Starting phenix.real_space_refine
on Fri Aug 22 19:27:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w2t_43758/08_2025/8w2t_43758_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w2t_43758/08_2025/8w2t_43758.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w2t_43758/08_2025/8w2t_43758_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w2t_43758/08_2025/8w2t_43758_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w2t_43758/08_2025/8w2t_43758.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w2t_43758/08_2025/8w2t_43758.map"
  }
  resolution = 2.52
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3298 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      26      5.16       5
     C    2846      2.51       5
     N     816      2.21       5
     O     798      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4488
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "D"
      Number of atoms: 2243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2243
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 8, 'TRANS': 275}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "Q"
      Number of atoms: 2243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2243
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 8, 'TRANS': 275}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "Q"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1635  SG  CYS D1081      55.052  15.823  63.245  1.00 73.54           S
  ATOM   1695  SG  CYS D1089      52.081  16.456  65.323  1.00 67.99           S
  ATOM   1721  SG  CYS D1092      54.777  18.829  65.304  1.00 66.89           S
  ATOM   3878  SG  CYS Q1081      12.251  34.067  11.902  1.00 85.28           S
  ATOM   3938  SG  CYS Q1089      14.760  32.502   9.703  1.00 77.24           S
  ATOM   3964  SG  CYS Q1092      15.927  35.341  12.028  1.00 75.79           S

  Time building chain proxies: 1.41, per 1000 atoms: 0.31
  Number of scatterers: 4488
  At special positions: 0
  Unit cell: (94.164, 100.772, 76.818, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      26     16.00
     O     798      8.00
     N     816      7.00
     C    2846      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: 0.38
  Conformation dependent library (CDL) restraints added in 174.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN D1201 "
        pdb="ZN    ZN D1201 " - pdb=" ND1 HIS D1084 "
        pdb="ZN    ZN D1201 " - pdb=" SG  CYS D1092 "
        pdb="ZN    ZN D1201 " - pdb=" SG  CYS D1089 "
        pdb="ZN    ZN D1201 " - pdb=" SG  CYS D1081 "
      pdb="  ZN Q1201 "
        pdb="ZN    ZN Q1201 " - pdb=" ND1 HIS Q1084 "
        pdb="ZN    ZN Q1201 " - pdb=" SG  CYS Q1089 "
        pdb="ZN    ZN Q1201 " - pdb=" SG  CYS Q1081 "
        pdb="ZN    ZN Q1201 " - pdb=" SG  CYS Q1092 "
      Number of angles added : 6


  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1020

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 4 sheets defined
      44.0% alpha, 16.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'D' and resid 875 through 886
      removed outlier: 4.365A  pdb=" N   THR D 879 " --> pdb=" O   ASP D 875 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 887 through 889
      No H-bonds generated for 'chain 'D' and resid 887 through 889'
    Processing helix  chain 'D' and resid 890 through 897
      removed outlier: 3.539A  pdb=" N   ARG D 896 " --> pdb=" O   ASP D 892 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 900 through 905
    Processing helix  chain 'D' and resid 908 through 916
    Processing helix  chain 'D' and resid 919 through 935
    Processing helix  chain 'D' and resid 937 through 940
    Processing helix  chain 'D' and resid 941 through 946
    Processing helix  chain 'D' and resid 962 through 975
      removed outlier: 3.525A  pdb=" N   THR D 975 " --> pdb=" O   GLU D 971 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1002 through 1019
    Processing helix  chain 'D' and resid 1035 through 1043
      removed outlier: 3.566A  pdb=" N   HIS D1041 " --> pdb=" O   ASN D1037 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1045 through 1049
    Processing helix  chain 'D' and resid 1064 through 1070
      removed outlier: 3.594A  pdb=" N   GLN D1070 " --> pdb=" O   SER D1066 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1074 through 1078
    Processing helix  chain 'D' and resid 1143 through 1145
      No H-bonds generated for 'chain 'D' and resid 1143 through 1145'
    Processing helix  chain 'Q' and resid 876 through 885
    Processing helix  chain 'Q' and resid 887 through 889
      No H-bonds generated for 'chain 'Q' and resid 887 through 889'
    Processing helix  chain 'Q' and resid 890 through 897
    Processing helix  chain 'Q' and resid 900 through 905
    Processing helix  chain 'Q' and resid 908 through 915
    Processing helix  chain 'Q' and resid 919 through 935
    Processing helix  chain 'Q' and resid 937 through 940
    Processing helix  chain 'Q' and resid 941 through 947
      removed outlier: 3.562A  pdb=" N   THR Q 945 " --> pdb=" O   ASN Q 941 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 962 through 975
      removed outlier: 3.609A  pdb=" N   THR Q 975 " --> pdb=" O   GLU Q 971 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 1002 through 1019
    Processing helix  chain 'Q' and resid 1035 through 1043
      removed outlier: 3.739A  pdb=" N   HIS Q1041 " --> pdb=" O   ASN Q1037 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 1045 through 1049
    Processing helix  chain 'Q' and resid 1064 through 1070
      removed outlier: 3.508A  pdb=" N   SER Q1068 " --> pdb=" O   ASN Q1064 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 1074 through 1078
    Processing helix  chain 'Q' and resid 1143 through 1145
      No H-bonds generated for 'chain 'Q' and resid 1143 through 1145'
    Processing sheet with id=AA1, first strand: chain 'D' and resid 954 through 957
      removed outlier: 5.264A  pdb=" N   ILE D 994 " --> pdb=" O   GLN D1156 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   GLN D1156 " --> pdb=" O   ILE D 994 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LYS D 996 " --> pdb=" O   THR D1154 " (cutoff:3.500A)
      removed outlier: 5.590A  pdb=" N   GLU D1150 " --> pdb=" O   VAL D1000 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   ALA D1147 " --> pdb=" O   THR D1102 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   THR D1102 " --> pdb=" O   ALA D1147 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ARG D1100 " --> pdb=" O   PRO D1149 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 1059 through 1061
      removed outlier: 6.253A  pdb=" N   PHE D1107 " --> pdb=" O   THR D1126 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'Q' and resid 954 through 957
      removed outlier: 6.294A  pdb=" N   TYR Q 992 " --> pdb=" O   MET Q1158 " (cutoff:3.500A)
      removed outlier: 6.019A  pdb=" N   MET Q1158 " --> pdb=" O   TYR Q 992 " (cutoff:3.500A)
      removed outlier: 5.301A  pdb=" N   ILE Q 994 " --> pdb=" O   GLN Q1156 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   GLN Q1156 " --> pdb=" O   ILE Q 994 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LYS Q 996 " --> pdb=" O   THR Q1154 " (cutoff:3.500A)
      removed outlier: 5.570A  pdb=" N   GLU Q1150 " --> pdb=" O   VAL Q1000 " (cutoff:3.500A)
      removed outlier: 6.036A  pdb=" N   ALA Q1147 " --> pdb=" O   THR Q1102 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   THR Q1102 " --> pdb=" O   ALA Q1147 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ARG Q1100 " --> pdb=" O   PRO Q1149 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'Q' and resid 1059 through 1062

