
  link_BETA1-4         : angle       1.71327 (    9)
  hydrogen bonds       : bond        0.03443 (  270)
  hydrogen bonds       : angle       4.73938 (  783)
  SS BOND              : bond        0.00135 (    3)
  SS BOND              : angle       1.61361 (    6)
  covalent geometry    : bond        0.00319 ( 6594)
  covalent geometry    : angle       0.61088 ( 8994)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 GLN cc_start: 0.7960 (pm20) cc_final: 0.7316 (pp30)
REVERT: A  259 ARG cc_start: 0.7619 (mtm110) cc_final: 0.7270 (mtm110)
REVERT: A  318 PHE cc_start: 0.7382 (t80) cc_final: 0.6961 (m-80)
REVERT: A  319 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7207 (tptt)
REVERT: B  147 MET cc_start: 0.7419 (mtp) cc_final: 0.7156 (mtt)
REVERT: B  172 GLN cc_start: 0.8630 (tt0) cc_final: 0.8423 (tp40)
REVERT: B  260 GLN cc_start: 0.8376 (pp30) cc_final: 0.7618 (pp30)
REVERT: B  309 LEU cc_start: 0.8247 (tp) cc_final: 0.7936 (tp)
REVERT: B  319 LYS cc_start: 0.7936 (ttpt) cc_final: 0.7408 (tttt)
REVERT: C  319 LYS cc_start: 0.7285 (ttpt) cc_final: 0.6984 (tppt)
REVERT: C  330 TRP cc_start: 0.7312 (t-100) cc_final: 0.6873 (t-100)
  outliers start: 17
  outliers final: 10
  residues processed: 144
  average time/residue: 0.2196
  time to fit residues: 42.4554
Evaluate side-chains
  125 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  319 LYS
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain C residue  295 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 29 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0770
   chunk 64 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 71 optimal weight:    0.6980
   chunk 46 optimal weight:    0.4980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.167031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.137038 restraints weight = 9113.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.141122 restraints weight = 7132.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.142447 restraints weight = 4411.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.4138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6612  Z= 0.134
  Angle     :  0.689  12.675   9045  Z= 0.322
  Chirality :  0.044   0.296   1062
  Planarity :  0.004   0.033   1131
  Dihedral  :  6.546  41.495   1209
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 29.45 %
    Favored  : 66.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.30), residues: 828
  helix:  1.84 (0.32), residues: 267
  sheet: -2.48 (0.29), residues: 261
  loop : -1.76 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 287 
 HIS   0.002   0.001   HIS A 131 
 PHE   0.019   0.002   PHE C 232 
 TYR   0.016   0.002   TYR C 156 
 ARG   0.005   0.001   ARG C 259 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00678 (   12)
  link_NAG-ASN         : angle       5.49315 (   36)
  link_BETA1-4         : bond        0.00283 (    3)
  link_BETA1-4         : angle       1.63412 (    9)
  hydrogen bonds       : bond        0.03298 (  270)
  hydrogen bonds       : angle       4.55338 (  783)
  SS BOND              : bond        0.00111 (    3)
  SS BOND              : angle       2.12194 (    6)
  covalent geometry    : bond        0.00308 ( 6594)
  covalent geometry    : angle       0.59211 ( 8994)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8197 (ttp)
REVERT: A  124 GLN cc_start: 0.8042 (pm20) cc_final: 0.7392 (pp30)
REVERT: A  259 ARG cc_start: 0.7634 (mtm110) cc_final: 0.7335 (mtm110)
REVERT: A  318 PHE cc_start: 0.7394 (t80) cc_final: 0.7101 (m-80)
REVERT: A  319 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7227 (tptt)
REVERT: B  238 THR cc_start: 0.9550 (OUTLIER) cc_final: 0.9306 (p)
REVERT: B  260 GLN cc_start: 0.8330 (pp30) cc_final: 0.7567 (pp30)
REVERT: B  309 LEU cc_start: 0.8303 (tp) cc_final: 0.7925 (tp)
REVERT: B  319 LYS cc_start: 0.7927 (ttpt) cc_final: 0.7645 (tttm)
REVERT: C  319 LYS cc_start: 0.7293 (ttpt) cc_final: 0.7083 (tppt)
REVERT: C  330 TRP cc_start: 0.7122 (t-100) cc_final: 0.6798 (t-100)
  outliers start: 24
  outliers final: 13
  residues processed: 149
  average time/residue: 0.2661
  time to fit residues: 55.0103
Evaluate side-chains
  135 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 1.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 MET
