Starting phenix.real_space_refine
on Sat May 10 11:18:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pds_17620/05_2025/8pds_17620.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pds_17620/05_2025/8pds_17620.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pds_17620/05_2025/8pds_17620.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pds_17620/05_2025/8pds_17620.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pds_17620/05_2025/8pds_17620.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pds_17620/05_2025/8pds_17620.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.025
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      14      5.49       5
     S      26      5.16       5
     C    3776      2.51       5
     N    1044      2.21       5
     O    1196      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6056
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 365, 2827
          Classifications: {'peptide': 365}
          Link IDs: {'PTRANS': 11, 'TRANS': 353}
    Chain: "E"
      Number of atoms: 280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 280
          Classifications: {'RNA': 14}
          Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 2, 'rna3p': 11}
    Chain: "B"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 61
          Classifications: {'peptide': 7}
          Link IDs: {'TRANS': 6}
    Chain: "C"
      Number of atoms: 2827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 365, 2827
          Classifications: {'peptide': 365}
          Link IDs: {'PTRANS': 11, 'TRANS': 353}
    Chain: "D"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 61
          Classifications: {'peptide': 7}
          Link IDs: {'TRANS': 6}
  Time building chain proxies: 5.30, per 1000 atoms: 0.88
  Number of scatterers: 6056
  At special positions: 0
  Unit cell: (110.25, 90.3, 89.25, 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      26     16.00
     P      14     15.00
     O    1196      8.00
     N    1044      7.00
     C    3776      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.41
  Conformation dependent library (CDL) restraints added in 804.6 milliseconds
  

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1380

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 4 sheets defined
      67.1% alpha, 5.1% beta
      0 base pairs and 10 stacking pairs defined.
    Time for finding SS restraints: 2.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 20
    Processing helix  chain 'A' and resid 37 through 39
      No H-bonds generated for 'chain 'A' and resid 37 through 39'
    Processing helix  chain 'A' and resid 40 through 51
      removed outlier: 3.636A  pdb=" N   LEU A  47 " --> pdb=" O   GLU A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 75
    Processing helix  chain 'A' and resid 75 through 86
    Processing helix  chain 'A' and resid 120 through 142
      removed outlier: 3.628A  pdb=" N   VAL A 124 " --> pdb=" O   GLU A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 151
      removed outlier: 3.646A  pdb=" N   GLN A 150 " --> pdb=" O   PRO A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 171
      removed outlier: 3.883A  pdb=" N   LYS A 171 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 191
      removed outlier: 3.795A  pdb=" N   ARG A 189 " --> pdb=" O   ARG A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 198
    Processing helix  chain 'A' and resid 202 through 217
    Processing helix  chain 'A' and resid 217 through 233
      removed outlier: 3.894A  pdb=" N   ARG A 221 " --> pdb=" O   LYS A 217 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   SER A 222 " --> pdb=" O   VAL A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 251
    Processing helix  chain 'A' and resid 256 through 268
      removed outlier: 3.719A  pdb=" N   ARG A 260 " --> pdb=" O   GLN A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 274
    Processing helix  chain 'A' and resid 275 through 280
    Processing helix  chain 'A' and resid 281 through 296
    Processing helix  chain 'A' and resid 297 through 300
      removed outlier: 3.527A  pdb=" N   GLY A 300 " --> pdb=" O   PRO A 297 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 297 through 300'
    Processing helix  chain 'A' and resid 318 through 332
    Processing helix  chain 'A' and resid 344 through 361
    Processing helix  chain 'B' and resid 10 through 14
