Starting phenix.real_space_refine
on Tue Feb 11 06:08:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7umq_26607/02_2025/7umq_26607.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7umq_26607/02_2025/7umq_26607.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7umq_26607/02_2025/7umq_26607.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7umq_26607/02_2025/7umq_26607.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7umq_26607/02_2025/7umq_26607.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7umq_26607/02_2025/7umq_26607.cif"
  }
  resolution = 3.29
  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=   1.000
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      30      5.16       5
     C    2760      2.51       5
     N     850      2.21       5
     O     740      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4380
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 438
          Classifications: {'peptide': 62}
          Link IDs: {'PTRANS': 4, 'TRANS': 57}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, J
  Time building chain proxies: 1.90, per 1000 atoms: 0.43
  Number of scatterers: 4380
  At special positions: 0
  Unit cell: (89.474, 123.97, 42.042, 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      30     16.00
     O     740      8.00
     N     850      7.00
     C    2760      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Time building additional restraints: 1.08
  Conformation dependent library (CDL) restraints added in 591.0 milliseconds
  

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  940

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 14 sheets defined
      0.0% alpha, 29.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'J' and resid 89 through 91
      removed outlier: 6.118A  pdb=" N   TRP J  89 " --> pdb=" O   GLY H  90 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   TRP H  89 " --> pdb=" O   GLY F  90 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   TRP D  89 " --> pdb=" O   GLY B  90 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 95 through 100
      removed outlier: 6.321A  pdb=" N   THR D  95 " --> pdb=" O   HIS F  96 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   GLN F  98 " --> pdb=" O   THR D  95 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   SER D  97 " --> pdb=" O   GLN F  98 " (cutoff:3.500A)
      removed outlier: 7.709A  pdb=" N   ASN F 100 " --> pdb=" O   SER D  97 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   TRP D  99 " --> pdb=" O   ASN F 100 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'J' and resid 106 through 107
      removed outlier: 6.655A  pdb=" N   LYS D 106 " --> pdb=" O   THR F 107 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'J' and resid 115 through 117
      removed outlier: 6.522A  pdb=" N   ALA D 115 " --> pdb=" O   ALA F 116 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'J' and resid 120 through 122
      removed outlier: 6.965A  pdb=" N   VAL J 121 " --> pdb=" O   VAL H 122 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   VAL H 121 " --> pdb=" O   VAL F 122 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   VAL D 121 " --> pdb=" O   VAL B 122 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'J' and resid 125 through 130
      removed outlier: 6.891A  pdb=" N   GLY J 126 " --> pdb=" O   LEU H 125 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   GLY H 127 " --> pdb=" O   GLY J 126 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   TYR J 128 " --> pdb=" O   GLY H 127 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   GLY H 126 " --> pdb=" O   LEU F 125 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   GLY F 127 " --> pdb=" O   GLY H 126 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   TYR H 128 " --> pdb=" O   GLY F 127 " (cutoff:3.500A)
      removed outlier: 9.074A  pdb=" N   LEU D 125 " --> pdb=" O   GLY F 126 " (cutoff:3.500A)
      removed outlier: 10.541A  pdb=" N   TYR F 128 " --> pdb=" O   LEU D 125 " (cutoff:3.500A)
      removed outlier: 5.178A  pdb=" N   GLY D 127 " --> pdb=" O   TYR F 128 " (cutoff:3.500A)
      removed outlier: 8.193A  pdb=" N   LEU F 130 " --> pdb=" O   GLY D 127 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   VAL D 129 " --> pdb=" O   LEU F 130 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   GLY D 126 " --> pdb=" O   LEU B 125 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   GLY B 127 " --> pdb=" O   GLY D 126 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   TYR D 128 " --> pdb=" O   GLY B 127 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'J' and resid 138 through 139
      removed outlier: 6.539A  pdb=" N   ILE J 138 " --> pdb=" O   ILE H 139 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   ILE H 138 " --> pdb=" O   ILE F 139 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   ILE D 138 " --> pdb=" O   ILE B 139 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'I' and resid 89 through 91
      removed outlier: 6.118A  pdb=" N   TRP I  89 " --> pdb=" O   GLY G  90 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   TRP G  89 " --> pdb=" O   GLY E  90 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   TRP C  89 " --> pdb=" O   GLY A  90 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'I' and resid 95 through 100
      removed outlier: 6.322A  pdb=" N   THR C  95 " --> pdb=" O   HIS E  96 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   GLN E  98 " --> pdb=" O   THR C  95 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   SER C  97 " --> pdb=" O   GLN E  98 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   ASN E 100 " --> pdb=" O   SER C  97 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   TRP C  99 " --> pdb=" O   ASN E 100 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'I' and resid 106 through 107
      removed outlier: 6.654A  pdb=" N   LYS C 106 " --> pdb=" O   THR E 107 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'I' and resid 115 through 117
      removed outlier: 6.522A  pdb=" N   ALA C 115 " --> pdb=" O   ALA E 116 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'I' and resid 120 through 122
      removed outlier: 6.965A  pdb=" N   VAL I 121 " --> pdb=" O   VAL G 122 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   VAL G 121 " --> pdb=" O   VAL E 122 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   VAL C 121 " --> pdb=" O   VAL A 122 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'I' and resid 125 through 130
      removed outlier: 6.891A  pdb=" N   GLY I 126 " --> pdb=" O   LEU G 125 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   GLY G 127 " --> pdb=" O   GLY I 126 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   TYR I 128 " --> pdb=" O   GLY G 127 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   GLY G 126 " --> pdb=" O   LEU E 125 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   GLY E 127 " --> pdb=" O   GLY G 126 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   TYR G 128 " --> pdb=" O   GLY E 127 " (cutoff:3.500A)
      removed outlier: 9.075A  pdb=" N   LEU C 125 " --> pdb=" O   GLY E 126 " (cutoff:3.500A)
      removed outlier: 10.541A  pdb=" N   TYR E 128 " --> pdb=" O   LEU C 125 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   GLY C 127 " --> pdb=" O   TYR E 128 " (cutoff:3.500A)
      removed outlier: 8.193A  pdb=" N   LEU E 130 " --> pdb=" O   GLY C 127 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   VAL C 129 " --> pdb=" O   LEU E 130 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   GLY C 126 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   GLY A 127 " --> pdb=" O   GLY C 126 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   TYR C 128 " --> pdb=" O   GLY A 127 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'I' and resid 138 through 139
      removed outlier: 6.539A  pdb=" N   ILE I 138 " --> pdb=" O   ILE G 139 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   ILE G 138 " --> pdb=" O   ILE E 139 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   ILE C 138 " --> pdb=" O   ILE A 139 " (cutoff:3.500A)

