Starting phenix.real_space_refine
on Wed Sep 17 12:20:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9i7p_52658/09_2025/9i7p_52658.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9i7p_52658/09_2025/9i7p_52658.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9i7p_52658/09_2025/9i7p_52658.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9i7p_52658/09_2025/9i7p_52658.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9i7p_52658/09_2025/9i7p_52658.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9i7p_52658/09_2025/9i7p_52658.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.068
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: 5
    Type Number    sf(0)   Gaussians
     P      11      5.49       5
     S      24      5.16       5
     C    5646      2.51       5
     N    1339      2.21       5
     O    1624      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8644
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "C"
      Number of atoms: 451
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 451
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 1, 'TRANS': 55}
    Chain: "E"
      Number of atoms: 326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 326
          Classifications: {'peptide': 43}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 39}
    Chain: "G"
      Number of atoms: 298
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 298
          Classifications: {'peptide': 41}
          Link IDs: {'TRANS': 40}
    Chain: "I"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 410
          Classifications: {'peptide': 51}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 46}
    Chain: "A"
      Number of atoms: 2466
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2466
          Classifications: {'peptide': 318}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 305}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 451
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 451
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 1, 'TRANS': 55}
    Chain: "C"
      Number of atoms: 124
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 124
          Unusual residues: {'DU0': 1, 'PC1': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 21
    Chain: "G"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 37
          Unusual residues: {'DU0': 1}
          Classifications: {'undetermined': 1}
    Chain: "I"
      Number of atoms: 47
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 47
          Unusual residues: {'PC1': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 7
    Chain: "A"
      Number of atoms: 142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 142
          Unusual residues: {'DU0': 2, 'PC1': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 40
    Chain: "D"
      Number of atoms: 166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 166
          Unusual residues: {'DU0': 1, 'PC1': 2, 'PLC': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 21
  Restraints were copied for chains:
    B, F, H, J
  Time building chain proxies: 2.70, per 1000 atoms: 0.31
  Number of scatterers: 8644
  At special positions: 0
  Unit cell: (112.995, 149.823, 92.07, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      24     16.00
     P      11     15.00
     O    1624      8.00
     N    1339      7.00
     C    5646      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.76
  Conformation dependent library (CDL) restraints added in 307.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1888

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 2 sheets defined
      38.8% alpha, 33.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'C' and resid 62 through 117
      Proline residue:  C 100  - end of helix
    Processing helix  chain 'E' and resid 11 through 50
      removed outlier: 3.545A  pdb=" N   ARG E  16 " --> pdb=" O   PRO E  12 " (cutoff:3.500A)
      Proline residue:  E  40  - end of helix
    Processing helix  chain 'G' and resid 17 through 26
      removed outlier: 3.877A  pdb=" N   ALA G  23 " --> pdb=" O   GLY G  19 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 48
    Processing helix  chain 'G' and resid 49 through 56
    Processing helix  chain 'I' and resid 23 through 57
      removed outlier: 5.536A  pdb=" N   LEU I  46 " --> pdb=" O   HIS I  42 " (cutoff:3.500A)
      Proline residue:  I  47  - end of helix
    Processing helix  chain 'I' and resid 64 through 68
    Processing helix  chain 'A' and resid 22 through 34
      removed outlier: 3.754A  pdb=" N   ALA A  27 " --> pdb=" O   ASP A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 46
    Processing helix  chain 'A' and resid 47 through 52
    Processing helix  chain 'D' and resid 62 through 117
      Proline residue:  D 100  - end of helix
    Processing helix  chain 'F' and resid 11 through 50
      removed outlier: 3.545A  pdb=" N   ARG F  16 " --> pdb=" O   PRO F  12 " (cutoff:3.500A)
      Proline residue:  F  40  - end of helix
    Processing helix  chain 'H' and resid 17 through 26
      removed outlier: 3.877A  pdb=" N   ALA H  23 " --> pdb=" O   GLY H  19 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 29 through 48
    Processing helix  chain 'H' and resid 49 through 56
    Processing helix  chain 'J' and resid 23 through 57
      removed outlier: 5.536A  pdb=" N   LEU J  46 " --> pdb=" O   HIS J  42 " (cutoff:3.500A)
      Proline residue:  J  47  - end of helix
    Processing helix  chain 'J' and resid 64 through 68
    Processing helix  chain 'B' and resid 22 through 34
      removed outlier: 3.754A  pdb=" N   ALA B  27 " --> pdb=" O   ASP B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 46
    Processing helix  chain 'B' and resid 47 through 52
    Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 73
      removed outlier: 6.466A  pdb=" N   PHE A  78 " --> pdb=" O   PHE A  72 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   ALA A 146 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   THR A 174 " --> pdb=" O   PRO A 166 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LYS A 293 " --> pdb=" O   ASP A 289 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 63 through 73
      removed outlier: 6.466A  pdb=" N   PHE B  78 " --> pdb=" O   PHE B  72 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   ALA B 146 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   THR B 174 " --> pdb=" O   PRO B 166 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LYS B 293 " --> pdb=" O   ASP B 289 " (cutoff:3.500A)

    594 hydrogen bonds defined for protein.