      removed outlier: 3.549A  pdb=" N   GLN B  13 " --> pdb=" O   ASP B  10 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU B  14 " --> pdb=" O   ILE B  11 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 10 through 14'
    Processing helix  chain 'C' and resid 9 through 20
    Processing helix  chain 'C' and resid 37 through 39
      No H-bonds generated for 'chain 'C' and resid 37 through 39'
    Processing helix  chain 'C' and resid 40 through 51
      removed outlier: 3.613A  pdb=" N   LEU C  47 " --> pdb=" O   GLU C  43 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 75
    Processing helix  chain 'C' and resid 75 through 86
    Processing helix  chain 'C' and resid 120 through 142
      removed outlier: 3.570A  pdb=" N   VAL C 124 " --> pdb=" O   GLU C 120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 151
    Processing helix  chain 'C' and resid 156 through 171
      removed outlier: 3.910A  pdb=" N   LYS C 171 " --> pdb=" O   LEU C 167 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 175 through 191
      removed outlier: 3.884A  pdb=" N   ARG C 189 " --> pdb=" O   ARG C 185 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 191 through 198
    Processing helix  chain 'C' and resid 202 through 217
    Processing helix  chain 'C' and resid 217 through 233
      removed outlier: 3.902A  pdb=" N   ARG C 221 " --> pdb=" O   LYS C 217 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   SER C 222 " --> pdb=" O   VAL C 218 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 251
    Processing helix  chain 'C' and resid 256 through 268
      removed outlier: 3.651A  pdb=" N   ARG C 260 " --> pdb=" O   GLN C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 270 through 274
    Processing helix  chain 'C' and resid 275 through 280
    Processing helix  chain 'C' and resid 281 through 296
    Processing helix  chain 'C' and resid 297 through 300
      removed outlier: 3.762A  pdb=" N   GLY C 300 " --> pdb=" O   PRO C 297 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 297 through 300'
    Processing helix  chain 'C' and resid 318 through 332
    Processing helix  chain 'C' and resid 344 through 361
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35
      removed outlier: 6.193A  pdb=" N   THR A  33 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 104
      removed outlier: 7.803A  pdb=" N   LEU A 111 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 32 through 35
    Processing sheet with id=AA4, first strand: chain 'C' and resid 96 through 104
      removed outlier: 7.875A  pdb=" N   LEU C 111 " --> pdb=" O   LEU C 100 " (cutoff:3.500A)

    338 hydrogen bonds defined for protein.
    987 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      10 stacking parallelities
  Total time for adding SS restraints: 1.74

  Time building geometry restraints manager: 1.68 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: 1949
        1.34 -     1.46: 815
        1.46 -     1.57: 3334
        1.57 -     1.69: 27
        1.69 -     1.81: 46
  Bond restraints: 6171
  Sorted by residual:
  bond pdb=" N   ILE B  11 "
       pdb=" CA  ILE B  11 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.30e-02 5.92e+03 7.53e+00
  bond pdb=" CB  VAL C  92 "
       pdb=" CG1 VAL C  92 "
    ideal  model  delta    sigma   weight residual
    1.521  1.466  0.055 3.30e-02 9.18e+02 2.74e+00
  bond pdb=" CB  VAL A  92 "
       pdb=" CG1 VAL A  92 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.45e+00
  bond pdb=" CB  VAL C 190 "
       pdb=" CG1 VAL C 190 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.89e+00
  bond pdb=" CG  LEU C 282 "
       pdb=" CD2 LEU C 282 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.07e+00
  ... (remaining 6166 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.17: 7950
        1.17 -     2.35: 360
        2.35 -     3.52: 53
        3.52 -     4.69: 17
        4.69 -     5.87: 4
  Bond angle restraints: 8384
  Sorted by residual:
  angle pdb=" CA  ILE B  11 "
        pdb=" C   ILE B  11 "
        pdb=" O   ILE B  11 "
      ideal   model   delta    sigma   weight residual
     120.47  117.86    2.61 1.08e+00 8.57e-01 5.86e+00
  angle pdb=" C   LEU C  52 "
        pdb=" N   TYR C  53 "
        pdb=" CA  TYR C  53 "
      ideal   model   delta    sigma   weight residual
     122.60  118.83    3.77 1.56e+00 4.11e-01 5.83e+00
  angle pdb=" C   LEU A  52 "
        pdb=" N   TYR A  53 "
        pdb=" CA  TYR A  53 "
      ideal   model   delta    sigma   weight residual