    70 hydrogen bonds defined for protein.
    210 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: 1.04

  Time building geometry restraints manager: 1.26 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1403
        1.33 -     1.45: 1147
        1.45 -     1.57: 1910
        1.57 -     1.69: 10
        1.69 -     1.81: 60
  Bond restraints: 4530
  Sorted by residual:
  bond pdb=" CG  HIS D 111 "
       pdb=" CD2 HIS D 111 "
    ideal  model  delta    sigma   weight residual
    1.354  1.271  0.083 1.10e-02 8.26e+03 5.63e+01
  bond pdb=" CG  HIS I 111 "
       pdb=" CD2 HIS I 111 "
    ideal  model  delta    sigma   weight residual
    1.354  1.272  0.082 1.10e-02 8.26e+03 5.61e+01
  bond pdb=" CG  HIS F 111 "
       pdb=" CD2 HIS F 111 "
    ideal  model  delta    sigma   weight residual
    1.354  1.272  0.082 1.10e-02 8.26e+03 5.60e+01
  bond pdb=" CG  HIS J 111 "
       pdb=" CD2 HIS J 111 "
    ideal  model  delta    sigma   weight residual
    1.354  1.272  0.082 1.10e-02 8.26e+03 5.59e+01
  bond pdb=" CG  HIS B 111 "
       pdb=" CD2 HIS B 111 "
    ideal  model  delta    sigma   weight residual
    1.354  1.272  0.082 1.10e-02 8.26e+03 5.59e+01
  ... (remaining 4525 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 3646
        1.45 -     2.89: 1494
        2.89 -     4.34: 644
        4.34 -     5.78: 202
        5.78 -     7.23: 124
  Bond angle restraints: 6110
  Sorted by residual:
  angle pdb=" C   ARG E 136 "
        pdb=" N   PRO E 137 "
        pdb=" CA  PRO E 137 "
      ideal   model   delta    sigma   weight residual
     119.85  126.78   -6.93 1.01e+00 9.80e-01 4.71e+01
  angle pdb=" C   ARG I 136 "
        pdb=" N   PRO I 137 "
        pdb=" CA  PRO I 137 "
      ideal   model   delta    sigma   weight residual
     119.85  126.75   -6.90 1.01e+00 9.80e-01 4.66e+01
  angle pdb=" C   ARG J 136 "
        pdb=" N   PRO J 137 "
        pdb=" CA  PRO J 137 "
      ideal   model   delta    sigma   weight residual
     119.85  126.74   -6.89 1.01e+00 9.80e-01 4.66e+01
  angle pdb=" C   ARG F 136 "
        pdb=" N   PRO F 137 "
        pdb=" CA  PRO F 137 "
      ideal   model   delta    sigma   weight residual
     119.85  126.73   -6.88 1.01e+00 9.80e-01 4.64e+01
  angle pdb=" C   ARG B 136 "
        pdb=" N   PRO B 137 "
        pdb=" CA  PRO B 137 "
      ideal   model   delta    sigma   weight residual
     119.85  126.73   -6.88 1.01e+00 9.80e-01 4.64e+01
  ... (remaining 6105 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.45: 2240
       10.45 -    20.91: 110
       20.91 -    31.36: 90
       31.36 -    41.81: 10
       41.81 -    52.26: 10
  Dihedral angle restraints: 2460
    sinusoidal: 900
      harmonic: 1560
  Sorted by residual:
  dihedral pdb=" C   TRP A  89 "
           pdb=" N   TRP A  89 "
           pdb=" CA  TRP A  89 "
           pdb=" CB  TRP A  89 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -129.47    6.87     0      2.50e+00 1.60e-01 7.56e+00
  dihedral pdb=" C   TRP B  89 "
           pdb=" N   TRP B  89 "
           pdb=" CA  TRP B  89 "
           pdb=" CB  TRP B  89 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -129.46    6.86     0      2.50e+00 1.60e-01 7.52e+00
  dihedral pdb=" C   TRP E  89 "
           pdb=" N   TRP E  89 "
           pdb=" CA  TRP E  89 "
           pdb=" CB  TRP E  89 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -129.45    6.85     0      2.50e+00 1.60e-01 7.50e+00
  ... (remaining 2457 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.066: 309
       0.066 -    0.129: 147
       0.129 -    0.192: 64
       0.192 -    0.255: 22
       0.255 -    0.319: 18
  Chirality restraints: 560
  Sorted by residual:
  chirality pdb=" CA  TRP D  89 "
            pdb=" N   TRP D  89 "
            pdb=" C   TRP D  89 "
            pdb=" CB  TRP D  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.54e+00
  chirality pdb=" CA  TRP E  89 "
            pdb=" N   TRP E  89 "
            pdb=" C   TRP E  89 "
            pdb=" CB  TRP E  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.53e+00
  chirality pdb=" CA  TRP J  89 "
            pdb=" N   TRP J  89 "
            pdb=" C   TRP J  89 "
            pdb=" CB  TRP J  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.52e+00
  ... (remaining 557 not shown)