    190 hydrogen bonds defined for protein.
    516 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: 0.66

  Time building geometry restraints manager: 0.50 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1500
        1.35 -     1.47: 1121
        1.47 -     1.59: 1929
        1.59 -     1.71: 0
        1.71 -     1.83: 42
  Bond restraints: 4592
  Sorted by residual:
  bond pdb=" CA  GLY D1133 "
       pdb=" C   GLY D1133 "
    ideal  model  delta    sigma   weight residual
    1.530  1.515  0.016 1.04e-02 9.25e+03 2.24e+00
  bond pdb=" N   GLY D1133 "
       pdb=" CA  GLY D1133 "
    ideal  model  delta    sigma   weight residual
    1.464  1.449  0.015 1.12e-02 7.97e+03 1.84e+00
  bond pdb=" CA  ASN Q 941 "
       pdb=" C   ASN Q 941 "
    ideal  model  delta    sigma   weight residual
    1.532  1.524  0.008 6.50e-03 2.37e+04 1.38e+00
  bond pdb=" C   ASN Q 941 "
       pdb=" O   ASN Q 941 "
    ideal  model  delta    sigma   weight residual
    1.233  1.238 -0.005 4.80e-03 4.34e+04 1.03e+00
  bond pdb=" CA  ILE Q 917 "
       pdb=" CB  ILE Q 917 "
    ideal  model  delta    sigma   weight residual
    1.527  1.539 -0.012 1.31e-02 5.83e+03 8.37e-01
  ... (remaining 4587 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.80: 5675
        0.80 -     1.59: 418
        1.59 -     2.39: 62
        2.39 -     3.18: 14
        3.18 -     3.98: 13
  Bond angle restraints: 6182
  Sorted by residual:
  angle pdb=" N   ASN D 947 "
        pdb=" CA  ASN D 947 "
        pdb=" CB  ASN D 947 "
      ideal   model   delta    sigma   weight residual
     112.78  109.70    3.08 1.53e+00 4.27e-01 4.06e+00
  angle pdb=" N   ILE D1051 "
        pdb=" CA  ILE D1051 "
        pdb=" C   ILE D1051 "
      ideal   model   delta    sigma   weight residual
     109.34  113.32   -3.98 2.08e+00 2.31e-01 3.66e+00
  angle pdb=" CA  ALA Q1057 "
        pdb=" C   ALA Q1057 "
        pdb=" N   GLY Q1058 "
      ideal   model   delta    sigma   weight residual
     114.60  117.08   -2.48 1.30e+00 5.92e-01 3.63e+00
  angle pdb=" CA  ALA Q1057 "
        pdb=" C   ALA Q1057 "
        pdb=" O   ALA Q1057 "
      ideal   model   delta    sigma   weight residual
     122.63  120.45    2.18 1.29e+00 6.01e-01 2.86e+00
  angle pdb=" N   GLY D1133 "
        pdb=" CA  GLY D1133 "
        pdb=" C   GLY D1133 "
      ideal   model   delta    sigma   weight residual
     111.67  113.22   -1.55 9.20e-01 1.18e+00 2.85e+00
  ... (remaining 6177 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 2407
       17.74 -    35.47: 202
       35.47 -    53.21: 72
       53.21 -    70.95: 15
       70.95 -    88.68: 8
  Dihedral angle restraints: 2704
    sinusoidal: 1090
      harmonic: 1614
  Sorted by residual:
  dihedral pdb=" CA  PHE Q1098 "
           pdb=" C   PHE Q1098 "
           pdb=" N   CYS Q1099 "
           pdb=" CA  CYS Q1099 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.82  -21.18     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  PHE D1098 "
           pdb=" C   PHE D1098 "
           pdb=" N   CYS D1099 "
           pdb=" CA  CYS D1099 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.18  -20.82     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" CA  GLU D1018 "
           pdb=" C   GLU D1018 "
           pdb=" N   GLU D1019 "
           pdb=" CA  GLU D1019 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.09   19.91     0      5.00e+00 4.00e-02 1.59e+01
  ... (remaining 2701 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 361
       0.027 -    0.053: 199
       0.053 -    0.080: 47
       0.080 -    0.107: 24
       0.107 -    0.133: 17
  Chirality restraints: 648
  Sorted by residual:
  chirality pdb=" CA  VAL D1000 "
            pdb=" N   VAL D1000 "
            pdb=" C   VAL D1000 "
            pdb=" CB  VAL D1000 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.44e-01
  chirality pdb=" CA  ILE Q1153 "
            pdb=" N   ILE Q1153 "
            pdb=" C   ILE Q1153 "
            pdb=" CB  ILE Q1153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.32e-01
  chirality pdb=" CA  ILE D 997 "
            pdb=" N   ILE D 997 "
            pdb=" C   ILE D 997 "
            pdb=" CB  ILE D 997 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.27e-01
  ... (remaining 645 not shown)