    1704 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.38

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1342
        1.32 -     1.44: 2320
        1.44 -     1.56: 5107
        1.56 -     1.68: 24
        1.68 -     1.80: 46
  Bond restraints: 8839
  Sorted by residual:
  bond pdb=" CG  LEU A 336 "
       pdb=" CD1 LEU A 336 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.88e+00
  bond pdb=" CG  LEU B 336 "
       pdb=" CD1 LEU B 336 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.88e+00
  bond pdb=" C09 DU0 B 402 "
       pdb=" O16 DU0 B 402 "
    ideal  model  delta    sigma   weight residual
    1.404  1.431 -0.027 2.00e-02 2.50e+03 1.88e+00
  bond pdb=" C09 DU0 A 402 "
       pdb=" O16 DU0 A 402 "
    ideal  model  delta    sigma   weight residual
    1.404  1.431 -0.027 2.00e-02 2.50e+03 1.88e+00
  bond pdb=" C09 DU0 D 204 "
       pdb=" O16 DU0 D 204 "
    ideal  model  delta    sigma   weight residual
    1.404  1.431 -0.027 2.00e-02 2.50e+03 1.86e+00
  ... (remaining 8834 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 11280
        1.57 -     3.13: 565
        3.13 -     4.70: 114
        4.70 -     6.27: 18
        6.27 -     7.84: 14
  Bond angle restraints: 11991
  Sorted by residual:
  angle pdb=" C   PRO A 343 "
        pdb=" N   ASN A 344 "
        pdb=" CA  ASN A 344 "
      ideal   model   delta    sigma   weight residual
     122.46  126.82   -4.36 1.41e+00 5.03e-01 9.57e+00
  angle pdb=" C   PRO B 343 "
        pdb=" N   ASN B 344 "
        pdb=" CA  ASN B 344 "
      ideal   model   delta    sigma   weight residual
     122.46  126.82   -4.36 1.41e+00 5.03e-01 9.57e+00
  angle pdb=" CD  ARG I  29 "
        pdb=" NE  ARG I  29 "
        pdb=" CZ  ARG I  29 "
      ideal   model   delta    sigma   weight residual
     124.40  127.91   -3.51 1.40e+00 5.10e-01 6.29e+00
  angle pdb=" CD  ARG J  29 "
        pdb=" NE  ARG J  29 "
        pdb=" CZ  ARG J  29 "
      ideal   model   delta    sigma   weight residual
     124.40  127.91   -3.51 1.40e+00 5.10e-01 6.29e+00
  angle pdb=" C   LYS A 103 "
        pdb=" N   MET A 104 "
        pdb=" CA  MET A 104 "
      ideal   model   delta    sigma   weight residual
     121.75  117.48    4.27 1.73e+00 3.34e-01 6.10e+00
  ... (remaining 11986 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.39: 5418
       27.39 -    54.77: 337
       54.77 -    82.16: 104
       82.16 -   109.55: 38
      109.55 -   136.93: 16
  Dihedral angle restraints: 5913
    sinusoidal: 2975
      harmonic: 2938
  Sorted by residual:
  dihedral pdb=" CD  ARG J  29 "
           pdb=" NE  ARG J  29 "
           pdb=" CZ  ARG J  29 "
           pdb=" NH1 ARG J  29 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   80.47  -80.47     1      1.00e+01 1.00e-02 8.01e+01
  dihedral pdb=" CD  ARG I  29 "
           pdb=" NE  ARG I  29 "
           pdb=" CZ  ARG I  29 "
           pdb=" NH1 ARG I  29 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   80.47  -80.47     1      1.00e+01 1.00e-02 8.01e+01
  dihedral pdb=" C26 DU0 B 403 "
           pdb=" C24 DU0 B 403 "
           pdb=" C25 DU0 B 403 "
           pdb=" O23 DU0 B 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     189.32   52.39  136.93     1      3.00e+01 1.11e-03 1.85e+01
  ... (remaining 5910 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 865
       0.041 -    0.081: 312
       0.081 -    0.122: 108
       0.122 -    0.163: 36
       0.163 -    0.203: 8
  Chirality restraints: 1329
  Sorted by residual:
  chirality pdb=" CA  ASN B 344 "
            pdb=" N   ASN B 344 "
            pdb=" C   ASN B 344 "
            pdb=" CB  ASN B 344 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  ASN A 344 "
            pdb=" N   ASN A 344 "
            pdb=" C   ASN A 344 "
            pdb=" CB  ASN A 344 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  ILE A 345 "
            pdb=" N   ILE A 345 "
            pdb=" C   ILE A 345 "
            pdb=" CB  ILE A 345 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.18 2.00e-01 2.50e+01 8.38e-01
  ... (remaining 1326 not shown)

  Planarity restraints: 1428
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG J  29 "    0.931 9.50e-02 1.11e+02   4.18e-01 1.17e+02
        pdb=" NE  ARG J  29 "   -0.077 2.00e-02 2.50e+03
        pdb=" CZ  ARG J  29 "    0.046 2.00e-02 2.50e+03
        pdb=" NH1 ARG J  29 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH2 ARG J  29 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG I  29 "   -0.931 9.50e-02 1.11e+02   4.18e-01 1.17e+02
        pdb=" NE  ARG I  29 "    0.077 2.00e-02 2.50e+03
        pdb=" CZ  ARG I  29 "   -0.046 2.00e-02 2.50e+03
        pdb=" NH1 ARG I  29 "    0.011 2.00e-02 2.50e+03
        pdb=" NH2 ARG I  29 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 301 "    0.196 9.50e-02 1.11e+02   8.84e-02 5.97e+00
        pdb=" NE  ARG A 301 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 301 "    0.017 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 301 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 301 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1425 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 181
