Starting phenix.real_space_refine
on Tue Feb 11 14:04:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tld_41367/02_2025/8tld_41367.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tld_41367/02_2025/8tld_41367.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tld_41367/02_2025/8tld_41367.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tld_41367/02_2025/8tld_41367.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tld_41367/02_2025/8tld_41367.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tld_41367/02_2025/8tld_41367.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.026
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      27      5.16       5
     C    3776      2.51       5
     N    1040      2.21       5
     O    1139      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5982
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "B"
      Number of atoms: 758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 758
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 9, 'TRANS': 84}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 862
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 3, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 879
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 879
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 3, 'TRANS': 105}
    Chain: "E"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 942
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 4, 'TRANS': 108}
    Chain: "F"
      Number of atoms: 2471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2471
          Classifications: {'peptide': 308}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 291}
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 4.08, per 1000 atoms: 0.68
  Number of scatterers: 5982
  At special positions: 0
  Unit cell: (80.972, 112.316, 124.07, 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      27     16.00
     O    1139      8.00
     N    1040      7.00
     C    3776      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  35 " - pdb=" SG  CYS B  45 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  72 " - pdb=" SG  CYS B  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  83 " - pdb=" SG  CYS B  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  64 " - pdb=" SG  CYS D 106 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 106 " - pdb=" SG  CYS D  64 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 134 " - pdb=" SG  CYS F 155 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 182 " - pdb=" SG  CYS F 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 269 " - pdb=" SG  CYS F 316 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG C 200 " - " ASN C  48 "
      " NAG F 501 " - " ASN F  35 "
      " NAG F 502 " - " ASN F 131 "
      " NAG F 503 " - " ASN F 216 "
      " NAG F 504 " - " ASN F 244 "
  Time building additional restraints: 1.23
  Conformation dependent library (CDL) restraints added in 907.4 milliseconds
  

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1400

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 11 sheets defined
      24.9% alpha, 31.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'B' and resid 27 through 33
    Processing helix  chain 'B' and resid 51 through 55
      removed outlier: 3.859A  pdb=" N   ARG B  55 " --> pdb=" O   GLN B  51 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 51 through 55'
    Processing helix  chain 'C' and resid 26 through 41
    Processing helix  chain 'C' and resid 41 through 46
    Processing helix  chain 'C' and resid 64 through 78
    Processing helix  chain 'C' and resid 84 through 105
      removed outlier: 3.673A  pdb=" N   ASN C  91 " --> pdb=" O   ARG C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 130
    Processing helix  chain 'D' and resid 29 through 41
    Processing helix  chain 'D' and resid 41 through 46
      removed outlier: 3.536A  pdb=" N   LEU D  45 " --> pdb=" O   HIS D  41 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 60 through 63
      removed outlier: 3.721A  pdb=" N   LEU D  63 " --> pdb=" O   ASN D  60 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 60 through 63'
    Processing helix  chain 'D' and resid 64 through 79
    Processing helix  chain 'D' and resid 83 through 106
      removed outlier: 4.037A  pdb=" N   ARG D  87 " --> pdb=" O   GLY D  83 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   TYR D  98 " --> pdb=" O   LEU D  94 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ILE D  99 " --> pdb=" O   ILE D  95 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 112 through 130
    Processing helix  chain 'E' and resid 382 through 386
    Processing helix  chain 'F' and resid 232 through 237
    Processing sheet with id=AA1, first strand: chain 'B' and resid 34 through 37
    Processing sheet with id=AA2, first strand: chain 'B' and resid 59 through 64
    Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 55
      removed outlier: 4.293A  pdb=" N   GLU D 109 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   SER F  95 " --> pdb=" O   ASN F  70 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 55
      removed outlier: 4.293A  pdb=" N   GLU D 109 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   SER F  95 " --> pdb=" O   ASN F  70 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 344 through 350
    Processing sheet with id=AA6, first strand: chain 'E' and resid 387 through 392
    Processing sheet with id=AA7, first strand: chain 'F' and resid 34 through 42
      removed outlier: 5.518A  pdb=" N   ASN F  35 " --> pdb=" O   LYS F  51 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   LYS F  51 " --> pdb=" O   ASN F  35 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LYS F  39 " --> pdb=" O   LEU F  47 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   THR F  41 " --> pdb=" O   GLN F  45 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   GLN F  45 " --> pdb=" O   THR F  41 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 130 through 140
      removed outlier: 5.696A  pdb=" N   ASN F 131 " --> pdb=" O   LEU F 158 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   LEU F 158 " --> pdb=" O   ASN F 131 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   VAL F 151 " --> pdb=" O   ARG F 200 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   ARG F 200 " --> pdb=" O   VAL F 151 " (cutoff:3.500A)
      removed outlier: 5.281A  pdb=" N   ILE F 194 " --> pdb=" O   TRP F 157 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   SER F 186 " --> pdb=" O   ILE F 194 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 178 through 181
    Processing sheet with id=AB1, first strand: chain 'F' and resid 246 through 250
    Processing sheet with id=AB2, first strand: chain 'F' and resid 284 through 289