     122.65  119.02    3.63 1.60e+00 3.91e-01 5.14e+00
  angle pdb=" N   ILE C  51 "
        pdb=" CA  ILE C  51 "
        pdb=" C   ILE C  51 "
      ideal   model   delta    sigma   weight residual
     113.00  110.37    2.63 1.30e+00 5.92e-01 4.10e+00
  angle pdb=" N   GLN C 216 "
        pdb=" CA  GLN C 216 "
        pdb=" CB  GLN C 216 "
      ideal   model   delta    sigma   weight residual
     110.07  112.91   -2.84 1.45e+00 4.76e-01 3.83e+00
  ... (remaining 8379 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 3444
       17.57 -    35.15: 281
       35.15 -    52.72: 44
       52.72 -    70.29: 15
       70.29 -    87.87: 25
  Dihedral angle restraints: 3809
    sinusoidal: 1657
      harmonic: 2152
  Sorted by residual:
  dihedral pdb=" CA  GLY C 311 "
           pdb=" C   GLY C 311 "
           pdb=" N   LEU C 312 "
           pdb=" CA  LEU C 312 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.62   18.38     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  ILE A 334 "
           pdb=" C   ILE A 334 "
           pdb=" N   ILE A 335 "
           pdb=" CA  ILE A 335 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.64  -16.36     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  ALA C 251 "
           pdb=" C   ALA C 251 "
           pdb=" N   TYR C 252 "
           pdb=" CA  TYR C 252 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.71  -16.29     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 3806 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 598
       0.032 -    0.065: 263
       0.065 -    0.097: 92
       0.097 -    0.129: 28
       0.129 -    0.162: 5
  Chirality restraints: 986
  Sorted by residual:
  chirality pdb=" CA  ILE B  11 "
            pdb=" N   ILE B  11 "
            pdb=" C   ILE B  11 "
            pdb=" CB  ILE B  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.53e-01
  chirality pdb=" CB  VAL A  35 "
            pdb=" CA  VAL A  35 "
            pdb=" CG1 VAL A  35 "
            pdb=" CG2 VAL A  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.42e-01
  chirality pdb=" CA  VAL C 119 "
            pdb=" N   VAL C 119 "
            pdb=" C   VAL C 119 "
            pdb=" CB  VAL C 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.66e-01
  ... (remaining 983 not shown)

  Planarity restraints: 1018
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C E  66 "   -0.021 2.00e-02 2.50e+03   1.11e-02 2.76e+00
        pdb=" N1    C E  66 "    0.024 2.00e-02 2.50e+03
        pdb=" C2    C E  66 "    0.001 2.00e-02 2.50e+03
        pdb=" O2    C E  66 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    C E  66 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    C E  66 "   -0.001 2.00e-02 2.50e+03
        pdb=" N4    C E  66 "   -0.007 2.00e-02 2.50e+03
        pdb=" C5    C E  66 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    C E  66 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C  53 "   -0.006 2.00e-02 2.50e+03   1.11e-02 2.46e+00
        pdb=" CG  TYR C  53 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR C  53 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR C  53 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR C  53 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR C  53 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR C  53 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C  53 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C E  73 "   -0.020 2.00e-02 2.50e+03   1.02e-02 2.33e+00
        pdb=" N1    C E  73 "    0.021 2.00e-02 2.50e+03
        pdb=" C2    C E  73 "    0.002 2.00e-02 2.50e+03
        pdb=" O2    C E  73 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    C E  73 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    C E  73 "   -0.001 2.00e-02 2.50e+03
        pdb=" N4    C E  73 "   -0.007 2.00e-02 2.50e+03
        pdb=" C5    C E  73 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    C E  73 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1015 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1066
        2.76 -     3.30: 5996
        3.30 -     3.83: 10436
        3.83 -     4.37: 12651
        4.37 -     4.90: 20723
  Nonbonded interactions: 50872
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 338 "
            pdb=" OP2   C E  74 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   LEU A  18 "
            pdb=" OG  SER C 233 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OG  SER A 307 "