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  319 LYS
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  162 ASN
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  128 CYS
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  295 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 8 optimal weight:    8.9990
   chunk 28 optimal weight:    9.9990
   chunk 67 optimal weight:    6.9990
   chunk 59 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0000
   overall best weight:    0.8788

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

Flipped N/Q/H residues before XYZ refinement:
** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.167670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.134056 restraints weight = 9015.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.138336 restraints weight = 5704.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.141134 restraints weight = 4314.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.4502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6612  Z= 0.149
  Angle     :  0.709  13.385   9045  Z= 0.331
  Chirality :  0.044   0.246   1062
  Planarity :  0.004   0.033   1131
  Dihedral  :  6.293  44.885   1209
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 28.22 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.30), residues: 828
  helix:  1.95 (0.31), residues: 267
  sheet: -2.51 (0.29), residues: 255
  loop : -1.55 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.001   TRP A 287 
 HIS   0.002   0.001   HIS A 131 
 PHE   0.017   0.002   PHE C 232 
 TYR   0.018   0.002   TYR B 156 
 ARG   0.005   0.000   ARG C 259 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00708 (   12)
  link_NAG-ASN         : angle       5.98852 (   36)
  link_BETA1-4         : bond        0.00401 (    3)
  link_BETA1-4         : angle       1.46666 (    9)
  hydrogen bonds       : bond        0.03266 (  270)
  hydrogen bonds       : angle       4.47528 (  783)
  SS BOND              : bond        0.00169 (    3)
  SS BOND              : angle       2.27136 (    6)
  covalent geometry    : bond        0.00346 ( 6594)
  covalent geometry    : angle       0.59752 ( 8994)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 130
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  259 ARG cc_start: 0.7713 (mtm110) cc_final: 0.7500 (mtm110)
REVERT: A  260 GLN cc_start: 0.8521 (pp30) cc_final: 0.7906 (pp30)
REVERT: A  305 ASN cc_start: 0.7488 (t0) cc_final: 0.7253 (t0)
REVERT: A  318 PHE cc_start: 0.7566 (t80) cc_final: 0.7192 (m-80)
REVERT: A  319 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7119 (tptt)
REVERT: B  260 GLN cc_start: 0.8372 (pp30) cc_final: 0.7889 (pp30)
REVERT: B  296 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7471 (pt0)
REVERT: B  319 LYS cc_start: 0.7673 (ttpt) cc_final: 0.7212 (tppt)
REVERT: C  253 ARG cc_start: 0.7200 (tpt170) cc_final: 0.6684 (tpt-90)
REVERT: C  287 TRP cc_start: 0.9190 (m100) cc_final: 0.8882 (m100)
REVERT: C  305 ASN cc_start: 0.7605 (t0) cc_final: 0.7405 (t0)
REVERT: C  318 PHE cc_start: 0.7108 (m-10) cc_final: 0.6593 (m-10)
REVERT: C  330 TRP cc_start: 0.7473 (t-100) cc_final: 0.7126 (t-100)
  outliers start: 29
  outliers final: 22
  residues processed: 148
  average time/residue: 0.2357
  time to fit residues: 48.5127
Evaluate side-chains
  147 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 1.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  319 LYS
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  162 ASN
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  296 GLN
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  128 CYS
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  225 SER
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  268 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 8 optimal weight:    8.9990
   chunk 7 optimal weight:    8.9990
   chunk 34 optimal weight:    7.9990
   chunk 17 optimal weight:    0.6980
   chunk 76 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.166331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.133086 restraints weight = 9051.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.137003 restraints weight = 7176.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.138568 restraints weight = 4767.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.4948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6612  Z= 0.183