    280 hydrogen bonds defined for protein.
    768 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.07

  Time building geometry restraints manager: 1.55 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1954
        1.34 -     1.46: 1304
        1.46 -     1.58: 2820
        1.58 -     1.70: 2
        1.70 -     1.82: 36
  Bond restraints: 6116
  Sorted by residual:
  bond pdb=" CG  PRO C  54 "
       pdb=" CD  PRO C  54 "
    ideal  model  delta    sigma   weight residual
    1.503  1.296  0.207 3.40e-02 8.65e+02 3.70e+01
  bond pdb=" CB  PRO C  54 "
       pdb=" CG  PRO C  54 "
    ideal  model  delta    sigma   weight residual
    1.492  1.668 -0.176 5.00e-02 4.00e+02 1.23e+01
  bond pdb=" N   PRO C  54 "
       pdb=" CD  PRO C  54 "
    ideal  model  delta    sigma   weight residual
    1.473  1.522 -0.049 1.40e-02 5.10e+03 1.21e+01
  bond pdb=" N   PRO C  54 "
       pdb=" CA  PRO C  54 "
    ideal  model  delta    sigma   weight residual
    1.469  1.438  0.030 1.28e-02 6.10e+03 5.64e+00
  bond pdb=" C1  NAG F 503 "
       pdb=" O5  NAG F 503 "
    ideal  model  delta    sigma   weight residual
    1.406  1.451 -0.045 2.00e-02 2.50e+03 5.14e+00
  ... (remaining 6111 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.60: 8264
        3.60 -     7.20: 37
        7.20 -    10.81: 5
       10.81 -    14.41: 1
       14.41 -    18.01: 1
  Bond angle restraints: 8308
  Sorted by residual:
  angle pdb=" CA  PRO C  54 "
        pdb=" N   PRO C  54 "
        pdb=" CD  PRO C  54 "
      ideal   model   delta    sigma   weight residual
     112.00   93.99   18.01 1.40e+00 5.10e-01 1.65e+02
  angle pdb=" N   PRO C  54 "
        pdb=" CD  PRO C  54 "
        pdb=" CG  PRO C  54 "
      ideal   model   delta    sigma   weight residual
     103.20   90.46   12.74 1.50e+00 4.44e-01 7.21e+01
  angle pdb=" CA  PRO C  54 "
        pdb=" CB  PRO C  54 "
        pdb=" CG  PRO C  54 "
      ideal   model   delta    sigma   weight residual
     104.50   94.84    9.66 1.90e+00 2.77e-01 2.59e+01
  angle pdb=" CA  PRO F 261 "
        pdb=" N   PRO F 261 "
        pdb=" CD  PRO F 261 "
      ideal   model   delta    sigma   weight residual
     112.00  106.01    5.99 1.40e+00 5.10e-01 1.83e+01
  angle pdb=" C   GLU D  24 "
        pdb=" N   ILE D  25 "
        pdb=" CA  ILE D  25 "
      ideal   model   delta    sigma   weight residual
     122.13  129.53   -7.40 1.85e+00 2.92e-01 1.60e+01
  ... (remaining 8303 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 3192
       17.71 -    35.41: 429
       35.41 -    53.12: 121
       53.12 -    70.82: 18
       70.82 -    88.53: 12
  Dihedral angle restraints: 3772
    sinusoidal: 1622
      harmonic: 2150
  Sorted by residual:
  dihedral pdb=" CA  GLN C 102 "
           pdb=" C   GLN C 102 "
           pdb=" N   LYS C 103 "
           pdb=" CA  LYS C 103 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.91   27.09     0      5.00e+00 4.00e-02 2.93e+01
  dihedral pdb=" CA  ASN C  48 "
           pdb=" C   ASN C  48 "
           pdb=" N   GLU C  49 "
           pdb=" CA  GLU C  49 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.26  -25.74     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CB  CYS C  64 "
           pdb=" SG  CYS C  64 "
           pdb=" SG  CYS D 106 "
           pdb=" CB  CYS D 106 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -45.06  -40.94     1      1.00e+01 1.00e-02 2.35e+01
  ... (remaining 3769 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 874
       0.084 -    0.167: 70
       0.167 -    0.251: 1
       0.251 -    0.334: 0
       0.334 -    0.418: 1
  Chirality restraints: 946
  Sorted by residual:
  chirality pdb=" C1  NAG C 200 "
            pdb=" ND2 ASN C  48 "
            pdb=" C2  NAG C 200 "
            pdb=" O5  NAG C 200 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.98   -0.42 2.00e-01 2.50e+01 4.36e+00
  chirality pdb=" CA  ASN D  60 "
            pdb=" N   ASN D  60 "
            pdb=" C   ASN D  60 "
            pdb=" CB  ASN D  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.18 2.00e-01 2.50e+01 7.67e-01
  chirality pdb=" C1  NAG F 501 "
            pdb=" ND2 ASN F  35 "
            pdb=" C2  NAG F 501 "
            pdb=" O5  NAG F 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.23   -0.17 2.00e-01 2.50e+01 6.89e-01
  ... (remaining 943 not shown)