            pdb=" O   SER C 235 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OP2   C E  67 "
            pdb=" OH  TYR C 338 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O2    C E  71 "
            pdb=" ND2 ASN C 246 "
     model   vdw
     2.315 3.120
  ... (remaining 50867 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 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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:             3.340
  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:         0.040
  Set scattering table:                    0.070
  Process input model:                     20.290
  Find NCS groups from input model:        0.140
  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:12.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
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      :  0.004   0.055   6171  Z= 0.193
  Angle     :  0.580   5.865   8384  Z= 0.331
  Chirality :  0.042   0.162    986
  Planarity :  0.004   0.028   1018
  Dihedral  : 15.092  87.867   2429
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.00 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.30), residues: 736
  helix:  0.32 (0.24), residues: 474
  sheet: -1.22 (0.64), residues: 42
  loop : -0.54 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 123 
 HIS   0.004   0.001   HIS C  56 
 PHE   0.016   0.002   PHE C 169 
 TYR   0.025   0.002   TYR C  53 
 ARG   0.007   0.000   ARG A  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12069 (  338)
  hydrogen bonds       : angle       6.23451 (  987)
  covalent geometry    : bond        0.00443 ( 6171)
  covalent geometry    : angle       0.58039 ( 8384)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.695 
Fit side-chains
REVERT: C  135 MET cc_start: 0.8191 (ttm) cc_final: 0.7928 (ttm)
  outliers start: 1
  outliers final: 0
  residues processed: 98
  average time/residue: 1.5603
  time to fit residues: 158.7240
Evaluate side-chains
  82 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 55 optimal weight:    0.5980
   chunk 30 optimal weight:    0.4980
   chunk 18 optimal weight:    0.2980
   chunk 37 optimal weight:    1.9990
   chunk 29 optimal weight:    0.2980
   chunk 57 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
C  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.144252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.117307 restraints weight = 6862.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 1.57
r_work: 0.3095 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.1066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6171  Z= 0.173
  Angle     :  0.540   5.788   8384  Z= 0.288
  Chirality :  0.041   0.141    986
  Planarity :  0.004   0.033   1018
  Dihedral  : 11.621  74.596   1031
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  8.04 %
    Favored  : 90.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.30), residues: 736
  helix:  0.85 (0.24), residues: 478
  sheet: -1.08 (0.64), residues: 42
  loop : -0.43 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 123 
 HIS   0.004   0.001   HIS C  56 
 PHE   0.014   0.002   PHE C 169 
 TYR   0.015   0.002   TYR C  69 
 ARG   0.006   0.001   ARG A  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04555 (  338)
  hydrogen bonds       : angle       4.56279 (  987)
  covalent geometry    : bond        0.00404 ( 6171)
  covalent geometry    : angle       0.53984 ( 8384)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.616 
Fit side-chains
REVERT: A   26 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7905 (mtmm)
REVERT: A  105 ASN cc_start: 0.7630 (OUTLIER) cc_final: 0.7133 (p0)
REVERT: A  208 ARG cc_start: 0.8287 (tpt-90) cc_final: 0.7548 (tpm-80)
REVERT: A  339 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7872 (mmt180)
REVERT: C  272 MET cc_start: 0.8525 (mmm) cc_final: 0.8298 (mmm)
REVERT: C  283 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7431 (mmpt)
REVERT: C  341 ARG cc_start: 0.8095 (ptt-90) cc_final: 0.7685 (ptm-80)
  outliers start: 11
  outliers final: 7
  residues processed: 88
  average time/residue: 1.4970
  time to fit residues: 136.9685
Evaluate side-chains
  88 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LYS
Chi-restraints excluded: chain A residue  105 ASN
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  339 ARG
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  283 LYS
Chi-restraints excluded: chain C residue  358 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 28 optimal weight:    0.2980