        2.68 -     3.24: 7779
        3.24 -     3.79: 12611
        3.79 -     4.35: 17347
        4.35 -     4.90: 30199
  Nonbonded interactions: 68117
  Sorted by model distance:
  nonbonded pdb=" NE  ARG J  38 "
            pdb=" OD2 ASP B 144 "
     model   vdw
     2.131 3.120
  nonbonded pdb=" NE  ARG I  38 "
            pdb=" OD2 ASP A 144 "
     model   vdw
     2.131 3.120
  nonbonded pdb=" O   TYR E  37 "
            pdb=" NH1 ARG A  32 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" O   TYR F  37 "
            pdb=" NH1 ARG B  32 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" NH2 ARG A 301 "
            pdb=" O   ALA A 304 "
     model   vdw
     2.295 3.120
  ... (remaining 68112 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 'A'
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'C' and (resid 62 through 118 or (resid 201 and (name N or name C1 or nam \ 
e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or  \ 
name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ 
 or name C29 or name C2A or name C2B or name C3 or name C31 or name C32 or name  \ 
C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or n \ 
ame C3A or name O11 or name O12 or name O13 or name O14 or name O21 or name O22  \ 
or name O31 or name O32 or name P )) or resid 203))
  selection = (chain 'D' and (resid 62 through 201 or (resid 203 and (name N or name C1 or nam \ 
e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or  \ 
name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ 
 or name C29 or name C2A or name C2B or name C3 or name C31 or name C32 or name  \ 
C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or n \ 
ame C3A or name O11 or name O12 or name O13 or name O14 or name O21 or name O22  \ 
or name O31 or name O32 or name P ))))
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'I'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     9.680
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
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      :  0.007   0.063   8839  Z= 0.287
  Angle     :  0.836   7.836  11991  Z= 0.405
  Chirality :  0.051   0.203   1329
  Planarity :  0.018   0.418   1428
  Dihedral  : 21.096 136.931   4025
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  1.46 %
    Favored  : 98.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.26), residues: 996
  helix:  0.13 (0.24), residues: 362
  sheet:  1.04 (0.25), residues: 408
  loop : -0.06 (0.44), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.057   0.004   ARG J  29 
 TYR   0.014   0.003   TYR D 111 
 PHE   0.018   0.002   PHE A 128 
 TRP   0.019   0.003   TRP G  50 
 HIS   0.004   0.001   HIS J  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00680 ( 8839)
  covalent geometry    : angle       0.83598 (11991)
  hydrogen bonds       : bond        0.18627 (  594)
  hydrogen bonds       : angle       7.65136 ( 1704)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 186
  time to evaluate  : 0.346 
Fit side-chains
REVERT: C   85 ARG cc_start: 0.8503 (tpt-90) cc_final: 0.8233 (tpt90)
REVERT: I   43 TYR cc_start: 0.8615 (m-80) cc_final: 0.8220 (m-80)
REVERT: A   33 GLN cc_start: 0.8063 (mt0) cc_final: 0.7684 (mp10)
REVERT: A  104 MET cc_start: 0.8658 (ptm) cc_final: 0.8450 (ptp)
REVERT: A  168 PHE cc_start: 0.6377 (t80) cc_final: 0.6164 (t80)
REVERT: A  207 ASP cc_start: 0.6757 (t0) cc_final: 0.6261 (p0)
REVERT: A  244 LYS cc_start: 0.8694 (mttm) cc_final: 0.8368 (mtmt)
REVERT: A  307 MET cc_start: 0.8287 (ttp) cc_final: 0.8002 (ttm)
REVERT: A  308 MET cc_start: 0.8529 (mmm) cc_final: 0.7806 (ttp)
REVERT: A  315 ASP cc_start: 0.7834 (t0) cc_final: 0.7623 (t0)
REVERT: D   85 ARG cc_start: 0.8503 (tpt-90) cc_final: 0.8233 (tpt90)
REVERT: J   43 TYR cc_start: 0.8612 (m-80) cc_final: 0.8219 (m-80)
REVERT: B   33 GLN cc_start: 0.8065 (mt0) cc_final: 0.7684 (mp10)
REVERT: B  104 MET cc_start: 0.8657 (ptm) cc_final: 0.8447 (ptp)
REVERT: B  168 PHE cc_start: 0.6370 (t80) cc_final: 0.6161 (t80)
REVERT: B  207 ASP cc_start: 0.6761 (t0) cc_final: 0.6266 (p0)
REVERT: B  244 LYS cc_start: 0.8692 (mttm) cc_final: 0.8362 (mtmt)
REVERT: B  307 MET cc_start: 0.8291 (ttp) cc_final: 0.8004 (ttm)
REVERT: B  308 MET cc_start: 0.8542 (mmm) cc_final: 0.7777 (ttp)
REVERT: B  315 ASP cc_start: 0.7833 (t0) cc_final: 0.7623 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 188
  average time/residue: 0.0896
  time to fit residues: 23.9165
Evaluate side-chains
  156 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0470
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
I  27 GLN
A  29 GLN
A 344 ASN
B  29 GLN
B 344 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.166720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.124693 restraints weight = 10663.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 2.38
r_work: 0.3335 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8839  Z= 0.150