  Planarity restraints: 804
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS D1084 "    0.005 2.00e-02 2.50e+03   1.19e-02 2.13e+00
        pdb=" CG  HIS D1084 "   -0.023 2.00e-02 2.50e+03
        pdb=" ND1 HIS D1084 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 HIS D1084 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 HIS D1084 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE2 HIS D1084 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER Q 959 "   -0.018 5.00e-02 4.00e+02   2.66e-02 1.13e+00
        pdb=" N   PRO Q 960 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO Q 960 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO Q 960 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D 959 "   -0.017 5.00e-02 4.00e+02   2.64e-02 1.11e+00
        pdb=" N   PRO D 960 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO D 960 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO D 960 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 801 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 52
        2.67 -     3.23: 4134
        3.23 -     3.79: 6719
        3.79 -     4.34: 9849
        4.34 -     4.90: 15580
  Nonbonded interactions: 36334
  Sorted by model distance:
  nonbonded pdb=" O   ILE Q1091 "
            pdb=" NE2 GLN Q1156 "
     model   vdw
     2.118 3.120
  nonbonded pdb=" NH2 ARG D1027 "
            pdb=" OE2 GLU D1063 "
     model   vdw
     2.171 3.120
  nonbonded pdb=" OG1 THR Q 900 "
            pdb=" OD1 ASP Q 902 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" OE2 GLU Q 964 "
            pdb=" OH  TYR Q1151 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OG  SER D1106 "
            pdb=" OG1 THR D1126 "
     model   vdw
     2.323 3.040
  ... (remaining 36329 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = chain 'Q'
}

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:             4.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.100
  Find NCS groups from input model:        0.070
  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:6.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
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      :  0.011   0.656   4600  Z= 0.388
  Angle     :  0.631  19.235   6188  Z= 0.306
  Chirality :  0.039   0.133    648
  Planarity :  0.003   0.027    804
  Dihedral  : 16.005  88.682   1684
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 1.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 11.90 %
    Favored  : 87.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.35), residues: 564
  helix:  0.72 (0.38), residues: 204
  sheet: -0.51 (0.41), residues: 132
  loop : -0.08 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG Q1087 
 TYR   0.009   0.001   TYR D1090 
 PHE   0.015   0.001   PHE D1055 
 TRP   0.006   0.001   TRP Q1006 
 HIS   0.017   0.001   HIS D1084 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 4592)
  covalent geometry    : angle       0.48940 ( 6182)
  hydrogen bonds       : bond        0.17126 (  190)
  hydrogen bonds       : angle       5.89281 (  516)
  metal coordination   : bond        0.25628 (    8)
  metal coordination   : angle      12.82236 (    6)