   chunk 52 optimal weight:    0.0970
   chunk 1 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0980
   chunk 70 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 21 optimal weight:    0.3980
   chunk 39 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 16 optimal weight:    0.4980
   overall best weight:    0.2778

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

Flipped N/Q/H residues before XYZ refinement:
A 112 GLN
A 284 GLN
C 150 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.146066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.119615 restraints weight = 6925.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 1.63
r_work: 0.3112 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.1315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6171  Z= 0.125
  Angle     :  0.482   6.907   8384  Z= 0.257
  Chirality :  0.039   0.137    986
  Planarity :  0.003   0.033   1018
  Dihedral  : 11.539  74.205   1031
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  :  9.78 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.31), residues: 736
  helix:  1.21 (0.24), residues: 478
  sheet: -0.93 (0.66), residues: 42
  loop : -0.34 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 123 
 HIS   0.002   0.001   HIS C  56 
 PHE   0.011   0.001   PHE C 169 
 TYR   0.012   0.001   TYR C  69 
 ARG   0.008   0.001   ARG C  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03990 (  338)
  hydrogen bonds       : angle       4.28948 (  987)
  covalent geometry    : bond        0.00282 ( 6171)
  covalent geometry    : angle       0.48227 ( 8384)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
REVERT: A  208 ARG cc_start: 0.8226 (tpt-90) cc_final: 0.7491 (tpm-80)
REVERT: C  283 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7374 (mmpt)
REVERT: C  341 ARG cc_start: 0.8017 (ptt-90) cc_final: 0.7613 (ptm-80)
  outliers start: 12
  outliers final: 8
  residues processed: 89
  average time/residue: 1.4723
  time to fit residues: 136.4190
Evaluate side-chains
  85 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  339 ARG
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  104 LYS
Chi-restraints excluded: chain C residue  283 LYS
Chi-restraints excluded: chain C residue  358 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 41 optimal weight:    0.6980
   chunk 67 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   chunk 43 optimal weight:    0.5980
   chunk 57 optimal weight:    0.5980
   chunk 56 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0870
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
C  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.144186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.118452 restraints weight = 7065.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 1.39
r_work: 0.3067 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.1355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6171  Z= 0.173
  Angle     :  0.526   6.679   8384  Z= 0.278
  Chirality :  0.041   0.136    986
  Planarity :  0.004   0.034   1018
  Dihedral  : 11.503  74.612   1031
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 11.67 %
    Favored  : 85.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.30), residues: 736
  helix:  1.12 (0.24), residues: 478
  sheet: -1.01 (0.65), residues: 42
  loop : -0.39 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 123 
 HIS   0.003   0.001   HIS C  56 
 PHE   0.015   0.002   PHE C 169 
 TYR   0.015   0.002   TYR C  69 
 ARG   0.009   0.001   ARG C  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04375 (  338)
  hydrogen bonds       : angle       4.34194 (  987)
  covalent geometry    : bond        0.00405 ( 6171)
  covalent geometry    : angle       0.52610 ( 8384)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7908 (mtmm)
REVERT: A  208 ARG cc_start: 0.8268 (tpt-90) cc_final: 0.7509 (tpm-80)
REVERT: A  339 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7834 (mmt180)
REVERT: C  283 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7381 (mmpt)
REVERT: C  341 ARG cc_start: 0.8050 (ptt-90) cc_final: 0.7641 (ptm-80)
  outliers start: 19
  outliers final: 13
  residues processed: 91
  average time/residue: 1.3733
  time to fit residues: 130.3783
Evaluate side-chains
  95 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ASP
Chi-restraints excluded: chain A residue   26 LYS
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  339 ARG