  Planarity restraints: 1059
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C  53 "   -0.102 5.00e-02 4.00e+02   1.39e-01 3.07e+01
        pdb=" N   PRO C  54 "    0.239 5.00e-02 4.00e+02
        pdb=" CA  PRO C  54 "   -0.066 5.00e-02 4.00e+02
        pdb=" CD  PRO C  54 "   -0.071 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 110 "   -0.371 9.50e-02 1.11e+02   1.67e-01 1.80e+01
        pdb=" NE  ARG C 110 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 110 "    0.022 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 110 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 110 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F 260 "    0.063 5.00e-02 4.00e+02   9.13e-02 1.33e+01
        pdb=" N   PRO F 261 "   -0.158 5.00e-02 4.00e+02
        pdb=" CA  PRO F 261 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO F 261 "    0.050 5.00e-02 4.00e+02
  ... (remaining 1056 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 343
        2.72 -     3.27: 5661
        3.27 -     3.81: 9630
        3.81 -     4.36: 11263
        4.36 -     4.90: 19145
  Nonbonded interactions: 46042
  Sorted by model distance:
  nonbonded pdb=" O   PRO E 343 "
            pdb=" OG  SER E 429 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" OG1 THR D  34 "
            pdb=" OD1 ASN D  91 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" OD2 ASP B 104 "
            pdb=" NH1 ARG C  87 "
     model   vdw
     2.185 3.120
  nonbonded pdb=" NZ  LYS F 260 "
            pdb=" O   PHE F 265 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" O   THR C  50 "
            pdb=" NH1 ARG C  52 "
     model   vdw
     2.211 3.120
  ... (remaining 46037 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'C' and resid 25 through 131)
  selection = (chain 'D' and resid 25 through 131)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.570
  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:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.150
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6565
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.207   6116  Z= 0.303
  Angle     :  0.732  18.009   8308  Z= 0.407
  Chirality :  0.045   0.418    946
  Planarity :  0.009   0.167   1054
  Dihedral  : 17.428  88.526   2348
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  3.76 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 24.13 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.32), residues: 719
  helix:  0.48 (0.41), residues: 169
  sheet:  0.65 (0.36), residues: 226
  loop : -0.96 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP F 322 
 HIS   0.006   0.001   HIS C  61 
 PHE   0.024   0.002   PHE D 116 
 TYR   0.009   0.001   TYR F 172 
 ARG   0.018   0.001   ARG C 110 

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 126
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
REVERT: D  123 PHE cc_start: 0.7327 (t80) cc_final: 0.6906 (t80)
REVERT: F  186 SER cc_start: 0.8080 (m) cc_final: 0.7838 (p)
REVERT: F  292 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.6940 (t0)
REVERT: F  324 GLU cc_start: 0.7743 (tp30) cc_final: 0.7373 (tp30)
  outliers start: 4
  outliers final: 0
  residues processed: 127
  average time/residue: 0.2151
  time to fit residues: 34.6274
Evaluate side-chains
  124 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  292 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 29 optimal weight:    4.9990
   chunk 18 optimal weight:    0.3980
   chunk 35 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0770
   chunk 33 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** C  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.149677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.132038 restraints weight = 9674.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.135129 restraints weight = 5759.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.137227 restraints weight = 3882.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6692
moved from start:          0.0843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   6116  Z= 0.223
  Angle     :  0.604   6.205   8308  Z= 0.318
  Chirality :  0.045   0.371    946
  Planarity :  0.006   0.089   1054
  Dihedral  :  6.731  54.288    903
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  3.76 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 23.68 %
    Favored  : 73.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.32), residues: 719
  helix:  1.03 (0.42), residues: 158
  sheet:  0.78 (0.36), residues: 227
  loop : -0.79 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP F 322 
 HIS   0.004   0.001   HIS F 277 
 PHE   0.012   0.002   PHE F 198 
 TYR   0.012   0.001   TYR E 376 
 ARG   0.007   0.001   ARG F 174 