  Angle     :  0.710  14.415   9045  Z= 0.335
  Chirality :  0.044   0.242   1062
  Planarity :  0.004   0.033   1131
  Dihedral  :  5.994  47.426   1209
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 29.28 %
    Favored  : 64.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.30), residues: 828
  helix:  1.99 (0.31), residues: 267
  sheet: -2.63 (0.27), residues: 279
  loop : -1.48 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP A 287 
 HIS   0.002   0.001   HIS B  98 
 PHE   0.018   0.002   PHE C 236 
 TYR   0.019   0.002   TYR A 111 
 ARG   0.005   0.001   ARG C 259 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00783 (   12)
  link_NAG-ASN         : angle       5.86010 (   36)
  link_BETA1-4         : bond        0.00359 (    3)
  link_BETA1-4         : angle       1.26846 (    9)
  hydrogen bonds       : bond        0.03335 (  270)
  hydrogen bonds       : angle       4.51063 (  783)
  SS BOND              : bond        0.00154 (    3)
  SS BOND              : angle       2.27477 (    6)
  covalent geometry    : bond        0.00429 ( 6594)
  covalent geometry    : angle       0.60344 ( 8994)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 136
  time to evaluate  : 2.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 GLN cc_start: 0.8597 (pp30) cc_final: 0.7904 (pp30)
REVERT: A  305 ASN cc_start: 0.7609 (t0) cc_final: 0.7351 (t0)
REVERT: A  319 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7284 (tppt)
REVERT: B  172 GLN cc_start: 0.8744 (tp40) cc_final: 0.8527 (tp40)
REVERT: B  260 GLN cc_start: 0.8405 (pp30) cc_final: 0.7842 (pp30)
REVERT: B  319 LYS cc_start: 0.7917 (ttpt) cc_final: 0.7394 (tppt)
REVERT: B  330 TRP cc_start: 0.7021 (t-100) cc_final: 0.6703 (t-100)
REVERT: C  253 ARG cc_start: 0.7267 (tpt170) cc_final: 0.6747 (tpt-90)
REVERT: C  287 TRP cc_start: 0.9256 (m100) cc_final: 0.8951 (m100)
REVERT: C  318 PHE cc_start: 0.6996 (m-10) cc_final: 0.6468 (m-10)
  outliers start: 33
  outliers final: 26
  residues processed: 155
  average time/residue: 0.2433
  time to fit residues: 54.3467
Evaluate side-chains
  157 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 130
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  319 LYS
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  162 ASN
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  298 ILE
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  127 SER
Chi-restraints excluded: chain C residue  128 CYS
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  225 SER
Chi-restraints excluded: chain C residue  230 TRP
Chi-restraints excluded: chain C residue  247 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 70 optimal weight:    0.4980
   chunk 31 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 75 optimal weight:    8.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 172 GLN
** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.165047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.132629 restraints weight = 8999.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.135382 restraints weight = 7196.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.136998 restraints weight = 5147.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.5283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   6612  Z= 0.196
  Angle     :  0.725  13.442   9045  Z= 0.346
  Chirality :  0.045   0.218   1062
  Planarity :  0.004   0.043   1131
  Dihedral  :  5.870  49.121   1209
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  6.53 %
    Allowed  : 28.92 %
    Favored  : 64.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.30), residues: 828
  helix:  2.05 (0.31), residues: 267
  sheet: -2.57 (0.29), residues: 255
  loop : -1.48 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 287 
 HIS   0.003   0.001   HIS B  98 
 PHE   0.021   0.002   PHE C 236 
 TYR   0.018   0.002   TYR C 156 
 ARG   0.005   0.001   ARG C 259 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00616 (   12)
  link_NAG-ASN         : angle       5.60281 (   36)
  link_BETA1-4         : bond        0.00454 (    3)
  link_BETA1-4         : angle       1.14392 (    9)
  hydrogen bonds       : bond        0.03358 (  270)