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  104 LYS
Chi-restraints excluded: chain C residue  283 LYS
Chi-restraints excluded: chain C residue  358 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 7 optimal weight:    0.4980
   chunk 66 optimal weight:    0.1980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
C 150 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.143654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.117260 restraints weight = 6938.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 1.38
r_work: 0.3071 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6171  Z= 0.182
  Angle     :  0.536   6.883   8384  Z= 0.282
  Chirality :  0.041   0.138    986
  Planarity :  0.004   0.039   1018
  Dihedral  : 11.485  74.688   1031
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 11.99 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.30), residues: 736
  helix:  1.08 (0.24), residues: 478
  sheet: -1.02 (0.65), residues: 42
  loop : -0.44 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 123 
 HIS   0.003   0.001   HIS C  56 
 PHE   0.015   0.002   PHE C 169 
 TYR   0.016   0.002   TYR C  69 
 ARG   0.010   0.001   ARG C  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04416 (  338)
  hydrogen bonds       : angle       4.35235 (  987)
  covalent geometry    : bond        0.00429 ( 6171)
  covalent geometry    : angle       0.53550 ( 8384)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 81
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7946 (mtmm)
REVERT: A  208 ARG cc_start: 0.8258 (tpt-90) cc_final: 0.7500 (tpm-80)
REVERT: C  249 MET cc_start: 0.9142 (mmp) cc_final: 0.8937 (mmp)
REVERT: C  341 ARG cc_start: 0.8064 (ptt-90) cc_final: 0.7642 (ptm-80)
  outliers start: 20
  outliers final: 14
  residues processed: 94
  average time/residue: 1.4938
  time to fit residues: 146.1680
Evaluate side-chains
  93 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ASP
Chi-restraints excluded: chain A residue   26 LYS
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  339 ARG
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  104 LYS
Chi-restraints excluded: chain C residue  358 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0870
   chunk 11 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0980
   chunk 17 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.4558

-------------------------------------------------------------------------------
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 = 0.3511 r_free = 0.3511 target = 0.143880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.118362 restraints weight = 6874.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 1.30
r_work: 0.3087 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.1465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6171  Z= 0.163
  Angle     :  0.526   7.092   8384  Z= 0.278
  Chirality :  0.040   0.138    986
  Planarity :  0.004   0.042   1018
  Dihedral  : 11.472  74.548   1031
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 11.99 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.30), residues: 736
  helix:  1.16 (0.24), residues: 478
  sheet: -1.03 (0.66), residues: 42
  loop : -0.45 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 123 
 HIS   0.002   0.001   HIS C  56 
 PHE   0.014   0.002   PHE C 169 
 TYR   0.014   0.002   TYR C  69 
 ARG   0.010   0.001   ARG C  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04238 (  338)
  hydrogen bonds       : angle       4.29755 (  987)
  covalent geometry    : bond        0.00381 ( 6171)
  covalent geometry    : angle       0.52576 ( 8384)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASN cc_start: 0.8477 (t0) cc_final: 0.8277 (t0)
REVERT: A  208 ARG cc_start: 0.8221 (tpt-90) cc_final: 0.7473 (tpm-80)
REVERT: C  341 ARG cc_start: 0.8002 (ptt-90) cc_final: 0.7609 (ptm-80)
REVERT: C  363 LYS cc_start: 0.7673 (mmtt) cc_final: 0.6988 (mtpm)
  outliers start: 22
  outliers final: 16
  residues processed: 94
  average time/residue: 1.3240
  time to fit residues: 130.1138
Evaluate side-chains
  100 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ASP
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  339 ARG
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   53 TYR
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  104 LYS
Chi-restraints excluded: chain C residue  358 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 27 optimal weight:    0.3980
   chunk 38 optimal weight:    0.6980