  Angle     :  0.649   6.896  11991  Z= 0.324
  Chirality :  0.043   0.214   1329
  Planarity :  0.005   0.036   1428
  Dihedral  : 17.833 123.466   2227
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  6.31 %
    Favored  : 92.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.27), residues: 996
  helix:  2.10 (0.26), residues: 362
  sheet:  1.14 (0.26), residues: 408
  loop :  0.18 (0.45), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 301 
 TYR   0.019   0.002   TYR C  66 
 PHE   0.012   0.001   PHE B 347 
 TRP   0.008   0.001   TRP B 221 
 HIS   0.001   0.000   HIS J  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8839)
  covalent geometry    : angle       0.64868 (11991)
  hydrogen bonds       : bond        0.04182 (  594)
  hydrogen bonds       : angle       5.15995 ( 1704)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 149
  time to evaluate  : 0.306 
Fit side-chains
REVERT: E   42 ILE cc_start: 0.7794 (mt) cc_final: 0.7566 (mm)
REVERT: A   33 GLN cc_start: 0.8134 (mt0) cc_final: 0.7825 (mp10)
REVERT: A  207 ASP cc_start: 0.7079 (t0) cc_final: 0.6872 (p0)
REVERT: A  244 LYS cc_start: 0.8778 (mttm) cc_final: 0.8550 (mtmt)
REVERT: A  308 MET cc_start: 0.8498 (mmm) cc_final: 0.8178 (ttp)
REVERT: F   42 ILE cc_start: 0.7796 (mt) cc_final: 0.7570 (mm)
REVERT: B   33 GLN cc_start: 0.8136 (mt0) cc_final: 0.7823 (mp10)
REVERT: B  207 ASP cc_start: 0.7107 (t0) cc_final: 0.6887 (p0)
REVERT: B  244 LYS cc_start: 0.8769 (mttm) cc_final: 0.8540 (mtmt)
REVERT: B  308 MET cc_start: 0.8521 (mmm) cc_final: 0.8136 (ttp)
  outliers start: 10
  outliers final: 4
  residues processed: 151
  average time/residue: 0.0820
  time to fit residues: 18.0208
Evaluate side-chains
  143 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 139
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  129 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 95 optimal weight:    5.9990
   chunk 73 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 90 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 94 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 150 HIS
B 150 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.162456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.119943 restraints weight = 10630.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 2.38
r_work: 0.3287 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   8839  Z= 0.233
  Angle     :  0.640   5.872  11991  Z= 0.329
  Chirality :  0.045   0.211   1329
  Planarity :  0.005   0.038   1428
  Dihedral  : 16.187 115.326   2227
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  9.71 %
    Favored  : 88.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.27), residues: 996
  helix:  2.26 (0.27), residues: 364
  sheet:  1.03 (0.27), residues: 408
  loop : -0.02 (0.43), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  52 
 TYR   0.012   0.002   TYR I  43 
 PHE   0.015   0.002   PHE B 168 
 TRP   0.011   0.002   TRP A 221 
 HIS   0.003   0.001   HIS B  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00548 ( 8839)
  covalent geometry    : angle       0.64044 (11991)
  hydrogen bonds       : bond        0.03752 (  594)
  hydrogen bonds       : angle       4.93419 ( 1704)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 0.345 
Fit side-chains
REVERT: E   42 ILE cc_start: 0.7894 (mt) cc_final: 0.7580 (mm)
REVERT: I   43 TYR cc_start: 0.8448 (m-80) cc_final: 0.8239 (m-80)
REVERT: A   33 GLN cc_start: 0.8163 (mt0) cc_final: 0.7805 (mp10)
REVERT: A  207 ASP cc_start: 0.7115 (t0) cc_final: 0.6820 (p0)
REVERT: A  244 LYS cc_start: 0.8864 (mttm) cc_final: 0.8548 (mtmt)
REVERT: A  289 ASP cc_start: 0.8446 (p0) cc_final: 0.8201 (p0)
REVERT: A  308 MET cc_start: 0.8491 (mmm) cc_final: 0.8186 (ttp)
REVERT: F   42 ILE cc_start: 0.7895 (mt) cc_final: 0.7580 (mm)
REVERT: J   43 TYR cc_start: 0.8450 (m-80) cc_final: 0.8243 (m-80)
REVERT: B   33 GLN cc_start: 0.8154 (mt0) cc_final: 0.7802 (mp10)
REVERT: B  207 ASP cc_start: 0.7121 (t0) cc_final: 0.6829 (p0)
REVERT: B  244 LYS cc_start: 0.8863 (mttm) cc_final: 0.8546 (mtmt)
REVERT: B  308 MET cc_start: 0.8521 (mmm) cc_final: 0.8150 (ttp)
  outliers start: 16
  outliers final: 12
  residues processed: 152
  average time/residue: 0.0671
  time to fit residues: 15.7249
Evaluate side-chains
  144 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   11 SER
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain F residue   11 SER
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  251 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 69 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 72 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 344 ASN
J  27 GLN
B 344 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.165856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.123466 restraints weight = 10730.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 2.41
r_work: 0.3320 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8839  Z= 0.131
  Angle     :  0.556   6.398  11991  Z= 0.283