  Planarity restraints: 800
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP F  81 "   -0.032 2.00e-02 2.50e+03   1.63e-02 6.62e+00
        pdb=" CG  TRP F  81 "    0.009 2.00e-02 2.50e+03
        pdb=" CD1 TRP F  81 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP F  81 "    0.017 2.00e-02 2.50e+03
        pdb=" NE1 TRP F  81 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP F  81 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP F  81 "    0.024 2.00e-02 2.50e+03
        pdb=" CZ2 TRP F  81 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ3 TRP F  81 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP F  81 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP E  81 "    0.032 2.00e-02 2.50e+03   1.62e-02 6.59e+00
        pdb=" CG  TRP E  81 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD1 TRP E  81 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP E  81 "   -0.017 2.00e-02 2.50e+03
        pdb=" NE1 TRP E  81 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP E  81 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP E  81 "   -0.024 2.00e-02 2.50e+03
        pdb=" CZ2 TRP E  81 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ3 TRP E  81 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP E  81 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP I  81 "    0.032 2.00e-02 2.50e+03   1.62e-02 6.54e+00
        pdb=" CG  TRP I  81 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD1 TRP I  81 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP I  81 "   -0.016 2.00e-02 2.50e+03
        pdb=" NE1 TRP I  81 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP I  81 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP I  81 "   -0.024 2.00e-02 2.50e+03
        pdb=" CZ2 TRP I  81 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ3 TRP I  81 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP I  81 "    0.021 2.00e-02 2.50e+03
  ... (remaining 797 not shown)

  Histogram of nonbonded interaction distances:
        2.54 -     3.01: 2414
        3.01 -     3.48: 4106
        3.48 -     3.96: 6913
        3.96 -     4.43: 8233
        4.43 -     4.90: 15076
  Nonbonded interactions: 36742
  Sorted by model distance:
  nonbonded pdb=" N   GLY G  93 "
            pdb=" O   GLY G  93 "
     model   vdw
     2.540 2.496
  nonbonded pdb=" N   GLY E  93 "
            pdb=" O   GLY E  93 "
     model   vdw
     2.541 2.496
  nonbonded pdb=" N   GLY H  93 "
            pdb=" O   GLY H  93 "
     model   vdw
     2.541 2.496
  nonbonded pdb=" N   GLY F  93 "
            pdb=" O   GLY F  93 "
     model   vdw
     2.541 2.496
  nonbonded pdb=" N   GLY D  93 "
            pdb=" O   GLY D  93 "
     model   vdw
     2.541 2.496
  ... (remaining 36737 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 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.750
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     13.670
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7234
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      :  0.023   0.101   4530  Z= 1.595
  Angle     :  2.110   7.226   6110  Z= 1.387
  Chirality :  0.102   0.319    560
  Planarity :  0.009   0.024    800
  Dihedral  :  9.850  52.261   1520
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 2.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  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: -3.35 (0.24), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.54 (0.19), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.007   TRP F  81 
 HIS   0.017   0.004   HIS B 111 
 PHE   0.010   0.005   PHE B 141 
 TYR   0.012   0.007   TYR D 128 
 ARG   0.001   0.000   ARG J 136 

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.485 
Fit side-chains
REVERT: B   91 GLN cc_start: 0.5935 (tt0) cc_final: 0.4891 (pm20)
REVERT: A   91 GLN cc_start: 0.5723 (tt0) cc_final: 0.4869 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.1533
  time to fit residues: 32.9040
Evaluate side-chains
  110 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 45 optimal weight:    6.9990
   chunk 25 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 47 optimal weight:    6.9990
   chunk 18 optimal weight:    7.9990
   chunk 28 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** H  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  85 HIS ** 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 = 0.4537 r_free = 0.4537 target = 0.160612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.151355 restraints weight = 8327.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.4450 rms_B_bonded: 3.16
r_work: 0.4357 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.4357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.4169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   4530  Z= 0.380
  Angle     :  0.807   5.048   6110  Z= 0.424
  Chirality :  0.046   0.164    560
  Planarity :  0.005   0.055    800
  Dihedral  :  5.174  13.688    630
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 15.48
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.67 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 13.08 %
    Favored  : 82.56 %
  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: -3.87 (0.22), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.94 (0.17), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP B  81 
 HIS   0.003   0.001   HIS D 140 
 PHE   0.006   0.001   PHE D 141 
 TYR   0.005   0.002   TYR I 128 
 ARG   0.007   0.001   ARG C 136 