   chunk 63 optimal weight:    0.2980
   chunk 35 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 20 optimal weight:    0.4980
   chunk 59 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.3515 r_free = 0.3515 target = 0.144099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.118251 restraints weight = 6955.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 1.38
r_work: 0.3063 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6171  Z= 0.169
  Angle     :  0.537   7.046   8384  Z= 0.282
  Chirality :  0.041   0.139    986
  Planarity :  0.004   0.046   1018
  Dihedral  : 11.459  74.604   1031
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 12.78 %
    Favored  : 84.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.30), residues: 736
  helix:  1.13 (0.24), residues: 480
  sheet: -0.99 (0.67), residues: 42
  loop : -0.42 (0.40), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 123 
 HIS   0.002   0.001   HIS C  56 
 PHE   0.014   0.002   PHE C 169 
 TYR   0.015   0.002   TYR C  69 
 ARG   0.012   0.001   ARG C  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04277 (  338)
  hydrogen bonds       : angle       4.30462 (  987)
  covalent geometry    : bond        0.00396 ( 6171)
  covalent geometry    : angle       0.53658 ( 8384)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.580 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ASN cc_start: 0.8430 (t0) cc_final: 0.8148 (t0)
REVERT: A  208 ARG cc_start: 0.8263 (tpt-90) cc_final: 0.7502 (tpm-80)
REVERT: A  282 LEU cc_start: 0.8562 (mm) cc_final: 0.8274 (mp)
REVERT: C  283 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7942 (pptt)
REVERT: C  341 ARG cc_start: 0.8077 (ptt-90) cc_final: 0.7646 (ptm-80)
REVERT: C  363 LYS cc_start: 0.7676 (mmtt) cc_final: 0.6989 (mtpm)
  outliers start: 19
  outliers final: 16
  residues processed: 92
  average time/residue: 1.3859
  time to fit residues: 132.9415
Evaluate side-chains
  97 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ASP
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  339 ARG
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   53 TYR
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  104 LYS
Chi-restraints excluded: chain C residue  283 LYS
Chi-restraints excluded: chain C residue  358 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 30 optimal weight:    0.1980
   chunk 3 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0870
   chunk 19 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
C 150 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.143912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.117481 restraints weight = 6970.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 1.38
r_work: 0.3065 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2949 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6171  Z= 0.174
  Angle     :  0.542   6.658   8384  Z= 0.285
  Chirality :  0.041   0.139    986
  Planarity :  0.004   0.051   1018
  Dihedral  : 11.452  74.618   1031
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 13.41 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.30), residues: 736
  helix:  1.12 (0.24), residues: 480
  sheet: -0.98 (0.67), residues: 42
  loop : -0.41 (0.40), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 123 
 HIS   0.002   0.001   HIS C  56 
 PHE   0.015   0.002   PHE C 169 
 TYR   0.015   0.002   TYR C  69 
 ARG   0.013   0.001   ARG C  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04324 (  338)
  hydrogen bonds       : angle       4.30941 (  987)
  covalent geometry    : bond        0.00407 ( 6171)
  covalent geometry    : angle       0.54173 ( 8384)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 TYR cc_start: 0.6636 (OUTLIER) cc_final: 0.5275 (p90)
REVERT: A  105 ASN cc_start: 0.8406 (t0) cc_final: 0.8137 (t0)
REVERT: A  208 ARG cc_start: 0.8250 (tpt-90) cc_final: 0.7489 (tpm-80)
REVERT: C    1 MET cc_start: 0.6201 (pmm) cc_final: 0.5996 (ppp)
REVERT: C  283 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7957 (pptt)
REVERT: C  341 ARG cc_start: 0.8021 (ptt-90) cc_final: 0.7609 (ptm-80)
REVERT: C  363 LYS cc_start: 0.7694 (mmtt) cc_final: 0.7022 (mtpt)
  outliers start: 21
  outliers final: 17
  residues processed: 92
  average time/residue: 1.4414
  time to fit residues: 138.1482
Evaluate side-chains
  98 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ASP
Chi-restraints excluded: chain A residue   53 TYR
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  339 ARG