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

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

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 100
  time to evaluate  : 0.197 
Fit side-chains
REVERT: D  963 LYS cc_start: 0.7675 (pttt) cc_final: 0.7468 (ptpp)
REVERT: Q 1087 ARG cc_start: 0.7116 (mtm-85) cc_final: 0.6826 (ttm110)
REVERT: Q 1113 MET cc_start: 0.7132 (ptt) cc_final: 0.6834 (pp-130)
  outliers start: 3
  outliers final: 0
  residues processed: 102
  average time/residue: 0.8272
  time to fit residues: 86.5513
Evaluate side-chains
  71 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    9.9990
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
D 941 ASN
D 966 GLN
D1041 HIS
Q 889 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.178403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.151573 restraints weight = 4724.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3820 rms_B_bonded: 1.85
r_work: 0.3718 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3617 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.167   4600  Z= 0.218
  Angle     :  0.597   8.212   6188  Z= 0.329
  Chirality :  0.045   0.147    648
  Planarity :  0.004   0.043    804
  Dihedral  :  5.131  22.092    628
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 12.99 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.36), residues: 564
  helix:  0.51 (0.37), residues: 210
  sheet:  0.00 (0.46), residues: 120
  loop :  0.13 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D1047 
 TYR   0.016   0.002   TYR Q 992 
 PHE   0.026   0.002   PHE D 881 
 TRP   0.006   0.002   TRP Q1006 
 HIS   0.005   0.002   HIS Q 924 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 4592)
  covalent geometry    : angle       0.57465 ( 6182)
  hydrogen bonds       : bond        0.05945 (  190)
  hydrogen bonds       : angle       4.94601 (  516)
  metal coordination   : bond        0.06013 (    8)
  metal coordination   : angle       5.20760 (    6)

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

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

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.195 
Fit side-chains
REVERT: D  963 LYS cc_start: 0.7488 (pttt) cc_final: 0.7260 (pttm)
REVERT: D 1138 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6668 (tt0)
REVERT: Q  896 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7071 (mmt-90)
REVERT: Q 1067 LYS cc_start: 0.7629 (ttmp) cc_final: 0.7264 (ttpm)
REVERT: Q 1087 ARG cc_start: 0.7267 (mtm-85) cc_final: 0.6837 (ttm110)
REVERT: Q 1113 MET cc_start: 0.7812 (ptt) cc_final: 0.7103 (pp-130)
  outliers start: 12
  outliers final: 4
  residues processed: 74
  average time/residue: 0.7218
  time to fit residues: 55.0457
Evaluate side-chains
  74 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  892 ASP
Chi-restraints excluded: chain D residue  954 ILE
Chi-restraints excluded: chain D residue  972 MET
Chi-restraints excluded: chain D residue 1138 GLU
Chi-restraints excluded: chain Q residue  896 ARG
Chi-restraints excluded: chain Q residue 1072 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0770
   chunk 27 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0970
   chunk 10 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.4736

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.180090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.153516 restraints weight = 4664.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 1.86
r_work: 0.3743 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3644 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   4600  Z= 0.130
  Angle     :  0.473   5.208   6188  Z= 0.265
  Chirality :  0.042   0.141    648
  Planarity :  0.003   0.029    804
  Dihedral  :  4.773  21.495    628
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 12.99 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.36), residues: 564
  helix:  0.68 (0.37), residues: 212
  sheet:  0.22 (0.46), residues: 116
  loop :  0.10 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Q1027 
 TYR   0.011   0.001   TYR D1142 
 PHE   0.016   0.002   PHE Q 881 
 TRP   0.004   0.001   TRP D1006 
 HIS   0.005   0.001   HIS Q 909 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 4592)
  covalent geometry    : angle       0.46596 ( 6182)
  hydrogen bonds       : bond        0.04651 (  190)
  hydrogen bonds       : angle       4.54468 (  516)
  metal coordination   : bond        0.02290 (    8)
  metal coordination   : angle       2.64405 (    6)

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

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

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.173 
Fit side-chains
REVERT: D  969 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7523 (tt0)
REVERT: Q 1067 LYS cc_start: 0.7733 (ttmp) cc_final: 0.7507 (tttp)
REVERT: Q 1087 ARG cc_start: 0.7280 (mtm-85) cc_final: 0.6850 (ttm110)
  outliers start: 14
  outliers final: 4
  residues processed: 76
  average time/residue: 0.6903
  time to fit residues: 54.0909
Evaluate side-chains
  71 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  892 ASP
Chi-restraints excluded: chain D residue  969 GLU
Chi-restraints excluded: chain D residue  972 MET
Chi-restraints excluded: chain Q residue  953 THR
Chi-restraints excluded: chain Q residue 1072 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 18 optimal weight:    0.1980
   chunk 10 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 54 optimal weight:    0.4980
   chunk 7 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
Q1070 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.170399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.142618 restraints weight = 4407.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 1.82
r_work: 0.3533 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3420 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.2786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   4600  Z= 0.178
  Angle     :  0.515   4.865   6188  Z= 0.288
  Chirality :  0.043   0.136    648
  Planarity :  0.003   0.031    804
  Dihedral  :  4.907  22.535    628
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 14.07 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.36), residues: 564
  helix:  0.51 (0.36), residues: 214
  sheet:  0.20 (0.47), residues: 116
  loop :  0.04 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D1027 
 TYR   0.012   0.002   TYR Q 992 
 PHE   0.019   0.002   PHE D 881 
 TRP   0.005   0.002   TRP D1006 
 HIS   0.005   0.001   HIS Q1021 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 4592)
  covalent geometry    : angle       0.50609 ( 6182)
  hydrogen bonds       : bond        0.05222 (  190)
  hydrogen bonds       : angle       4.64046 (  516)
  metal coordination   : bond        0.02321 (    8)
  metal coordination   : angle       3.03976 (    6)