  hydrogen bonds       : angle       4.48629 (  783)
  SS BOND              : bond        0.00123 (    3)
  SS BOND              : angle       2.42785 (    6)
  covalent geometry    : bond        0.00463 ( 6594)
  covalent geometry    : angle       0.63011 ( 8994)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 143
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 GLN cc_start: 0.8623 (pp30) cc_final: 0.7924 (pp30)
REVERT: A  319 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7638 (tttt)
REVERT: B  172 GLN cc_start: 0.8738 (tp40) cc_final: 0.8494 (tp40)
REVERT: B  260 GLN cc_start: 0.8462 (pp30) cc_final: 0.7934 (pp30)
REVERT: B  296 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7649 (pt0)
REVERT: B  319 LYS cc_start: 0.8005 (ttpt) cc_final: 0.7379 (tppt)
REVERT: B  330 TRP cc_start: 0.7085 (t-100) cc_final: 0.6848 (t-100)
REVERT: C  253 ARG cc_start: 0.7266 (tpt170) cc_final: 0.6755 (tpt-90)
REVERT: C  318 PHE cc_start: 0.7075 (m-10) cc_final: 0.6462 (m-10)
  outliers start: 37
  outliers final: 30
  residues processed: 160
  average time/residue: 0.2654
  time to fit residues: 59.7020
Evaluate side-chains
  162 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 130
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  319 LYS
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  162 ASN
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  296 GLN
Chi-restraints excluded: chain B residue  298 ILE
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  127 SER
Chi-restraints excluded: chain C residue  128 CYS
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  225 SER
Chi-restraints excluded: chain C residue  230 TRP
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain C residue  298 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 24 optimal weight:    0.0470
   chunk 77 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0040
   chunk 11 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.5694

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

Flipped N/Q/H residues before XYZ refinement:
** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.168563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.136914 restraints weight = 9004.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.140268 restraints weight = 6737.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.141403 restraints weight = 4605.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.5550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6612  Z= 0.135
  Angle     :  0.726  14.296   9045  Z= 0.340
  Chirality :  0.044   0.211   1062
  Planarity :  0.004   0.036   1131
  Dihedral  :  5.686  50.461   1209
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 30.34 %
    Favored  : 65.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.30), residues: 828
  helix:  2.16 (0.32), residues: 267
  sheet: -2.53 (0.27), residues: 294
  loop : -1.45 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP C 287 
 HIS   0.002   0.001   HIS A 131 
 PHE   0.016   0.002   PHE B 232 
 TYR   0.019   0.002   TYR B 156 
 ARG   0.009   0.001   ARG C  93 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01006 (   12)
  link_NAG-ASN         : angle       6.09488 (   36)
  link_BETA1-4         : bond        0.00386 (    3)
  link_BETA1-4         : angle       1.01667 (    9)
  hydrogen bonds       : bond        0.03222 (  270)
  hydrogen bonds       : angle       4.35557 (  783)
  SS BOND              : bond        0.00105 (    3)
  SS BOND              : angle       2.26148 (    6)
  covalent geometry    : bond        0.00310 ( 6594)
  covalent geometry    : angle       0.61435 ( 8994)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 140
  time to evaluate  : 1.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 GLN cc_start: 0.8541 (pp30) cc_final: 0.7919 (pp30)
REVERT: A  287 TRP cc_start: 0.8948 (m100) cc_final: 0.8708 (m100)
REVERT: A  304 TRP cc_start: 0.8255 (m100) cc_final: 0.8030 (m100)
REVERT: A  305 ASN cc_start: 0.7763 (t0) cc_final: 0.7545 (t0)
REVERT: A  319 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7191 (tppt)
REVERT: B  260 GLN cc_start: 0.8447 (pp30) cc_final: 0.7895 (pp30)
REVERT: B  287 TRP cc_start: 0.9301 (m100) cc_final: 0.8531 (m100)
REVERT: B  296 GLN cc_start: 0.7789 (pt0) cc_final: 0.7551 (pt0)