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  141 PHE cc_start: 0.7240 (t80) cc_final: 0.6194 (p90)
REVERT: H   85 HIS cc_start: 0.7925 (m-70) cc_final: 0.7650 (m-70)
REVERT: H  100 ASN cc_start: 0.9134 (t0) cc_final: 0.8806 (t0)
REVERT: H  112 MET cc_start: 0.8788 (mpp) cc_final: 0.8401 (mpp)
REVERT: H  134 MET cc_start: 0.7952 (mtt) cc_final: 0.7720 (mtt)
REVERT: D  112 MET cc_start: 0.8864 (mpp) cc_final: 0.8642 (mpp)
REVERT: D  134 MET cc_start: 0.7967 (mtt) cc_final: 0.7695 (mtt)
REVERT: I   81 TRP cc_start: 0.7255 (m-10) cc_final: 0.6532 (m100)
REVERT: I  141 PHE cc_start: 0.7469 (t80) cc_final: 0.6036 (p90)
REVERT: G   85 HIS cc_start: 0.8138 (m-70) cc_final: 0.7893 (m90)
REVERT: G  100 ASN cc_start: 0.9140 (t0) cc_final: 0.8827 (t0)
REVERT: G  112 MET cc_start: 0.8785 (mpp) cc_final: 0.8374 (mpp)
REVERT: C  112 MET cc_start: 0.8908 (mpp) cc_final: 0.8678 (mpp)
REVERT: C  121 VAL cc_start: 0.9211 (t) cc_final: 0.9010 (m)
REVERT: E   85 HIS cc_start: 0.8012 (m90) cc_final: 0.7623 (m-70)
  outliers start: 17
  outliers final: 14
  residues processed: 134
  average time/residue: 0.0947
  time to fit residues: 17.9863
Evaluate side-chains
  129 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  122 VAL
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain D residue  122 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain I residue  122 VAL
Chi-restraints excluded: chain G residue  122 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain E residue  122 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 54 optimal weight:   10.0000
   chunk 55 optimal weight:    9.9990
   chunk 52 optimal weight:   20.0000
   chunk 11 optimal weight:    9.9990
   chunk 36 optimal weight:    8.9990
   chunk 31 optimal weight:    9.9990
   chunk 3 optimal weight:   20.0000
   chunk 13 optimal weight:    4.9990
   chunk 34 optimal weight:   10.0000
   chunk 51 optimal weight:    0.0870
   overall best weight:    5.8166

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

Flipped N/Q/H residues before XYZ refinement:
J 100 ASN
** H  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 100 ASN
G 140 HIS
** C  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  83 GLN
E 140 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.151194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.142758 restraints weight = 8718.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.4412 rms_B_bonded: 3.10
r_work: 0.4312 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.4312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.5307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   4530  Z= 0.393
  Angle     :  0.777   7.724   6110  Z= 0.398
  Chirality :  0.045   0.161    560
  Planarity :  0.004   0.032    800
  Dihedral  :  5.207  15.367    630
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.00 %
    Favored  : 89.00 %
  Rotamer:
    Outliers :  7.95 %
    Allowed  : 14.87 %
    Favored  : 77.18 %
  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: -4.18 (0.22), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.17), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP C  99 
 HIS   0.006   0.001   HIS I  85 
 PHE   0.011   0.003   PHE J 141 
 TYR   0.012   0.002   TYR H 128 
 ARG   0.003   0.001   ARG I 136 

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 0.454 
Fit side-chains
REVERT: J   81 TRP cc_start: 0.5121 (OUTLIER) cc_final: 0.3426 (m100)
REVERT: J  141 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6124 (p90)
REVERT: H  112 MET cc_start: 0.8867 (mpp) cc_final: 0.8600 (mpp)
REVERT: D  112 MET cc_start: 0.8900 (mpp) cc_final: 0.8692 (mpp)
REVERT: D  134 MET cc_start: 0.7948 (mtt) cc_final: 0.7592 (mtt)
REVERT: D  136 ARG cc_start: 0.6579 (ptt180) cc_final: 0.5796 (mtm180)
REVERT: B   81 TRP cc_start: 0.8154 (m-10) cc_final: 0.7409 (m-10)
REVERT: F   85 HIS cc_start: 0.8267 (m-70) cc_final: 0.7719 (m-70)
REVERT: I   81 TRP cc_start: 0.7128 (m-10) cc_final: 0.6166 (m100)
REVERT: I  141 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6227 (p90)
REVERT: G  112 MET cc_start: 0.8829 (mpp) cc_final: 0.8568 (mpp)
REVERT: G  136 ARG cc_start: 0.8489 (ttm170) cc_final: 0.8264 (mtp180)
REVERT: G  139 ILE cc_start: 0.8585 (mt) cc_final: 0.8385 (mt)
REVERT: C  112 MET cc_start: 0.8935 (mpp) cc_final: 0.8716 (mpp)
REVERT: A  134 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7404 (mtt)
REVERT: E   85 HIS cc_start: 0.7990 (m90) cc_final: 0.7652 (m-70)
  outliers start: 31
  outliers final: 20
  residues processed: 132
  average time/residue: 0.1158
  time to fit residues: 20.6872
Evaluate side-chains
  139 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   81 TRP
Chi-restraints excluded: chain J residue  122 VAL
Chi-restraints excluded: chain J residue  141 PHE
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain H residue  141 PHE
Chi-restraints excluded: chain D residue  122 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  141 PHE
Chi-restraints excluded: chain I residue  122 VAL
Chi-restraints excluded: chain I residue  141 PHE
Chi-restraints excluded: chain G residue  122 VAL
Chi-restraints excluded: chain G residue  141 PHE
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  141 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 34 optimal weight:   10.0000
   chunk 21 optimal weight:   20.0000
   chunk 24 optimal weight:    9.9990
   chunk 2 optimal weight:    6.9990
   chunk 30 optimal weight:   10.0000
   chunk 31 optimal weight:   20.0000
   chunk 49 optimal weight:    8.9990
   chunk 11 optimal weight:    6.9990
   chunk 58 optimal weight:    4.9990
   chunk 51 optimal weight:   10.0000
   overall best weight:    5.7988