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

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

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.205 
Fit side-chains
REVERT: D  991 ARG cc_start: 0.7963 (ptp-170) cc_final: 0.7623 (ptp-170)
REVERT: D 1138 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6501 (tt0)
REVERT: Q  991 ARG cc_start: 0.7568 (ttt180) cc_final: 0.7010 (ttt90)
REVERT: Q 1014 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7616 (ttmt)
REVERT: Q 1067 LYS cc_start: 0.7750 (ttmp) cc_final: 0.7127 (ttpm)
REVERT: Q 1087 ARG cc_start: 0.7291 (mtm-85) cc_final: 0.6852 (ttm110)
  outliers start: 17
  outliers final: 8
  residues processed: 75
  average time/residue: 0.5946
  time to fit residues: 46.1321
Evaluate side-chains
  73 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  892 ASP
Chi-restraints excluded: chain D residue  972 MET
Chi-restraints excluded: chain D residue 1138 GLU
Chi-restraints excluded: chain Q residue  896 ARG
Chi-restraints excluded: chain Q residue  934 ILE
Chi-restraints excluded: chain Q residue  953 THR
Chi-restraints excluded: chain Q residue 1014 LYS
Chi-restraints excluded: chain Q residue 1072 VAL
Chi-restraints excluded: chain Q residue 1099 CYS
Chi-restraints excluded: chain Q residue 1102 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
D 922 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.176011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.147274 restraints weight = 4742.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3778 rms_B_bonded: 1.84
r_work: 0.3698 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3598 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.2972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   4600  Z= 0.190
  Angle     :  0.526   4.873   6188  Z= 0.295
  Chirality :  0.044   0.139    648
  Planarity :  0.004   0.032    804
  Dihedral  :  4.977  23.237    628
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 13.64 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.35), residues: 564
  helix:  0.39 (0.36), residues: 214
  sheet:  0.05 (0.46), residues: 116
  loop :  0.00 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D1027 
 TYR   0.012   0.002   TYR Q 992 
 PHE   0.019   0.002   PHE D 881 
 TRP   0.005   0.002   TRP D1006 
 HIS   0.006   0.001   HIS Q1021 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 4592)
  covalent geometry    : angle       0.51893 ( 6182)
  hydrogen bonds       : bond        0.05308 (  190)
  hydrogen bonds       : angle       4.68109 (  516)
  metal coordination   : bond        0.02269 (    8)
  metal coordination   : angle       2.85499 (    6)

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

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

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 69
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
REVERT: Q  991 ARG cc_start: 0.7514 (ttt180) cc_final: 0.6995 (ttt90)
REVERT: Q 1014 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7692 (ttmt)
REVERT: Q 1067 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7239 (ttpm)
REVERT: Q 1087 ARG cc_start: 0.7379 (mtm-85) cc_final: 0.6901 (ttm110)
  outliers start: 21
  outliers final: 12
  residues processed: 80
  average time/residue: 0.6122
  time to fit residues: 50.5897
Evaluate side-chains
  81 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  882 VAL
Chi-restraints excluded: chain D residue  892 ASP
Chi-restraints excluded: chain D residue  972 MET
Chi-restraints excluded: chain D residue 1140 VAL
Chi-restraints excluded: chain D residue 1143 ARG
Chi-restraints excluded: chain Q residue  896 ARG
Chi-restraints excluded: chain Q residue  934 ILE
Chi-restraints excluded: chain Q residue  953 THR
Chi-restraints excluded: chain Q residue 1014 LYS
Chi-restraints excluded: chain Q residue 1067 LYS
Chi-restraints excluded: chain Q residue 1072 VAL
Chi-restraints excluded: chain Q residue 1099 CYS
Chi-restraints excluded: chain Q residue 1102 THR
Chi-restraints excluded: chain Q residue 1106 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 53 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0770
   chunk 9 optimal weight:    0.0970
   chunk 39 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.4936

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

Flipped N/Q/H residues before XYZ refinement:
D 941 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.177689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.150989 restraints weight = 4870.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3809 rms_B_bonded: 1.85
r_work: 0.3708 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3610 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4600  Z= 0.134
  Angle     :  0.471   4.301   6188  Z= 0.265
  Chirality :  0.041   0.138    648
  Planarity :  0.003   0.031    804
  Dihedral  :  4.725  22.295    628
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 14.72 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.36), residues: 564
  helix:  0.56 (0.36), residues: 214
  sheet:  0.05 (0.46), residues: 116
  loop :  0.08 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG Q1027 
 TYR   0.010   0.001   TYR D1142 
 PHE   0.015   0.001   PHE Q 881 
 TRP   0.004   0.001   TRP D1006 
 HIS   0.004   0.001   HIS Q 924 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 4592)
  covalent geometry    : angle       0.46727 ( 6182)
  hydrogen bonds       : bond        0.04474 (  190)
  hydrogen bonds       : angle       4.47283 (  516)
  metal coordination   : bond        0.01352 (    8)
  metal coordination   : angle       1.86748 (    6)