REVERT: B  319 LYS cc_start: 0.7990 (ttpt) cc_final: 0.7526 (tppp)
REVERT: C  318 PHE cc_start: 0.7026 (m-10) cc_final: 0.6488 (m-10)
  outliers start: 25
  outliers final: 22
  residues processed: 154
  average time/residue: 0.3163
  time to fit residues: 67.3621
Evaluate side-chains
  156 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  319 LYS
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  162 ASN
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  127 SER
Chi-restraints excluded: chain C residue  128 CYS
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  230 TRP
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  268 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 77 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 10 optimal weight:    0.4980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.167860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.135459 restraints weight = 8995.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.139125 restraints weight = 6934.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.140452 restraints weight = 4730.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.5800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6612  Z= 0.145
  Angle     :  0.766  17.534   9045  Z= 0.353
  Chirality :  0.047   0.495   1062
  Planarity :  0.004   0.034   1131
  Dihedral  :  5.679  50.094   1209
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 30.51 %
    Favored  : 64.55 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.30), residues: 828
  helix:  2.18 (0.32), residues: 267
  sheet: -2.52 (0.26), residues: 291
  loop : -1.39 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 287 
 HIS   0.002   0.001   HIS C 131 
 PHE   0.017   0.002   PHE B 232 
 TYR   0.018   0.002   TYR A 156 
 ARG   0.008   0.001   ARG B  93 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00764 (   12)
  link_NAG-ASN         : angle       6.72060 (   36)
  link_BETA1-4         : bond        0.00460 (    3)
  link_BETA1-4         : angle       1.00580 (    9)
  hydrogen bonds       : bond        0.03147 (  270)
  hydrogen bonds       : angle       4.30539 (  783)
  SS BOND              : bond        0.00385 (    3)
  SS BOND              : angle       3.06715 (    6)
  covalent geometry    : bond        0.00332 ( 6594)
  covalent geometry    : angle       0.63349 ( 8994)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 136
  time to evaluate  : 1.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 GLN cc_start: 0.8567 (pp30) cc_final: 0.7762 (pp30)
REVERT: A  305 ASN cc_start: 0.7855 (t0) cc_final: 0.7652 (t0)
REVERT: A  319 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7811 (tttm)
REVERT: B  260 GLN cc_start: 0.8490 (pp30) cc_final: 0.7880 (pp30)
REVERT: B  287 TRP cc_start: 0.9294 (m100) cc_final: 0.8582 (m100)
REVERT: B  296 GLN cc_start: 0.7758 (pt0) cc_final: 0.7511 (pt0)
REVERT: B  319 LYS cc_start: 0.8017 (ttpt) cc_final: 0.7448 (tppt)
REVERT: C  318 PHE cc_start: 0.7051 (m-10) cc_final: 0.6546 (m-10)
  outliers start: 28
  outliers final: 24
  residues processed: 153
  average time/residue: 0.3282
  time to fit residues: 72.7298
Evaluate side-chains
  155 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 2.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  319 LYS
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  162 ASN
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  127 SER
Chi-restraints excluded: chain C residue  128 CYS
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  225 SER
Chi-restraints excluded: chain C residue  230 TRP
Chi-restraints excluded: chain C residue  247 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0970
   chunk 70 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0570
   chunk 36 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   overall best weight:    1.0300

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

Flipped N/Q/H residues before XYZ refinement:
B 279 GLN
** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.166853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.136192 restraints weight = 9028.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.137431 restraints weight = 6260.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.140575 restraints weight = 4951.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.6088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6612  Z= 0.159
  Angle     :  0.732  18.776   9045  Z= 0.342