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   54 PRO cc_start: 0.6862 (Cg_exo) cc_final: 0.6636 (Cg_endo)
REVERT: D  112 ARG cc_start: 0.7471 (mmt-90) cc_final: 0.7004 (mpt180)
REVERT: D  123 PHE cc_start: 0.6981 (t80) cc_final: 0.6740 (t80)
REVERT: F   40 VAL cc_start: 0.8317 (t) cc_final: 0.8068 (m)
REVERT: F  292 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7051 (t0)
REVERT: F  324 GLU cc_start: 0.7667 (tp30) cc_final: 0.7350 (tp30)
  outliers start: 20
  outliers final: 9
  residues processed: 147
  average time/residue: 0.2255
  time to fit residues: 41.9665
Evaluate side-chains
  142 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 132
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain C residue   39 SER
Chi-restraints excluded: chain C residue   46 ILE
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain E residue  426 SER
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue  196 CYS
Chi-restraints excluded: chain F residue  220 LYS
Chi-restraints excluded: chain F residue  289 LEU
Chi-restraints excluded: chain F residue  292 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 25 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
** C  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 102 GLN
D  81 GLN
** F  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.147628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.130710 restraints weight = 9722.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.133666 restraints weight = 5854.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.135657 restraints weight = 4004.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6788
moved from start:          0.1361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.107   6116  Z= 0.336
  Angle     :  0.652   7.584   8308  Z= 0.339
  Chirality :  0.046   0.360    946
  Planarity :  0.006   0.073   1054
  Dihedral  :  6.799  54.781    903
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  4.31 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 22.78 %
    Favored  : 72.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.32), residues: 719
  helix:  0.74 (0.41), residues: 164
  sheet:  0.58 (0.35), residues: 230
  loop : -0.89 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP F 322 
 HIS   0.007   0.002   HIS F 106 
 PHE   0.019   0.002   PHE F 198 
 TYR   0.016   0.002   TYR E 376 
 ARG   0.004   0.001   ARG F  59 

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 132
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   84 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7944 (m)
REVERT: D  112 ARG cc_start: 0.7434 (mmt-90) cc_final: 0.7066 (mpt180)
REVERT: F   40 VAL cc_start: 0.8363 (t) cc_final: 0.8138 (m)
REVERT: F   85 LYS cc_start: 0.7819 (mttp) cc_final: 0.7588 (mttp)
REVERT: F  292 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7234 (t0)
REVERT: F  322 TRP cc_start: 0.7900 (m100) cc_final: 0.7693 (m-10)
  outliers start: 29
  outliers final: 19
  residues processed: 148
  average time/residue: 0.2121
  time to fit residues: 39.6240
Evaluate side-chains
  152 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain C residue   39 SER
Chi-restraints excluded: chain C residue   46 ILE
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain D residue  131 TRP
Chi-restraints excluded: chain E residue  426 SER
Chi-restraints excluded: chain E residue  433 SER
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue   61 VAL
Chi-restraints excluded: chain F residue  156 THR
Chi-restraints excluded: chain F residue  186 SER
Chi-restraints excluded: chain F residue  196 CYS
Chi-restraints excluded: chain F residue  218 SER
Chi-restraints excluded: chain F residue  259 GLU
Chi-restraints excluded: chain F residue  289 LEU
Chi-restraints excluded: chain F residue  292 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 25 optimal weight:    0.5980
   chunk 35 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** C  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  49 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 = 0.3872 r_free = 0.3872 target = 0.149011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.131561 restraints weight = 9781.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.134694 restraints weight = 5885.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.136793 restraints weight = 3988.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6741
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   6116  Z= 0.241
  Angle     :  0.589   6.913   8308  Z= 0.306
  Chirality :  0.044   0.336    946
  Planarity :  0.005   0.075   1054
  Dihedral  :  6.496  55.778    903
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  3.89 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 23.08 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.31), residues: 719
  helix:  0.87 (0.41), residues: 164
  sheet:  0.55 (0.35), residues: 230
  loop : -0.79 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP F 322 
 HIS   0.004   0.001   HIS C  61 
 PHE   0.012   0.002   PHE F 198 
 TYR   0.013   0.002   TYR E 376 
 ARG   0.002   0.000   ARG E 327 