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

Flipped N/Q/H residues before XYZ refinement:
J 140 HIS
** H  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 140 HIS
** D  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 140 HIS
B  83 GLN
** B  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 140 HIS
** F  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 140 HIS
I 140 HIS
** G  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 140 HIS
** A  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 140 HIS
** E  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.149486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.141385 restraints weight = 8996.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.4384 rms_B_bonded: 3.10
r_work: 0.4279 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.5804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   4530  Z= 0.379
  Angle     :  0.755   6.866   6110  Z= 0.385
  Chirality :  0.045   0.157    560
  Planarity :  0.004   0.034    800
  Dihedral  :  5.057  14.765    630
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.17 %
    Favored  : 88.83 %
  Rotamer:
    Outliers :  7.18 %
    Allowed  : 18.46 %
    Favored  : 74.36 %
  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: -4.38 (0.22), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.33 (0.17), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP C  99 
 HIS   0.005   0.001   HIS H  85 
 PHE   0.009   0.002   PHE E 141 
 TYR   0.010   0.002   TYR G 128 
 ARG   0.003   0.001   ARG J 136 

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 118
  time to evaluate  : 0.451 
Fit side-chains
REVERT: J   81 TRP cc_start: 0.4957 (OUTLIER) cc_final: 0.3788 (m100)
REVERT: J  141 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.6247 (p90)
REVERT: H  122 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8323 (p)
REVERT: D  112 MET cc_start: 0.8869 (mpp) cc_final: 0.8667 (mpp)
REVERT: B   81 TRP cc_start: 0.8430 (m-10) cc_final: 0.8215 (m-10)
REVERT: F   85 HIS cc_start: 0.8353 (m-70) cc_final: 0.8046 (m-70)
REVERT: I   81 TRP cc_start: 0.7082 (m-10) cc_final: 0.5972 (m100)
REVERT: I  141 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.6192 (p90)
REVERT: G   85 HIS cc_start: 0.8355 (m-70) cc_final: 0.8153 (m-70)
REVERT: G  122 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8328 (p)
REVERT: G  136 ARG cc_start: 0.8534 (ttm170) cc_final: 0.7952 (mtp180)
REVERT: C  112 MET cc_start: 0.8897 (mpp) cc_final: 0.8672 (mpp)
REVERT: A  134 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7336 (mtt)
REVERT: E   81 TRP cc_start: 0.8961 (m-10) cc_final: 0.8099 (m-10)
  outliers start: 28
  outliers final: 17
  residues processed: 122
  average time/residue: 0.1025
  time to fit residues: 17.3500
Evaluate side-chains
  136 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   81 TRP
Chi-restraints excluded: chain J residue  122 VAL
Chi-restraints excluded: chain J residue  141 PHE
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain H residue  141 PHE
Chi-restraints excluded: chain D residue  122 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  141 PHE
Chi-restraints excluded: chain I residue  122 VAL
Chi-restraints excluded: chain I residue  141 PHE
Chi-restraints excluded: chain G residue  122 VAL
Chi-restraints excluded: chain G residue  141 PHE
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  141 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 21 optimal weight:   20.0000
   chunk 24 optimal weight:    8.9990
   chunk 12 optimal weight:    4.9990
   chunk 1 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 38 optimal weight:    7.9990
   chunk 57 optimal weight:   20.0000
   chunk 58 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
** H  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  83 GLN
** C  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  98 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 = 0.4414 r_free = 0.4414 target = 0.146269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.138041 restraints weight = 9248.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.4337 rms_B_bonded: 3.16
r_work: 0.4230 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.4230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.6085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   4530  Z= 0.438
  Angle     :  0.785   5.946   6110  Z= 0.404
  Chirality :  0.046   0.155    560
  Planarity :  0.005   0.032    800
  Dihedral  :  5.174  15.446    630
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 15.48
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 11.67 %
    Favored  : 88.17 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 18.97 %
    Favored  : 74.10 %
  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: -4.66 (0.21), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.54 (0.16), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP H  99 
 HIS   0.006   0.001   HIS A  85 
 PHE   0.012   0.002   PHE E 141 
 TYR   0.009   0.002   TYR H 128 
 ARG   0.003   0.001   ARG I 136 