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

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

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.182 
Fit side-chains
REVERT: D  969 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7552 (tt0)
REVERT: D 1007 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8138 (mt-10)
REVERT: Q  991 ARG cc_start: 0.7561 (ttt180) cc_final: 0.7162 (ttt90)
REVERT: Q 1014 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7692 (ttmt)
REVERT: Q 1067 LYS cc_start: 0.7864 (ttmp) cc_final: 0.7242 (ttpm)
REVERT: Q 1087 ARG cc_start: 0.7400 (mtm-85) cc_final: 0.6937 (ttm110)
  outliers start: 19
  outliers final: 7
  residues processed: 77
  average time/residue: 0.6599
  time to fit residues: 52.3894
Evaluate side-chains
  79 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  882 VAL
Chi-restraints excluded: chain D residue  892 ASP
Chi-restraints excluded: chain D residue  969 GLU
Chi-restraints excluded: chain D residue  972 MET
Chi-restraints excluded: chain D residue 1007 GLU
Chi-restraints excluded: chain Q residue  953 THR
Chi-restraints excluded: chain Q residue 1014 LYS
Chi-restraints excluded: chain Q residue 1072 VAL
Chi-restraints excluded: chain Q residue 1099 CYS
Chi-restraints excluded: chain Q residue 1106 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 25 optimal weight:    8.9990
   chunk 3 optimal weight:    0.3980
   chunk 20 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
D 941 ASN
D1022 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.176982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.148538 restraints weight = 4830.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3790 rms_B_bonded: 1.84
r_work: 0.3708 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3608 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4600  Z= 0.154
  Angle     :  0.494   6.630   6188  Z= 0.276
  Chirality :  0.042   0.136    648
  Planarity :  0.003   0.031    804
  Dihedral  :  4.761  22.450    628
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 14.72 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.35), residues: 564
  helix:  0.53 (0.36), residues: 214
  sheet:  0.04 (0.46), residues: 116
  loop :  0.05 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D1027 
 TYR   0.017   0.002   TYR Q1071 
 PHE   0.015   0.002   PHE Q 881 
 TRP   0.004   0.001   TRP D1006 
 HIS   0.004   0.001   HIS Q1021 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 4592)
  covalent geometry    : angle       0.48977 ( 6182)
  hydrogen bonds       : bond        0.04782 (  190)
  hydrogen bonds       : angle       4.51117 (  516)
  metal coordination   : bond        0.01467 (    8)
  metal coordination   : angle       2.20491 (    6)

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

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

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
REVERT: D  969 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7553 (tt0)
REVERT: D 1007 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8158 (mt-10)
REVERT: Q  910 LYS cc_start: 0.7969 (mmmt) cc_final: 0.7567 (ttpp)
REVERT: Q  991 ARG cc_start: 0.7534 (ttt180) cc_final: 0.7101 (ttt90)
REVERT: Q 1014 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7652 (ttmt)
REVERT: Q 1067 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7398 (tttp)
REVERT: Q 1087 ARG cc_start: 0.7378 (mtm-85) cc_final: 0.6891 (ttm110)
  outliers start: 17
  outliers final: 10
  residues processed: 80
  average time/residue: 0.6819
  time to fit residues: 56.1403
Evaluate side-chains
  83 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  882 VAL
Chi-restraints excluded: chain D residue  892 ASP
Chi-restraints excluded: chain D residue  969 GLU
Chi-restraints excluded: chain D residue  972 MET
Chi-restraints excluded: chain D residue 1007 GLU
Chi-restraints excluded: chain D residue 1115 MET
Chi-restraints excluded: chain D residue 1143 ARG
Chi-restraints excluded: chain Q residue  953 THR
Chi-restraints excluded: chain Q residue 1014 LYS
Chi-restraints excluded: chain Q residue 1067 LYS
Chi-restraints excluded: chain Q residue 1072 VAL
Chi-restraints excluded: chain Q residue 1099 CYS
Chi-restraints excluded: chain Q residue 1102 THR
Chi-restraints excluded: chain Q residue 1106 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0030
   chunk 30 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0060
   chunk 0 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0170
   chunk 44 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 55 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.2844