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 131
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   70 VAL cc_start: 0.8267 (t) cc_final: 0.8002 (p)
REVERT: C   84 THR cc_start: 0.8052 (OUTLIER) cc_final: 0.7765 (m)
REVERT: D  112 ARG cc_start: 0.7453 (mmt-90) cc_final: 0.7041 (mpt180)
REVERT: E  421 TYR cc_start: 0.8338 (m-80) cc_final: 0.7623 (m-80)
REVERT: F   40 VAL cc_start: 0.8385 (t) cc_final: 0.8147 (m)
REVERT: F  135 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7914 (p)
REVERT: F  292 ASN cc_start: 0.8302 (t0) cc_final: 0.7217 (t0)
REVERT: F  322 TRP cc_start: 0.7966 (m100) cc_final: 0.7612 (m-10)
  outliers start: 30
  outliers final: 21
  residues processed: 149
  average time/residue: 0.2072
  time to fit residues: 39.6295
Evaluate side-chains
  148 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 125
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   85 HIS
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain C residue   39 SER
Chi-restraints excluded: chain C residue   46 ILE
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain D residue  131 TRP
Chi-restraints excluded: chain E residue  380 THR
Chi-restraints excluded: chain E residue  412 VAL
Chi-restraints excluded: chain E residue  426 SER
Chi-restraints excluded: chain E residue  433 SER
Chi-restraints excluded: chain F residue   28 ILE
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue   47 LEU
Chi-restraints excluded: chain F residue  135 THR
Chi-restraints excluded: chain F residue  186 SER
Chi-restraints excluded: chain F residue  196 CYS
Chi-restraints excluded: chain F residue  218 SER
Chi-restraints excluded: chain F residue  259 GLU
Chi-restraints excluded: chain F residue  260 LYS
Chi-restraints excluded: chain F residue  289 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 10 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 20 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** C  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  49 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.147006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.129448 restraints weight = 9748.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.132610 restraints weight = 5847.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.134725 restraints weight = 3958.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6775
moved from start:          0.1802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.095   6116  Z= 0.312
  Angle     :  0.647  10.472   8308  Z= 0.335
  Chirality :  0.045   0.334    946
  Planarity :  0.006   0.084   1054
  Dihedral  :  6.426  55.803    901
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  5.01 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 22.62 %
    Favored  : 71.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.31), residues: 719
  helix:  0.84 (0.41), residues: 164
  sheet:  0.44 (0.34), residues: 230
  loop : -0.87 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP F 322 
 HIS   0.006   0.001   HIS F 106 
 PHE   0.018   0.002   PHE F 198 
 TYR   0.015   0.002   TYR E 376 
 ARG   0.004   0.001   ARG D  52 

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 131
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  112 ARG cc_start: 0.7408 (mmt-90) cc_final: 0.6965 (mpt180)
REVERT: D  123 PHE cc_start: 0.7249 (t80) cc_final: 0.7006 (t80)
REVERT: E  421 TYR cc_start: 0.8366 (m-80) cc_final: 0.7549 (m-80)
REVERT: F  220 LYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6783 (pttt)
REVERT: F  292 ASN cc_start: 0.8301 (t0) cc_final: 0.7162 (t0)
REVERT: F  309 ARG cc_start: 0.6593 (mtp180) cc_final: 0.6087 (mtp180)
REVERT: F  317 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6888 (ttm170)
REVERT: F  322 TRP cc_start: 0.7972 (m100) cc_final: 0.7452 (m-10)
  outliers start: 36
  outliers final: 25
  residues processed: 154
  average time/residue: 0.1946
  time to fit residues: 38.5699
Evaluate side-chains
  156 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain C residue   39 SER
Chi-restraints excluded: chain C residue   46 ILE
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain D residue  131 TRP
Chi-restraints excluded: chain E residue  380 THR
Chi-restraints excluded: chain E residue  412 VAL
Chi-restraints excluded: chain E residue  426 SER
Chi-restraints excluded: chain E residue  433 SER
Chi-restraints excluded: chain F residue   28 ILE
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue   47 LEU
Chi-restraints excluded: chain F residue  156 THR
Chi-restraints excluded: chain F residue  186 SER
Chi-restraints excluded: chain F residue  196 CYS
Chi-restraints excluded: chain F residue  218 SER
Chi-restraints excluded: chain F residue  220 LYS
Chi-restraints excluded: chain F residue  259 GLU
Chi-restraints excluded: chain F residue  289 LEU
Chi-restraints excluded: chain F residue  317 ARG
Chi-restraints excluded: chain F residue  326 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 5 optimal weight:    0.2980
   chunk 27 optimal weight:    5.9990
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** C  78 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 = 0.3868 r_free = 0.3868 target = 0.148630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.131730 restraints weight = 9580.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.134671 restraints weight = 5853.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.136683 restraints weight = 4018.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6767
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   6116  Z= 0.227
  Angle     :  0.594   7.985   8308  Z= 0.309
  Chirality :  0.044   0.322    946
  Planarity :  0.005   0.087   1054
  Dihedral  :  6.291  56.471    901
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  3.62 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 23.98 %
    Favored  : 70.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.00 (0.32), residues: 719
  helix:  0.86 (0.40), residues: 169
  sheet:  0.47 (0.34), residues: 230
  loop : -0.78 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP F  50 
 HIS   0.004   0.001   HIS C  61 
 PHE   0.019   0.002   PHE D 123 
 TYR   0.012   0.001   TYR E 376 
 ARG   0.004   0.000   ARG F 174 