  Chirality :  0.041   0.239   1329
  Planarity :  0.004   0.042   1428
  Dihedral  : 14.869 103.637   2227
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 10.19 %
    Favored  : 87.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.27), residues: 996
  helix:  2.59 (0.27), residues: 362
  sheet:  1.02 (0.26), residues: 406
  loop : -0.10 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  52 
 TYR   0.008   0.001   TYR J  43 
 PHE   0.015   0.001   PHE B 168 
 TRP   0.010   0.001   TRP B 197 
 HIS   0.001   0.000   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 8839)
  covalent geometry    : angle       0.55586 (11991)
  hydrogen bonds       : bond        0.03069 (  594)
  hydrogen bonds       : angle       4.59523 ( 1704)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 0.332 
Fit side-chains
REVERT: E   42 ILE cc_start: 0.7849 (mt) cc_final: 0.7534 (mm)
REVERT: A   33 GLN cc_start: 0.8120 (mt0) cc_final: 0.7821 (mp10)
REVERT: A  207 ASP cc_start: 0.7038 (t0) cc_final: 0.6780 (p0)
REVERT: A  244 LYS cc_start: 0.8856 (mttm) cc_final: 0.8483 (mtmm)
REVERT: A  268 GLU cc_start: 0.8261 (tt0) cc_final: 0.7883 (tp30)
REVERT: A  308 MET cc_start: 0.8424 (mmm) cc_final: 0.8159 (ttp)
REVERT: A  318 THR cc_start: 0.9148 (p) cc_final: 0.8948 (t)
REVERT: F   42 ILE cc_start: 0.7851 (mt) cc_final: 0.7535 (mm)
REVERT: B   33 GLN cc_start: 0.8112 (mt0) cc_final: 0.7816 (mp10)
REVERT: B  207 ASP cc_start: 0.7047 (t0) cc_final: 0.6796 (p0)
REVERT: B  244 LYS cc_start: 0.8853 (mttm) cc_final: 0.8479 (mtmm)
REVERT: B  268 GLU cc_start: 0.8264 (tt0) cc_final: 0.7871 (tp30)
REVERT: B  308 MET cc_start: 0.8498 (mmm) cc_final: 0.8148 (ttp)
REVERT: B  318 THR cc_start: 0.9146 (p) cc_final: 0.8945 (t)
  outliers start: 18
  outliers final: 14
  residues processed: 159
  average time/residue: 0.0718
  time to fit residues: 17.3635
Evaluate side-chains
  155 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 141
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   11 SER
Chi-restraints excluded: chain G residue   21 TYR
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain F residue   11 SER
Chi-restraints excluded: chain H residue   21 TYR
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  251 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 94 optimal weight:    0.5980
   chunk 41 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   overall best weight:    1.0582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.164755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.122471 restraints weight = 10696.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 2.38
r_work: 0.3305 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8839  Z= 0.168
  Angle     :  0.570   7.655  11991  Z= 0.291
  Chirality :  0.042   0.224   1329
  Planarity :  0.004   0.040   1428
  Dihedral  : 14.253  97.017   2227
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 11.53 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.92 (0.27), residues: 996
  helix:  2.50 (0.27), residues: 374
  sheet:  0.99 (0.26), residues: 406
  loop : -0.32 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  52 
 TYR   0.009   0.001   TYR I  43 
 PHE   0.012   0.001   PHE A 128 
 TRP   0.010   0.001   TRP B 197 
 HIS   0.002   0.001   HIS B  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 8839)
  covalent geometry    : angle       0.57049 (11991)
  hydrogen bonds       : bond        0.03118 (  594)
  hydrogen bonds       : angle       4.53136 ( 1704)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 0.255 
Fit side-chains
REVERT: E   42 ILE cc_start: 0.7866 (mt) cc_final: 0.7564 (mm)
REVERT: A   33 GLN cc_start: 0.8163 (mt0) cc_final: 0.7770 (mp10)
REVERT: A  207 ASP cc_start: 0.6989 (t0) cc_final: 0.6702 (p0)
REVERT: A  244 LYS cc_start: 0.8875 (mttm) cc_final: 0.8509 (mtmm)
REVERT: A  268 GLU cc_start: 0.8229 (tt0) cc_final: 0.7826 (tp30)
REVERT: F   42 ILE cc_start: 0.7862 (mt) cc_final: 0.7560 (mm)
REVERT: B   33 GLN cc_start: 0.8151 (mt0) cc_final: 0.7764 (mp10)
REVERT: B  207 ASP cc_start: 0.7012 (t0) cc_final: 0.6727 (p0)
REVERT: B  244 LYS cc_start: 0.8869 (mttm) cc_final: 0.8506 (mtmm)
REVERT: B  268 GLU cc_start: 0.8225 (tt0) cc_final: 0.7824 (tp30)
REVERT: B  308 MET cc_start: 0.8496 (mmm) cc_final: 0.8144 (ttp)
  outliers start: 18
  outliers final: 16
  residues processed: 146
  average time/residue: 0.0758
  time to fit residues: 16.7750
Evaluate side-chains
  148 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   11 SER
Chi-restraints excluded: chain E residue   30 ILE
Chi-restraints excluded: chain G residue   21 TYR
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain F residue   11 SER
Chi-restraints excluded: chain F residue   30 ILE
Chi-restraints excluded: chain H residue   21 TYR
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  251 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   chunk 68 optimal weight:    6.9990
   chunk 76 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 344 ASN