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 117
  time to evaluate  : 0.519 
Fit side-chains
REVERT: J   81 TRP cc_start: 0.4982 (OUTLIER) cc_final: 0.3786 (m100)
REVERT: J  141 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.6247 (p90)
REVERT: H   85 HIS cc_start: 0.8337 (m-70) cc_final: 0.8109 (m-70)
REVERT: H  112 MET cc_start: 0.8615 (mpp) cc_final: 0.8394 (mpp)
REVERT: B   81 TRP cc_start: 0.8620 (m-10) cc_final: 0.8279 (m-10)
REVERT: B  112 MET cc_start: 0.8615 (mpp) cc_final: 0.8311 (mpp)
REVERT: F   85 HIS cc_start: 0.8403 (m-70) cc_final: 0.8147 (m-70)
REVERT: I   81 TRP cc_start: 0.7088 (m-10) cc_final: 0.5873 (m100)
REVERT: I  141 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.6231 (p90)
REVERT: G  112 MET cc_start: 0.8579 (mpp) cc_final: 0.8368 (mpp)
REVERT: G  122 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8241 (p)
REVERT: C   81 TRP cc_start: 0.8776 (m-10) cc_final: 0.8477 (m-10)
REVERT: A  112 MET cc_start: 0.8627 (mpp) cc_final: 0.8329 (mpp)
REVERT: A  134 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7381 (mtt)
  outliers start: 27
  outliers final: 22
  residues processed: 123
  average time/residue: 0.1015
  time to fit residues: 17.4934
Evaluate side-chains
  137 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 110
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   81 TRP
Chi-restraints excluded: chain J residue  103 SER
Chi-restraints excluded: chain J residue  122 VAL
Chi-restraints excluded: chain J residue  141 PHE
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain H residue  141 PHE
Chi-restraints excluded: chain D residue  122 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  141 PHE
Chi-restraints excluded: chain I residue  103 SER
Chi-restraints excluded: chain I residue  122 VAL
Chi-restraints excluded: chain I residue  141 PHE
Chi-restraints excluded: chain G residue  122 VAL
Chi-restraints excluded: chain G residue  141 PHE
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  141 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 40 optimal weight:    9.9990
   chunk 16 optimal weight:    0.3980
   chunk 36 optimal weight:    6.9990
   chunk 24 optimal weight:   20.0000
   chunk 53 optimal weight:    7.9990
   chunk 41 optimal weight:    5.9990
   chunk 27 optimal weight:   20.0000
   chunk 44 optimal weight:    6.9990
   chunk 30 optimal weight:    8.9990
   chunk 33 optimal weight:   20.0000
   overall best weight:    5.4788

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

Flipped N/Q/H residues before XYZ refinement:
** H  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  98 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 = 0.4450 r_free = 0.4450 target = 0.148977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.140705 restraints weight = 8982.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.4367 rms_B_bonded: 3.13
r_work: 0.4264 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.4264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.6243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   4530  Z= 0.363
  Angle     :  0.740   6.437   6110  Z= 0.376
  Chirality :  0.045   0.165    560
  Planarity :  0.004   0.032    800
  Dihedral  :  4.927  14.303    630
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.00 %
    Favored  : 89.00 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 19.23 %
    Favored  : 74.10 %
  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: -4.83 (0.20), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.68 (0.16), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP H  99 
 HIS   0.005   0.001   HIS A  85 
 PHE   0.010   0.002   PHE E 141 
 TYR   0.009   0.002   TYR I 128 
 ARG   0.003   0.001   ARG J 136 

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 113
  time to evaluate  : 0.488 
Fit side-chains
REVERT: J   81 TRP cc_start: 0.4886 (OUTLIER) cc_final: 0.3889 (m100)
REVERT: J  130 LEU cc_start: 0.7653 (tp) cc_final: 0.7411 (tp)
REVERT: J  141 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.6249 (p90)
REVERT: H  122 VAL cc_start: 0.8662 (OUTLIER) cc_final: 0.8106 (p)
REVERT: B   81 TRP cc_start: 0.8711 (m-10) cc_final: 0.8322 (m-10)
REVERT: B  112 MET cc_start: 0.8547 (mpp) cc_final: 0.8220 (mpp)
REVERT: F  134 MET cc_start: 0.7676 (mtt) cc_final: 0.7409 (mmt)
REVERT: I   81 TRP cc_start: 0.7079 (m-10) cc_final: 0.5815 (m100)
REVERT: I  141 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.6217 (p90)
REVERT: G  122 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8118 (p)
REVERT: C   81 TRP cc_start: 0.8837 (m-10) cc_final: 0.8553 (m-10)
REVERT: A  112 MET cc_start: 0.8560 (mpp) cc_final: 0.8235 (mpp)
  outliers start: 26
  outliers final: 20
  residues processed: 118
  average time/residue: 0.1057
  time to fit residues: 17.4787
Evaluate side-chains
  135 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   81 TRP
Chi-restraints excluded: chain J residue  122 VAL
Chi-restraints excluded: chain J residue  141 PHE
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain H residue  141 PHE
Chi-restraints excluded: chain D residue  122 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  141 PHE
Chi-restraints excluded: chain I residue  122 VAL
Chi-restraints excluded: chain I residue  141 PHE
Chi-restraints excluded: chain G residue  122 VAL
Chi-restraints excluded: chain G residue  141 PHE
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  141 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 15 optimal weight:   30.0000
   chunk 43 optimal weight:   20.0000
   chunk 7 optimal weight:   20.0000
   chunk 50 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:   20.0000
   chunk 39 optimal weight:   20.0000
   chunk 3 optimal weight:   20.0000
   chunk 10 optimal weight:    8.9990
   chunk 23 optimal weight:    7.9990
   overall best weight:    7.5992

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

Flipped N/Q/H residues before XYZ refinement:
** J 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  98 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 = 0.4413 r_free = 0.4413 target = 0.145752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.137654 restraints weight = 9043.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.4333 rms_B_bonded: 3.12
r_work: 0.4229 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.4229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.6359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050   4530  Z= 0.480
  Angle     :  0.805   5.444   6110  Z= 0.415
  Chirality :  0.047   0.181    560
  Planarity :  0.004   0.031    800
  Dihedral  :  5.188  15.797    630
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 13.83 %
    Favored  : 86.00 %
  Rotamer:
    Outliers :  7.69 %
    Allowed  : 18.21 %
    Favored  : 74.10 %
  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: -5.05 (0.20), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.84 (0.15), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP G  99 
 HIS   0.007   0.001   HIS A  85 
 PHE   0.015   0.003   PHE E 141 
 TYR   0.008   0.002   TYR J 128 
 ARG   0.004   0.001   ARG J 136 