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

Flipped N/Q/H residues before XYZ refinement:
D 941 ASN
** Q1064 ASN ** 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 = 0.4101 r_free = 0.4101 target = 0.179759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.151590 restraints weight = 4751.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 1.83
r_work: 0.3746 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3649 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.3260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4600  Z= 0.099
  Angle     :  0.440   6.855   6188  Z= 0.245
  Chirality :  0.040   0.140    648
  Planarity :  0.003   0.029    804
  Dihedral  :  4.467  21.276    628
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 15.80 %
    Favored  : 81.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.36), residues: 564
  helix:  0.75 (0.36), residues: 214
  sheet:  0.05 (0.46), residues: 116
  loop :  0.05 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG Q1027 
 TYR   0.009   0.001   TYR D1142 
 PHE   0.013   0.001   PHE Q 881 
 TRP   0.003   0.001   TRP D1006 
 HIS   0.004   0.001   HIS Q 909 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 4592)
  covalent geometry    : angle       0.43884 ( 6182)
  hydrogen bonds       : bond        0.03843 (  190)
  hydrogen bonds       : angle       4.27864 (  516)
  metal coordination   : bond        0.00893 (    8)
  metal coordination   : angle       1.30078 (    6)

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

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

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
REVERT: D  932 ARG cc_start: 0.7578 (mtm-85) cc_final: 0.7351 (ttp-110)
REVERT: D 1007 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.8041 (mt-10)
REVERT: D 1115 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7496 (ptp)
REVERT: D 1138 GLU cc_start: 0.7027 (tt0) cc_final: 0.6792 (mt-10)
REVERT: Q  910 LYS cc_start: 0.7898 (mmmt) cc_final: 0.7531 (ttpp)
REVERT: Q  991 ARG cc_start: 0.7525 (ttt180) cc_final: 0.7140 (ttt90)
REVERT: Q 1014 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7573 (ttmt)
REVERT: Q 1067 LYS cc_start: 0.7774 (ttmp) cc_final: 0.7391 (tttp)
REVERT: Q 1087 ARG cc_start: 0.7396 (mtm-85) cc_final: 0.6915 (ttm110)
REVERT: Q 1108 LEU cc_start: 0.8582 (mp) cc_final: 0.8119 (mp)
  outliers start: 13
  outliers final: 9
  residues processed: 86
  average time/residue: 0.6303
  time to fit residues: 56.0009
Evaluate side-chains
  84 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  882 VAL
Chi-restraints excluded: chain D residue  892 ASP
Chi-restraints excluded: chain D residue  972 MET
Chi-restraints excluded: chain D residue 1007 GLU
Chi-restraints excluded: chain D residue 1115 MET
Chi-restraints excluded: chain D residue 1140 VAL
Chi-restraints excluded: chain D residue 1143 ARG
Chi-restraints excluded: chain Q residue 1014 LYS
Chi-restraints excluded: chain Q residue 1072 VAL
Chi-restraints excluded: chain Q residue 1099 CYS
Chi-restraints excluded: chain Q residue 1102 THR
Chi-restraints excluded: chain Q residue 1106 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0980
   chunk 41 optimal weight:    0.2980
   chunk 42 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 48 optimal weight:   10.0000
   chunk 5 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 20 optimal weight:    0.1980
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
D1022 ASN
** Q1064 ASN ** 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 = 0.4094 r_free = 0.4094 target = 0.178710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.150491 restraints weight = 4744.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3812 rms_B_bonded: 1.83
r_work: 0.3735 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3638 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.3240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4600  Z= 0.117
  Angle     :  0.458   6.919   6188  Z= 0.253
  Chirality :  0.041   0.137    648
  Planarity :  0.003   0.029    804
  Dihedral  :  4.499  21.489    628
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 16.23 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.36), residues: 564
  helix:  0.73 (0.36), residues: 214
  sheet:  0.06 (0.46), residues: 116
  loop :  0.08 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG Q 883 
 TYR   0.014   0.001   TYR Q1071 
 PHE   0.013   0.001   PHE Q 881 
 TRP   0.004   0.001   TRP D1006 
 HIS   0.004   0.001   HIS Q 924 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 4592)
  covalent geometry    : angle       0.45535 ( 6182)
  hydrogen bonds       : bond        0.04155 (  190)
  hydrogen bonds       : angle       4.33977 (  516)
  metal coordination   : bond        0.01020 (    8)
  metal coordination   : angle       1.64185 (    6)