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 121
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   70 VAL cc_start: 0.8222 (t) cc_final: 0.7969 (p)
REVERT: C   84 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7869 (m)
REVERT: D   42 ARG cc_start: 0.5954 (OUTLIER) cc_final: 0.5163 (ttm110)
REVERT: D  112 ARG cc_start: 0.7230 (mmt-90) cc_final: 0.6930 (mpt180)
REVERT: D  123 PHE cc_start: 0.7328 (t80) cc_final: 0.6231 (t80)
REVERT: E  421 TYR cc_start: 0.8378 (m-80) cc_final: 0.7552 (m-80)
REVERT: F  220 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6581 (pttt)
REVERT: F  272 TYR cc_start: 0.7713 (m-80) cc_final: 0.7331 (m-80)
REVERT: F  292 ASN cc_start: 0.8274 (t0) cc_final: 0.7199 (t0)
REVERT: F  317 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7028 (ttm170)
  outliers start: 36
  outliers final: 23
  residues processed: 142
  average time/residue: 0.2081
  time to fit residues: 37.4942
Evaluate side-chains
  146 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 119
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 GLN
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue   85 HIS
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain C residue   39 SER
Chi-restraints excluded: chain C residue   46 ILE
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain D residue   42 ARG
Chi-restraints excluded: chain E residue  380 THR
Chi-restraints excluded: chain E residue  412 VAL
Chi-restraints excluded: chain E residue  426 SER
Chi-restraints excluded: chain F residue   28 ILE
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue  131 ASN
Chi-restraints excluded: chain F residue  186 SER
Chi-restraints excluded: chain F residue  196 CYS
Chi-restraints excluded: chain F residue  218 SER
Chi-restraints excluded: chain F residue  220 LYS
Chi-restraints excluded: chain F residue  259 GLU
Chi-restraints excluded: chain F residue  289 LEU
Chi-restraints excluded: chain F residue  317 ARG
Chi-restraints excluded: chain F residue  326 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 50 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 68 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** C  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  45 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.148446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.131133 restraints weight = 9610.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.134264 restraints weight = 5807.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.136376 restraints weight = 3948.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6754
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086   6116  Z= 0.253
  Angle     :  0.616   7.430   8308  Z= 0.317
  Chirality :  0.044   0.320    946
  Planarity :  0.005   0.063   1054
  Dihedral  :  6.324  55.931    901
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  4.73 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 23.23 %
    Favored  : 71.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.32), residues: 719
  helix:  0.86 (0.40), residues: 169
  sheet:  0.43 (0.34), residues: 232
  loop : -0.82 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP F  50 
 HIS   0.005   0.001   HIS D  61 
 PHE   0.016   0.002   PHE D 123 
 TYR   0.012   0.002   TYR E 376 
 ARG   0.004   0.000   ARG F 174 

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 119
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   70 VAL cc_start: 0.8172 (t) cc_final: 0.7917 (p)
REVERT: C   84 THR cc_start: 0.8022 (OUTLIER) cc_final: 0.7723 (m)
REVERT: D   42 ARG cc_start: 0.5932 (OUTLIER) cc_final: 0.5135 (ttm110)
REVERT: D  112 ARG cc_start: 0.7238 (mmt-90) cc_final: 0.6921 (mpt180)
REVERT: E  421 TYR cc_start: 0.8360 (m-80) cc_final: 0.7453 (m-80)
REVERT: F  220 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6758 (pttt)
REVERT: F  272 TYR cc_start: 0.7695 (m-80) cc_final: 0.7317 (m-80)
REVERT: F  292 ASN cc_start: 0.8302 (t0) cc_final: 0.7145 (t0)
REVERT: F  317 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6891 (ttm170)
  outliers start: 35
  outliers final: 27
  residues processed: 142
  average time/residue: 0.2019
  time to fit residues: 36.5655
Evaluate side-chains
  150 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 119
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue   51 GLN
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   85 HIS
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain C residue   39 SER
Chi-restraints excluded: chain C residue   46 ILE
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain D residue   42 ARG
Chi-restraints excluded: chain E residue  380 THR
Chi-restraints excluded: chain E residue  412 VAL
Chi-restraints excluded: chain E residue  426 SER
Chi-restraints excluded: chain E residue  433 SER
Chi-restraints excluded: chain F residue   28 ILE
Chi-restraints excluded: chain F residue   40 VAL
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue   47 LEU
Chi-restraints excluded: chain F residue  131 ASN
Chi-restraints excluded: chain F residue  186 SER
Chi-restraints excluded: chain F residue  196 CYS
Chi-restraints excluded: chain F residue  218 SER
Chi-restraints excluded: chain F residue  220 LYS
Chi-restraints excluded: chain F residue  225 ARG
Chi-restraints excluded: chain F residue  289 LEU
Chi-restraints excluded: chain F residue  317 ARG
Chi-restraints excluded: chain F residue  326 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 8 optimal weight:    0.2980
   chunk 51 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** C  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 331 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.149077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.131528 restraints weight = 9678.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.134711 restraints weight = 5834.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.136852 restraints weight = 3951.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6739
moved from start:          0.2052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   6116  Z= 0.224
  Angle     :  0.606   8.823   8308  Z= 0.311
  Chirality :  0.044   0.315    946
  Planarity :  0.005   0.063   1054
  Dihedral  :  6.255  56.093    901
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  3.76 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 23.83 %
    Favored  : 71.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.00 (0.32), residues: 719
  helix:  0.91 (0.40), residues: 169
  sheet:  0.47 (0.35), residues: 231
  loop : -0.81 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP F 322 
 HIS   0.004   0.001   HIS C  61 
 PHE   0.014   0.002   PHE F 198 
 TYR   0.011   0.001   TYR E 376 
 ARG   0.002   0.000   ARG C 111 