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 105
  time to evaluate  : 0.481 
Fit side-chains
REVERT: J   81 TRP cc_start: 0.4891 (OUTLIER) cc_final: 0.3976 (m100)
REVERT: J  125 LEU cc_start: 0.8887 (pp) cc_final: 0.8637 (pp)
REVERT: H  122 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8195 (p)
REVERT: B   81 TRP cc_start: 0.8695 (m-10) cc_final: 0.8295 (m-10)
REVERT: B  112 MET cc_start: 0.8563 (mpp) cc_final: 0.8293 (mpp)
REVERT: I   81 TRP cc_start: 0.7080 (m-10) cc_final: 0.5799 (m100)
REVERT: G  122 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8211 (p)
REVERT: A  112 MET cc_start: 0.8592 (mpp) cc_final: 0.8322 (mpp)
  outliers start: 30
  outliers final: 23
  residues processed: 112
  average time/residue: 0.1129
  time to fit residues: 17.3339
Evaluate side-chains
  126 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   81 TRP
Chi-restraints excluded: chain J residue  103 SER
Chi-restraints excluded: chain J residue  122 VAL
Chi-restraints excluded: chain H residue  109 MET
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain H residue  141 PHE
Chi-restraints excluded: chain D residue  122 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  141 PHE
Chi-restraints excluded: chain I residue  103 SER
Chi-restraints excluded: chain I residue  122 VAL
Chi-restraints excluded: chain G residue  109 MET
Chi-restraints excluded: chain G residue  122 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  141 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 50 optimal weight:    7.9990
   chunk 9 optimal weight:   30.0000
   chunk 59 optimal weight:    4.9990
   chunk 12 optimal weight:   10.0000
   chunk 31 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 7 optimal weight:   20.0000
   chunk 34 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
** D  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  98 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 = 0.4487 r_free = 0.4487 target = 0.151996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.143487 restraints weight = 8802.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.4405 rms_B_bonded: 3.16
r_work: 0.4304 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.4304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.6489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4530  Z= 0.284
  Angle     :  0.681   5.480   6110  Z= 0.344
  Chirality :  0.046   0.175    560
  Planarity :  0.004   0.031    800
  Dihedral  :  4.698  14.126    630
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 13.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.00 %
    Favored  : 89.00 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 18.97 %
    Favored  : 74.10 %
  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: -5.07 (0.20), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.86 (0.15), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP G  99 
 HIS   0.003   0.001   HIS A  85 
 PHE   0.009   0.002   PHE E 141 
 TYR   0.012   0.002   TYR I 128 
 ARG   0.002   0.001   ARG C 136 

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 0.450 
Fit side-chains
REVERT: J   81 TRP cc_start: 0.4755 (OUTLIER) cc_final: 0.3919 (m100)
REVERT: H  122 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8076 (p)
REVERT: B   81 TRP cc_start: 0.8665 (m-10) cc_final: 0.8348 (m-10)
REVERT: F  134 MET cc_start: 0.7538 (mtt) cc_final: 0.7320 (mmt)
REVERT: I   81 TRP cc_start: 0.7029 (m-10) cc_final: 0.5651 (m100)
REVERT: G  122 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8080 (p)
REVERT: C   81 TRP cc_start: 0.8801 (m-10) cc_final: 0.8427 (m-10)
  outliers start: 27
  outliers final: 22
  residues processed: 115
  average time/residue: 0.1067
  time to fit residues: 17.0536
Evaluate side-chains
  131 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   81 TRP
Chi-restraints excluded: chain J residue  103 SER
Chi-restraints excluded: chain J residue  122 VAL
Chi-restraints excluded: chain H residue  109 MET
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain D residue  122 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  141 PHE
Chi-restraints excluded: chain I residue  103 SER
Chi-restraints excluded: chain I residue  122 VAL
Chi-restraints excluded: chain G residue  109 MET
Chi-restraints excluded: chain G residue  122 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  141 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 27 optimal weight:   10.0000
   chunk 37 optimal weight:   30.0000
   chunk 13 optimal weight:   10.0000
   chunk 48 optimal weight:    7.9990
   chunk 14 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 7 optimal weight:   20.0000
   chunk 32 optimal weight:    0.0470
   chunk 44 optimal weight:    7.9990
   chunk 52 optimal weight:    9.9990
   overall best weight:    4.8086

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

Flipped N/Q/H residues before XYZ refinement:
** D  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  98 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 = 0.4464 r_free = 0.4464 target = 0.149654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.141288 restraints weight = 8836.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.4385 rms_B_bonded: 3.13
r_work: 0.4285 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.4285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.6530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   4530  Z= 0.321
  Angle     :  0.705   9.791   6110  Z= 0.352
  Chirality :  0.045   0.151    560
  Planarity :  0.004   0.031    800
  Dihedral  :  4.700  13.985    630
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.00 %
    Favored  : 88.00 %
  Rotamer:
    Outliers :  7.18 %
    Allowed  : 18.46 %
    Favored  : 74.36 %
  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: -5.11 (0.20), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.89 (0.15), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP G  99 
 HIS   0.004   0.001   HIS A  85 
 PHE   0.010   0.002   PHE E 141 
 TYR   0.012   0.002   TYR G 128 
 ARG   0.003   0.001   ARG I 136 