B 344 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.164508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.121463 restraints weight = 10671.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.40
r_work: 0.3288 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.2758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8839  Z= 0.197
  Angle     :  0.588   7.823  11991  Z= 0.299
  Chirality :  0.042   0.215   1329
  Planarity :  0.004   0.041   1428
  Dihedral  : 13.835  89.814   2227
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 12.01 %
    Favored  : 85.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.77 (0.27), residues: 996
  helix:  2.48 (0.27), residues: 374
  sheet:  0.81 (0.26), residues: 408
  loop : -0.39 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG J  29 
 TYR   0.010   0.001   TYR A 181 
 PHE   0.013   0.002   PHE A 128 
 TRP   0.011   0.001   TRP A 197 
 HIS   0.002   0.001   HIS A 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 8839)
  covalent geometry    : angle       0.58841 (11991)
  hydrogen bonds       : bond        0.03170 (  594)
  hydrogen bonds       : angle       4.58503 ( 1704)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 0.349 
Fit side-chains
REVERT: E   42 ILE cc_start: 0.7931 (mt) cc_final: 0.7644 (mm)
REVERT: I   32 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7624 (pttt)
REVERT: A   33 GLN cc_start: 0.8196 (mt0) cc_final: 0.7772 (mp10)
REVERT: A  207 ASP cc_start: 0.6991 (t0) cc_final: 0.6652 (p0)
REVERT: A  244 LYS cc_start: 0.8870 (mttm) cc_final: 0.8508 (mtmm)
REVERT: A  268 GLU cc_start: 0.8217 (tt0) cc_final: 0.7816 (tp30)
REVERT: F   42 ILE cc_start: 0.7912 (mt) cc_final: 0.7626 (mm)
REVERT: J   32 LYS cc_start: 0.8219 (mtmt) cc_final: 0.7627 (pttt)
REVERT: B   33 GLN cc_start: 0.8190 (mt0) cc_final: 0.7765 (mp10)
REVERT: B  207 ASP cc_start: 0.6988 (t0) cc_final: 0.6644 (p0)
REVERT: B  244 LYS cc_start: 0.8872 (mttm) cc_final: 0.8511 (mtmm)
REVERT: B  268 GLU cc_start: 0.8212 (tt0) cc_final: 0.7828 (tp30)
REVERT: B  289 ASP cc_start: 0.8479 (p0) cc_final: 0.8237 (p0)
REVERT: B  294 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8668 (tp)
REVERT: B  308 MET cc_start: 0.8415 (mmm) cc_final: 0.8128 (ttp)
  outliers start: 19
  outliers final: 16
  residues processed: 142
  average time/residue: 0.0742
  time to fit residues: 16.1499
Evaluate side-chains
  146 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   11 SER
Chi-restraints excluded: chain E residue   30 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain F residue   11 SER
Chi-restraints excluded: chain F residue   30 ILE
Chi-restraints excluded: chain F residue   46 VAL
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  251 MET
Chi-restraints excluded: chain B residue  294 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 49 optimal weight:   10.0000
   chunk 18 optimal weight:    6.9990
   chunk 17 optimal weight:    0.2980
   chunk 45 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 54 optimal weight:    0.0670
   chunk 14 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
A 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.165359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.123187 restraints weight = 10757.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 2.40
r_work: 0.3323 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8839  Z= 0.112
  Angle     :  0.528   8.750  11991  Z= 0.271
  Chirality :  0.039   0.153   1329
  Planarity :  0.004   0.043   1428
  Dihedral  : 13.153  84.070   2227
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 12.99 %
    Favored  : 85.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.27), residues: 996
  helix:  2.66 (0.27), residues: 374
  sheet:  0.94 (0.26), residues: 404
  loop : -0.31 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  52 
 TYR   0.006   0.001   TYR J  45 
 PHE   0.010   0.001   PHE H  45 
 TRP   0.010   0.001   TRP B 197 
 HIS   0.001   0.000   HIS B 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 8839)
  covalent geometry    : angle       0.52764 (11991)
  hydrogen bonds       : bond        0.02754 (  594)
  hydrogen bonds       : angle       4.35775 ( 1704)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 146
  time to evaluate  : 0.331 
Fit side-chains
REVERT: E   42 ILE cc_start: 0.7878 (mt) cc_final: 0.7600 (mm)
REVERT: I   32 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7599 (pttt)
REVERT: A   33 GLN cc_start: 0.8185 (mt0) cc_final: 0.7771 (mp10)
REVERT: A  207 ASP cc_start: 0.6901 (t0) cc_final: 0.6604 (p0)
REVERT: A  244 LYS cc_start: 0.8890 (mttm) cc_final: 0.8546 (mtmm)
REVERT: A  268 GLU cc_start: 0.8205 (tt0) cc_final: 0.7823 (tp30)
REVERT: F   42 ILE cc_start: 0.7880 (mt) cc_final: 0.7601 (mm)
REVERT: J   32 LYS cc_start: 0.8199 (mtmt) cc_final: 0.7602 (pttt)
REVERT: B   33 GLN cc_start: 0.8185 (mt0) cc_final: 0.7768 (mp10)
REVERT: B  207 ASP cc_start: 0.6937 (t0) cc_final: 0.6626 (p0)
REVERT: B  244 LYS cc_start: 0.8878 (mttm) cc_final: 0.8533 (mtmm)