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 120
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   70 VAL cc_start: 0.8167 (t) cc_final: 0.7904 (p)
REVERT: C   84 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7710 (m)
REVERT: D   42 ARG cc_start: 0.5850 (OUTLIER) cc_final: 0.5043 (ttm110)
REVERT: D  112 ARG cc_start: 0.7162 (mmt-90) cc_final: 0.6846 (mpt180)
REVERT: D  127 MET cc_start: 0.6580 (mmp) cc_final: 0.6326 (mmm)
REVERT: F  220 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6754 (pttt)
REVERT: F  292 ASN cc_start: 0.8295 (t0) cc_final: 0.7201 (t0)
REVERT: F  317 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6944 (ttm170)
REVERT: F  322 TRP cc_start: 0.7910 (m100) cc_final: 0.7548 (m-10)
  outliers start: 33
  outliers final: 28
  residues processed: 143
  average time/residue: 0.2009
  time to fit residues: 36.9227
Evaluate side-chains
  151 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 119
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue   51 GLN
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue   85 HIS
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain C residue   39 SER
Chi-restraints excluded: chain C residue   46 ILE
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain D residue   42 ARG
Chi-restraints excluded: chain E residue  380 THR
Chi-restraints excluded: chain E residue  412 VAL
Chi-restraints excluded: chain E residue  426 SER
Chi-restraints excluded: chain F residue   28 ILE
Chi-restraints excluded: chain F residue   40 VAL
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue   47 LEU
Chi-restraints excluded: chain F residue  131 ASN
Chi-restraints excluded: chain F residue  186 SER
Chi-restraints excluded: chain F residue  196 CYS
Chi-restraints excluded: chain F residue  220 LYS
Chi-restraints excluded: chain F residue  225 ARG
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  289 LEU
Chi-restraints excluded: chain F residue  317 ARG
Chi-restraints excluded: chain F residue  326 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0000
   chunk 32 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.5384

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

Flipped N/Q/H residues before XYZ refinement:
** C  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  91 ASN
F  45 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.148959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.131512 restraints weight = 9778.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.134592 restraints weight = 5975.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.136691 restraints weight = 4095.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6725
moved from start:          0.2156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   6116  Z= 0.199
  Angle     :  0.590   7.646   8308  Z= 0.302
  Chirality :  0.043   0.308    946
  Planarity :  0.005   0.063   1054
  Dihedral  :  6.187  56.125    901
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  4.03 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 23.08 %
    Favored  : 71.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.32), residues: 719
  helix:  1.12 (0.41), residues: 164
  sheet:  0.64 (0.35), residues: 226
  loop : -0.77 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E 434 
 HIS   0.004   0.001   HIS D  61 
 PHE   0.027   0.002   PHE D 123 
 TYR   0.014   0.001   TYR F 172 
 ARG   0.003   0.000   ARG F 174 

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 119
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   70 VAL cc_start: 0.8141 (t) cc_final: 0.7899 (p)
REVERT: C   84 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.7734 (m)
REVERT: C  112 ARG cc_start: 0.6645 (OUTLIER) cc_final: 0.6174 (tpp80)
REVERT: D   42 ARG cc_start: 0.5851 (OUTLIER) cc_final: 0.5082 (ttm110)
REVERT: D  123 PHE cc_start: 0.7131 (t80) cc_final: 0.6375 (t80)
REVERT: D  127 MET cc_start: 0.6565 (mmp) cc_final: 0.6004 (mmp)
REVERT: E  421 TYR cc_start: 0.8441 (m-80) cc_final: 0.7698 (m-80)
REVERT: F  193 ASN cc_start: 0.7631 (m-40) cc_final: 0.7415 (m110)
REVERT: F  292 ASN cc_start: 0.8266 (t0) cc_final: 0.7164 (t0)
REVERT: F  317 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6804 (ttm170)
REVERT: F  322 TRP cc_start: 0.7869 (m100) cc_final: 0.7525 (m-10)
  outliers start: 37
  outliers final: 29
  residues processed: 144
  average time/residue: 0.1956
  time to fit residues: 36.0996
Evaluate side-chains
  148 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 115
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 GLN
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue   85 HIS
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain C residue   39 SER
Chi-restraints excluded: chain C residue   46 ILE
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  112 ARG
Chi-restraints excluded: chain D residue   42 ARG
Chi-restraints excluded: chain D residue   91 ASN
Chi-restraints excluded: chain E residue  380 THR
Chi-restraints excluded: chain E residue  426 SER
Chi-restraints excluded: chain E residue  433 SER
Chi-restraints excluded: chain F residue   28 ILE
Chi-restraints excluded: chain F residue   40 VAL
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue  131 ASN
Chi-restraints excluded: chain F residue  156 THR
Chi-restraints excluded: chain F residue  186 SER
Chi-restraints excluded: chain F residue  196 CYS
Chi-restraints excluded: chain F residue  225 ARG
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  289 LEU
Chi-restraints excluded: chain F residue  317 ARG
Chi-restraints excluded: chain F residue  326 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 17 optimal weight:    0.2980
   chunk 27 optimal weight:    4.9990
   chunk 68 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 40 optimal weight:    0.6980
   chunk 6 optimal weight:    0.2980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** C  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  91 ASN
F  45 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.147029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.129373 restraints weight = 9785.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.132427 restraints weight = 6036.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.134501 restraints weight = 4168.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6763
moved from start:          0.2225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090   6116  Z= 0.282
  Angle     :  0.659  11.072   8308  Z= 0.335
  Chirality :  0.045   0.311    946
  Planarity :  0.005   0.061   1054
  Dihedral  :  6.350  55.457    901
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  4.45 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 23.38 %
    Favored  : 71.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.32), residues: 719
  helix:  1.00 (0.41), residues: 164
  sheet:  0.44 (0.35), residues: 233
  loop : -0.83 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP E 434 
 HIS   0.005   0.001   HIS C  61 
 PHE   0.023   0.002   PHE D 123 
 TYR   0.013   0.002   TYR E 376 
 ARG   0.006   0.001   ARG E 377 