  Chirality :  0.045   0.303   1062
  Planarity :  0.004   0.036   1131
  Dihedral  :  5.375  50.128   1209
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 30.34 %
    Favored  : 65.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.30), residues: 828
  helix:  2.22 (0.32), residues: 267
  sheet: -2.65 (0.26), residues: 291
  loop : -1.36 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP A 287 
 HIS   0.003   0.001   HIS B  98 
 PHE   0.018   0.002   PHE C 236 
 TYR   0.018   0.002   TYR A 156 
 ARG   0.008   0.001   ARG C 259 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00632 (   12)
  link_NAG-ASN         : angle       6.06604 (   36)
  link_BETA1-4         : bond        0.00432 (    3)
  link_BETA1-4         : angle       0.83750 (    9)
  hydrogen bonds       : bond        0.03153 (  270)
  hydrogen bonds       : angle       4.30658 (  783)
  SS BOND              : bond        0.00125 (    3)
  SS BOND              : angle       2.29541 (    6)
  covalent geometry    : bond        0.00372 ( 6594)
  covalent geometry    : angle       0.62252 ( 8994)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 137
  time to evaluate  : 1.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 GLN cc_start: 0.8586 (pp30) cc_final: 0.7762 (pp30)
REVERT: A  319 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7824 (tttm)
REVERT: B  260 GLN cc_start: 0.8550 (pp30) cc_final: 0.7861 (pp30)
REVERT: B  287 TRP cc_start: 0.9327 (m100) cc_final: 0.8612 (m100)
REVERT: B  296 GLN cc_start: 0.7800 (pt0) cc_final: 0.7535 (pt0)
REVERT: B  319 LYS cc_start: 0.8144 (ttpt) cc_final: 0.7698 (tppt)
REVERT: C  101 MET cc_start: 0.8674 (tmm) cc_final: 0.8414 (ttp)
REVERT: C  318 PHE cc_start: 0.7096 (m-10) cc_final: 0.6568 (m-10)
  outliers start: 26
  outliers final: 24
  residues processed: 151
  average time/residue: 0.1593
  time to fit residues: 35.3344
Evaluate side-chains
  160 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 135
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  319 LYS
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  162 ASN
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain C residue  104 SER
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  127 SER
Chi-restraints excluded: chain C residue  128 CYS
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  225 SER
Chi-restraints excluded: chain C residue  230 TRP
Chi-restraints excluded: chain C residue  247 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.165562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.135301 restraints weight = 9084.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.137551 restraints weight = 5960.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.138921 restraints weight = 5616.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.6496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6612  Z= 0.182
  Angle     :  0.729  13.362   9045  Z= 0.344
  Chirality :  0.048   0.385   1062
  Planarity :  0.005   0.040   1131
  Dihedral  :  5.377  52.262   1209
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 28.92 %
    Favored  : 66.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.30), residues: 828
  helix:  2.23 (0.32), residues: 261
  sheet: -2.69 (0.26), residues: 297
  loop : -1.38 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP A 287 
 HIS   0.003   0.001   HIS B  98 
 PHE   0.023   0.002   PHE A 236 
 TYR   0.019   0.002   TYR B 156 
 ARG   0.008   0.001   ARG C 259 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00630 (   12)
  link_NAG-ASN         : angle       5.34055 (   36)
  link_BETA1-4         : bond        0.00402 (    3)
  link_BETA1-4         : angle       0.83950 (    9)
  hydrogen bonds       : bond        0.03275 (  270)
  hydrogen bonds       : angle       4.38849 (  783)
  SS BOND              : bond        0.00141 (    3)
  SS BOND              : angle       2.32222 (    6)
  covalent geometry    : bond        0.00425 ( 6594)
  covalent geometry    : angle       0.64475 ( 8994)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3350.04 seconds
wall clock time: 64 minutes 44.75 seconds (3884.75 seconds total)