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.483 
Fit side-chains
REVERT: J   81 TRP cc_start: 0.4801 (OUTLIER) cc_final: 0.3235 (m100)
REVERT: H  122 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8184 (p)
REVERT: H  125 LEU cc_start: 0.8988 (pp) cc_final: 0.8775 (pt)
REVERT: B   81 TRP cc_start: 0.8674 (m-10) cc_final: 0.8315 (m-10)
REVERT: B  112 MET cc_start: 0.8610 (mpp) cc_final: 0.8094 (mpp)
REVERT: F  134 MET cc_start: 0.7579 (mtt) cc_final: 0.7366 (mmt)
REVERT: I   81 TRP cc_start: 0.7038 (m-10) cc_final: 0.5660 (m100)
REVERT: A  112 MET cc_start: 0.8589 (mpp) cc_final: 0.8076 (mpp)
  outliers start: 28
  outliers final: 23
  residues processed: 115
  average time/residue: 0.1088
  time to fit residues: 17.2741
Evaluate side-chains
  131 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   81 TRP
Chi-restraints excluded: chain J residue  103 SER
Chi-restraints excluded: chain J residue  122 VAL
Chi-restraints excluded: chain H residue  109 MET
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain D residue  122 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  141 PHE
Chi-restraints excluded: chain I residue  103 SER
Chi-restraints excluded: chain I residue  122 VAL
Chi-restraints excluded: chain G residue  109 MET
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  134 MET
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  141 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   chunk 25 optimal weight:   20.0000
   chunk 27 optimal weight:    8.9990
   chunk 13 optimal weight:    6.9990
   chunk 33 optimal weight:   20.0000
   chunk 40 optimal weight:   10.0000
   chunk 43 optimal weight:   20.0000
   chunk 14 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** D  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  98 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 = 0.4432 r_free = 0.4432 target = 0.146913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.138683 restraints weight = 8852.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.4355 rms_B_bonded: 3.18
r_work: 0.4260 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.4260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.6576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   4530  Z= 0.407
  Angle     :  0.764   8.882   6110  Z= 0.387
  Chirality :  0.047   0.154    560
  Planarity :  0.004   0.030    800
  Dihedral  :  4.919  14.272    630
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 15.95
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 12.67 %
    Favored  : 87.17 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 19.23 %
    Favored  : 73.85 %
  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: -5.21 (0.20), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.96 (0.15), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP G  99 
 HIS   0.005   0.001   HIS A  85 
 PHE   0.012   0.002   PHE E 141 
 TYR   0.012   0.002   TYR G 128 
 ARG   0.003   0.001   ARG I 136 

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

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

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1200 Ramachandran restraints generated.
    600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 110
  time to evaluate  : 0.480 
Fit side-chains
REVERT: J   81 TRP cc_start: 0.4766 (OUTLIER) cc_final: 0.3068 (m100)
REVERT: H  100 ASN cc_start: 0.9055 (t0) cc_final: 0.8474 (t0)
REVERT: B   81 TRP cc_start: 0.8674 (m-10) cc_final: 0.8355 (m-10)
REVERT: B  112 MET cc_start: 0.8645 (mpp) cc_final: 0.8061 (mpp)
REVERT: F  134 MET cc_start: 0.7630 (mtt) cc_final: 0.7412 (mmt)
REVERT: I   81 TRP cc_start: 0.7048 (m-10) cc_final: 0.5689 (m100)
REVERT: G  100 ASN cc_start: 0.9071 (t0) cc_final: 0.8496 (t0)
REVERT: A  112 MET cc_start: 0.8620 (mpp) cc_final: 0.8040 (mpp)
  outliers start: 27
  outliers final: 23
  residues processed: 118
  average time/residue: 0.0991
  time to fit residues: 16.2010
Evaluate side-chains
  131 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   81 TRP
Chi-restraints excluded: chain J residue  103 SER
Chi-restraints excluded: chain J residue  122 VAL
Chi-restraints excluded: chain H residue  109 MET
Chi-restraints excluded: chain D residue  122 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  141 PHE
Chi-restraints excluded: chain I residue  103 SER
Chi-restraints excluded: chain I residue  122 VAL
Chi-restraints excluded: chain G residue  109 MET
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  125 LEU
Chi-restraints excluded: chain C residue  134 MET
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  141 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 58 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 31 optimal weight:    9.9990
   chunk 6 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   chunk 51 optimal weight:   20.0000
   chunk 25 optimal weight:    8.9990
   chunk 32 optimal weight:    8.9990
   chunk 33 optimal weight:   20.0000
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
** D  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  98 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 = 0.4431 r_free = 0.4431 target = 0.146587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.138493 restraints weight = 8986.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.4352 rms_B_bonded: 3.16
r_work: 0.4251 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.4251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.6616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   4530  Z= 0.437
  Angle     :  0.782   6.997   6110  Z= 0.397
  Chirality :  0.047   0.154    560
  Planarity :  0.004   0.030    800
  Dihedral  :  5.033  14.510    630
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 16.65
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 13.50 %
    Favored  : 86.17 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 19.74 %
    Favored  : 73.33 %
  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: -5.30 (0.19), residues: 600
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.03 (0.15), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP G  99 
 HIS   0.006   0.001   HIS A  85 
 PHE   0.013   0.002   PHE E 141 
 TYR   0.011   0.002   TYR G 128 
 ARG   0.003   0.001   ARG I 136 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1814.45 seconds
wall clock time: 33 minutes 21.49 seconds (2001.49 seconds total)