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

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

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: D  932 ARG cc_start: 0.7604 (mtm-85) cc_final: 0.7373 (ttp-110)
REVERT: D 1007 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8038 (mt-10)
REVERT: D 1115 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7397 (ptp)
REVERT: D 1138 GLU cc_start: 0.7032 (tt0) cc_final: 0.6788 (mt-10)
REVERT: Q  991 ARG cc_start: 0.7536 (ttt180) cc_final: 0.7139 (ttt90)
REVERT: Q 1014 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7666 (ttmt)
REVERT: Q 1067 LYS cc_start: 0.7818 (ttmp) cc_final: 0.7203 (ttpm)
REVERT: Q 1087 ARG cc_start: 0.7410 (mtm-85) cc_final: 0.6925 (ttm110)
REVERT: Q 1108 LEU cc_start: 0.8533 (mp) cc_final: 0.8088 (mp)
  outliers start: 13
  outliers final: 9
  residues processed: 84
  average time/residue: 0.6982
  time to fit residues: 60.5104
Evaluate side-chains
  83 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  882 VAL
Chi-restraints excluded: chain D residue  892 ASP
Chi-restraints excluded: chain D residue  972 MET
Chi-restraints excluded: chain D residue 1007 GLU
Chi-restraints excluded: chain D residue 1115 MET
Chi-restraints excluded: chain D residue 1140 VAL
Chi-restraints excluded: chain D residue 1143 ARG
Chi-restraints excluded: chain Q residue 1014 LYS
Chi-restraints excluded: chain Q residue 1072 VAL
Chi-restraints excluded: chain Q residue 1099 CYS
Chi-restraints excluded: chain Q residue 1102 THR
Chi-restraints excluded: chain Q residue 1106 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0980
   chunk 52 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 4 optimal weight:    0.0970
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
Q1064 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.177429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.149028 restraints weight = 4760.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3797 rms_B_bonded: 1.83
r_work: 0.3720 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3621 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.3301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4600  Z= 0.145
  Angle     :  0.505   7.382   6188  Z= 0.276
  Chirality :  0.042   0.136    648
  Planarity :  0.003   0.030    804
  Dihedral  :  4.618  22.019    628
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 16.02 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.36), residues: 564
  helix:  0.65 (0.36), residues: 214
  sheet:  0.07 (0.46), residues: 116
  loop :  0.01 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG Q1027 
 TYR   0.011   0.002   TYR D1142 
 PHE   0.013   0.002   PHE D 965 
 TRP   0.004   0.001   TRP D1006 
 HIS   0.004   0.001   HIS Q1021 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 4592)
  covalent geometry    : angle       0.50104 ( 6182)
  hydrogen bonds       : bond        0.04536 (  190)
  hydrogen bonds       : angle       4.43452 (  516)
  metal coordination   : bond        0.01287 (    8)
  metal coordination   : angle       1.99524 (    6)

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

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

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1128 Ramachandran restraints generated.
    564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: D  969 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7523 (tt0)
REVERT: D 1007 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8107 (mt-10)
REVERT: D 1115 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7511 (ptp)
REVERT: D 1138 GLU cc_start: 0.7065 (tt0) cc_final: 0.6830 (mt-10)
REVERT: Q  910 LYS cc_start: 0.7992 (mmmt) cc_final: 0.7607 (ttpp)
REVERT: Q  991 ARG cc_start: 0.7554 (ttt180) cc_final: 0.7165 (ttt90)
REVERT: Q 1014 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7694 (ttmt)
REVERT: Q 1067 LYS cc_start: 0.7898 (ttmp) cc_final: 0.7285 (ttpm)
REVERT: Q 1087 ARG cc_start: 0.7430 (mtm-85) cc_final: 0.6957 (ttm110)
  outliers start: 16
  outliers final: 10
  residues processed: 82
  average time/residue: 0.6954
  time to fit residues: 58.8157
Evaluate side-chains
  84 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  882 VAL
Chi-restraints excluded: chain D residue  892 ASP
Chi-restraints excluded: chain D residue  969 GLU
Chi-restraints excluded: chain D residue  972 MET
Chi-restraints excluded: chain D residue 1007 GLU
Chi-restraints excluded: chain D residue 1115 MET
Chi-restraints excluded: chain D residue 1140 VAL
Chi-restraints excluded: chain D residue 1143 ARG
Chi-restraints excluded: chain Q residue  953 THR
Chi-restraints excluded: chain Q residue 1014 LYS
Chi-restraints excluded: chain Q residue 1072 VAL
Chi-restraints excluded: chain Q residue 1099 CYS
Chi-restraints excluded: chain Q residue 1102 THR
Chi-restraints excluded: chain Q residue 1106 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 8 optimal weight:    0.1980
   chunk 33 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.176940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.148291 restraints weight = 4805.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3791 rms_B_bonded: 1.85
r_work: 0.3710 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3612 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4600  Z= 0.154
  Angle     :  0.511   8.483   6188  Z= 0.279
  Chirality :  0.042   0.136    648
  Planarity :  0.003   0.030    804
  Dihedral  :  4.694  22.418    628
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 16.45 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.36), residues: 564
  helix:  0.56 (0.36), residues: 214
  sheet:  0.08 (0.46), residues: 116
  loop :  0.00 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D1027 
 TYR   0.015   0.002   TYR Q1071 
 PHE   0.013   0.002   PHE D 881 
 TRP   0.004   0.001   TRP D1006 
 HIS   0.005   0.001   HIS Q1021 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 4592)
  covalent geometry    : angle       0.50706 ( 6182)
  hydrogen bonds       : bond        0.04670 (  190)
  hydrogen bonds       : angle       4.48588 (  516)
  metal coordination   : bond        0.01396 (    8)
  metal coordination   : angle       2.17422 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2318.83 seconds
wall clock time: 40 minutes 6.38 seconds (2406.38 seconds total)