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 121
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   70 VAL cc_start: 0.8161 (t) cc_final: 0.7910 (p)
REVERT: D   42 ARG cc_start: 0.6061 (OUTLIER) cc_final: 0.5464 (ttm110)
REVERT: D  112 ARG cc_start: 0.7107 (mmt-90) cc_final: 0.6751 (mpt180)
REVERT: D  123 PHE cc_start: 0.7210 (t80) cc_final: 0.6408 (t80)
REVERT: D  127 MET cc_start: 0.6570 (mmp) cc_final: 0.6079 (mmp)
REVERT: F  193 ASN cc_start: 0.7675 (m-40) cc_final: 0.7470 (m110)
REVERT: F  220 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6716 (pttt)
REVERT: F  292 ASN cc_start: 0.8338 (t0) cc_final: 0.7182 (t0)
REVERT: F  317 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6739 (ttm170)
REVERT: F  322 TRP cc_start: 0.7908 (m100) cc_final: 0.7534 (m-10)
  outliers start: 35
  outliers final: 28
  residues processed: 144
  average time/residue: 0.2040
  time to fit residues: 37.7956
Evaluate side-chains
  149 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 118
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   39 TYR
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue   85 HIS
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   93 CYS
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain C residue   39 SER
Chi-restraints excluded: chain C residue   46 ILE
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain D residue   42 ARG
Chi-restraints excluded: chain E residue  380 THR
Chi-restraints excluded: chain E residue  426 SER
Chi-restraints excluded: chain E residue  433 SER
Chi-restraints excluded: chain F residue   28 ILE
Chi-restraints excluded: chain F residue   40 VAL
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain F residue   47 LEU
Chi-restraints excluded: chain F residue  131 ASN
Chi-restraints excluded: chain F residue  156 THR
Chi-restraints excluded: chain F residue  186 SER
Chi-restraints excluded: chain F residue  196 CYS
Chi-restraints excluded: chain F residue  220 LYS
Chi-restraints excluded: chain F residue  225 ARG
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  289 LEU
Chi-restraints excluded: chain F residue  317 ARG
Chi-restraints excluded: chain F residue  326 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 63 optimal weight:    0.0000
   chunk 30 optimal weight:    0.4980
   chunk 6 optimal weight:    0.0060
   overall best weight:    0.3800

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

Flipped N/Q/H residues before XYZ refinement:
** C  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 331 HIS
F  45 GLN
F 229 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.149239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.131599 restraints weight = 9842.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.134714 restraints weight = 6018.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.136862 restraints weight = 4128.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6721
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6116  Z= 0.189
  Angle     :  0.614  10.692   8308  Z= 0.309
  Chirality :  0.043   0.301    946
  Planarity :  0.005   0.064   1054
  Dihedral  :  6.350  56.176    901
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  3.06 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 23.83 %
    Favored  : 71.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.32), residues: 719
  helix:  1.17 (0.41), residues: 164
  sheet:  0.73 (0.36), residues: 227
  loop : -0.83 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP E 434 
 HIS   0.004   0.001   HIS D  61 
 PHE   0.025   0.002   PHE D 123 
 TYR   0.017   0.002   TYR F 272 
 ARG   0.006   0.000   ARG F 174 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2181.31 seconds
wall clock time: 39 minutes 45.89 seconds (2385.89 seconds total)