REVERT: B  268 GLU cc_start: 0.8212 (tt0) cc_final: 0.7844 (tp30)
REVERT: B  308 MET cc_start: 0.8421 (mmm) cc_final: 0.8102 (ttp)
  outliers start: 10
  outliers final: 10
  residues processed: 150
  average time/residue: 0.0737
  time to fit residues: 16.7491
Evaluate side-chains
  148 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 138
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  251 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 92 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 344 ASN
B 147 GLN
B 344 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.163816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.121479 restraints weight = 10678.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 2.37
r_work: 0.3298 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.2940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8839  Z= 0.189
  Angle     :  0.567   8.905  11991  Z= 0.290
  Chirality :  0.041   0.161   1329
  Planarity :  0.004   0.042   1428
  Dihedral  : 13.324  84.558   2227
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 13.35 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.82 (0.27), residues: 996
  helix:  2.61 (0.26), residues: 374
  sheet:  0.75 (0.26), residues: 406
  loop : -0.33 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG I  56 
 TYR   0.010   0.001   TYR B 181 
 PHE   0.012   0.001   PHE D 101 
 TRP   0.011   0.001   TRP A 197 
 HIS   0.002   0.001   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 8839)
  covalent geometry    : angle       0.56714 (11991)
  hydrogen bonds       : bond        0.03019 (  594)
  hydrogen bonds       : angle       4.46891 ( 1704)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 0.306 
Fit side-chains
REVERT: E   42 ILE cc_start: 0.7968 (mt) cc_final: 0.7696 (mm)
REVERT: I   32 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7627 (pttt)
REVERT: A   33 GLN cc_start: 0.8213 (mt0) cc_final: 0.7779 (mp10)
REVERT: A  207 ASP cc_start: 0.6957 (t0) cc_final: 0.6641 (p0)
REVERT: A  244 LYS cc_start: 0.8855 (mttm) cc_final: 0.8508 (mtmm)
REVERT: A  268 GLU cc_start: 0.8181 (tt0) cc_final: 0.7793 (tp30)
REVERT: A  294 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8649 (tp)
REVERT: F   42 ILE cc_start: 0.7962 (mt) cc_final: 0.7691 (mm)
REVERT: J   32 LYS cc_start: 0.8222 (mtmt) cc_final: 0.7621 (pttt)
REVERT: B   33 GLN cc_start: 0.8218 (mt0) cc_final: 0.7778 (mp10)
REVERT: B  207 ASP cc_start: 0.6942 (t0) cc_final: 0.6630 (p0)
REVERT: B  244 LYS cc_start: 0.8847 (mttm) cc_final: 0.8498 (mtmm)
REVERT: B  268 GLU cc_start: 0.8161 (tt0) cc_final: 0.7792 (tp30)
REVERT: B  289 ASP cc_start: 0.8458 (p0) cc_final: 0.8203 (p0)
REVERT: B  308 MET cc_start: 0.8409 (mmm) cc_final: 0.8111 (ttp)
  outliers start: 14
  outliers final: 12
  residues processed: 135
  average time/residue: 0.0733
  time to fit residues: 14.9536
Evaluate side-chains
  138 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   11 SER
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain F residue   11 SER
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  251 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 61 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 230 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.166753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.124332 restraints weight = 10651.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 2.40
r_work: 0.3326 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.3090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8839  Z= 0.117
  Angle     :  0.526   9.549  11991  Z= 0.269
  Chirality :  0.039   0.155   1329
  Planarity :  0.004   0.043   1428
  Dihedral  : 12.871  83.142   2227
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 13.35 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.27), residues: 996
  helix:  2.73 (0.26), residues: 374
  sheet:  0.84 (0.26), residues: 406
  loop : -0.22 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  52 
 TYR   0.006   0.001   TYR C  69 
 PHE   0.010   0.001   PHE H  45 
 TRP   0.010   0.001   TRP B 197 
 HIS   0.001   0.000   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8839)
  covalent geometry    : angle       0.52583 (11991)
  hydrogen bonds       : bond        0.02704 (  594)
  hydrogen bonds       : angle       4.30507 ( 1704)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 138
  time to evaluate  : 0.332 
Fit side-chains
REVERT: E   42 ILE cc_start: 0.7941 (mt) cc_final: 0.7590 (mm)
REVERT: I   32 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7606 (pttt)
REVERT: A   33 GLN cc_start: 0.8242 (mt0) cc_final: 0.7815 (mp10)
REVERT: A  207 ASP cc_start: 0.6886 (t0) cc_final: 0.6575 (p0)
REVERT: A  244 LYS cc_start: 0.8879 (mttm) cc_final: 0.8547 (mtmm)
REVERT: A  268 GLU cc_start: 0.8193 (tt0) cc_final: 0.7828 (tp30)
REVERT: A  307 MET cc_start: 0.8217 (tpp) cc_final: 0.7938 (tpt)
REVERT: F   42 ILE cc_start: 0.7948 (mt) cc_final: 0.7601 (mm)
REVERT: J   32 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7611 (pttt)
REVERT: B   33 GLN cc_start: 0.8242 (mt0) cc_final: 0.7812 (mp10)
REVERT: B  207 ASP cc_start: 0.6882 (t0) cc_final: 0.6568 (p0)
REVERT: B  244 LYS cc_start: 0.8865 (mttm) cc_final: 0.8541 (mtmm)
REVERT: B  268 GLU cc_start: 0.8169 (tt0) cc_final: 0.7824 (tp30)
REVERT: B  294 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8650 (tp)
REVERT: B  308 MET cc_start: 0.8398 (mmm) cc_final: 0.8095 (ttp)
  outliers start: 12
  outliers final: 10
  residues processed: 144
  average time/residue: 0.0708
  time to fit residues: 15.4599
Evaluate side-chains
  145 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 134
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  251 MET
Chi-restraints excluded: chain B residue  294 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 84 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 49 optimal weight:   10.0000
   chunk 73 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 344 ASN
B 344 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.164650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.122310 restraints weight = 10708.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 2.38
r_work: 0.3303 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8839  Z= 0.180
  Angle     :  0.560   9.541  11991  Z= 0.287
  Chirality :  0.041   0.160   1329
  Planarity :  0.004   0.043   1428
  Dihedral  : 12.982  83.471   2227
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.96 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.87 (0.27), residues: 996
  helix:  2.66 (0.26), residues: 374
  sheet:  0.75 (0.26), residues: 406
  loop : -0.27 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 215 
 TYR   0.011   0.001   TYR A 277 
 PHE   0.011   0.001   PHE D 101 
 TRP   0.010   0.001   TRP A 197 
 HIS   0.002   0.001   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 8839)
  covalent geometry    : angle       0.56002 (11991)
  hydrogen bonds       : bond        0.02927 (  594)
  hydrogen bonds       : angle       4.35121 ( 1704)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 139
  time to evaluate  : 0.313 
Fit side-chains
REVERT: E   42 ILE cc_start: 0.7995 (mt) cc_final: 0.7646 (mm)
REVERT: I   32 LYS cc_start: 0.8190 (mtmt) cc_final: 0.7595 (pttt)
REVERT: A   33 GLN cc_start: 0.8261 (mt0) cc_final: 0.7821 (mp10)
REVERT: A  207 ASP cc_start: 0.6941 (t0) cc_final: 0.6639 (p0)
REVERT: A  244 LYS cc_start: 0.8840 (mttm) cc_final: 0.8501 (mtmm)
REVERT: A  268 GLU cc_start: 0.8163 (tt0) cc_final: 0.7795 (tp30)
REVERT: F   42 ILE cc_start: 0.7994 (mt) cc_final: 0.7650 (mm)
REVERT: J   32 LYS cc_start: 0.8186 (mtmt) cc_final: 0.7597 (pttt)
REVERT: B   33 GLN cc_start: 0.8252 (mt0) cc_final: 0.7813 (mp10)
REVERT: B  207 ASP cc_start: 0.6946 (t0) cc_final: 0.6637 (p0)
REVERT: B  244 LYS cc_start: 0.8834 (mttm) cc_final: 0.8491 (mtmm)
REVERT: B  268 GLU cc_start: 0.8142 (tt0) cc_final: 0.7791 (tp30)
REVERT: B  289 ASP cc_start: 0.8438 (p0) cc_final: 0.8161 (p0)
REVERT: B  294 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8669 (tp)
REVERT: B  308 MET cc_start: 0.8409 (mmm) cc_final: 0.8110 (ttp)
  outliers start: 13
  outliers final: 12
  residues processed: 146
  average time/residue: 0.0716
  time to fit residues: 15.6511
Evaluate side-chains
  145 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   11 SER
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain F residue   11 SER
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  251 MET
Chi-restraints excluded: chain B residue  294 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 73 optimal weight:    3.9990
   chunk 94 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0270
   overall best weight:    0.6038

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.166658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.124688 restraints weight = 10611.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 2.38
r_work: 0.3331 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.3184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8839  Z= 0.119
  Angle     :  0.532  10.017  11991  Z= 0.274
  Chirality :  0.040   0.156   1329
  Planarity :  0.004   0.044   1428
  Dihedral  : 12.590  82.367   2227
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 13.71 %
    Favored  : 84.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.98 (0.27), residues: 996
  helix:  2.75 (0.26), residues: 374
  sheet:  0.79 (0.26), residues: 406
  loop : -0.16 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  52 
 TYR   0.007   0.001   TYR J  51 
 PHE   0.009   0.001   PHE H  45 
 TRP   0.011   0.001   TRP B 197 
 HIS   0.001   0.000   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8839)
  covalent geometry    : angle       0.53231 (11991)
  hydrogen bonds       : bond        0.02709 (  594)
  hydrogen bonds       : angle       4.19701 ( 1704)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2176.38 seconds
wall clock time: 38 minutes 2.51 seconds (2282.51 seconds total)