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   53 TYR
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  104 LYS
Chi-restraints excluded: chain C residue  283 LYS
Chi-restraints excluded: chain C residue  358 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 22 optimal weight:    0.4980
   chunk 18 optimal weight:    0.4980
   chunk 34 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.142800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.116790 restraints weight = 6997.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 1.32
r_work: 0.3068 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6171  Z= 0.204
  Angle     :  0.574   7.198   8384  Z= 0.301
  Chirality :  0.042   0.138    986
  Planarity :  0.004   0.054   1018
  Dihedral  : 11.476  74.806   1031
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 14.20 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.30), residues: 736
  helix:  1.02 (0.24), residues: 478
  sheet: -1.04 (0.68), residues: 42
  loop : -0.46 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 123 
 HIS   0.002   0.001   HIS C  56 
 PHE   0.017   0.002   PHE C 169 
 TYR   0.017   0.002   TYR C  69 
 ARG   0.013   0.001   ARG C  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04584 (  338)
  hydrogen bonds       : angle       4.39120 (  987)
  covalent geometry    : bond        0.00484 ( 6171)
  covalent geometry    : angle       0.57414 ( 8384)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 TYR cc_start: 0.6777 (OUTLIER) cc_final: 0.5287 (p90)
REVERT: A  208 ARG cc_start: 0.8239 (tpt-90) cc_final: 0.7488 (tpm-80)
REVERT: C  216 GLN cc_start: 0.8294 (mt0) cc_final: 0.7903 (tp40)
REVERT: C  283 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7910 (pptt)
REVERT: C  341 ARG cc_start: 0.8013 (ptt-90) cc_final: 0.7624 (ptm-80)
REVERT: C  363 LYS cc_start: 0.7721 (mmtt) cc_final: 0.7057 (mtpt)
  outliers start: 18
  outliers final: 15
  residues processed: 87
  average time/residue: 1.4229
  time to fit residues: 128.9772
Evaluate side-chains
  94 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ASP
Chi-restraints excluded: chain A residue   53 TYR
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  339 ARG
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   53 TYR
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  104 LYS
Chi-restraints excluded: chain C residue  283 LYS
Chi-restraints excluded: chain C residue  358 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 16 optimal weight:    0.2980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.142912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.117335 restraints weight = 7014.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 1.27
r_work: 0.3065 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.1566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6171  Z= 0.205
  Angle     :  0.585   8.111   8384  Z= 0.305
  Chirality :  0.042   0.139    986
  Planarity :  0.004   0.058   1018
  Dihedral  : 11.505  74.801   1031
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 14.20 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.30), residues: 736
  helix:  1.00 (0.24), residues: 478
  sheet: -1.03 (0.68), residues: 42
  loop : -0.48 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 123 
 HIS   0.002   0.001   HIS C  56 
 PHE   0.016   0.002   PHE C 169 
 TYR   0.016   0.002   TYR C  69 
 ARG   0.014   0.001   ARG C  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04552 (  338)
  hydrogen bonds       : angle       4.38458 (  987)
  covalent geometry    : bond        0.00487 ( 6171)
  covalent geometry    : angle       0.58459 ( 8384)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 TYR cc_start: 0.6818 (OUTLIER) cc_final: 0.5322 (p90)
REVERT: A  208 ARG cc_start: 0.8242 (tpt-90) cc_final: 0.7499 (tpm-80)
REVERT: C  216 GLN cc_start: 0.8288 (mt0) cc_final: 0.7898 (tp40)
REVERT: C  283 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7916 (pptt)
REVERT: C  341 ARG cc_start: 0.7973 (ptt-90) cc_final: 0.7588 (ptm-80)
REVERT: C  363 LYS cc_start: 0.7739 (mmtt) cc_final: 0.7088 (mtpt)
  outliers start: 18
  outliers final: 15
  residues processed: 88
  average time/residue: 1.3919
  time to fit residues: 127.7980
Evaluate side-chains
  93 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ASP
Chi-restraints excluded: chain A residue   53 TYR
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain C residue   25 ILE
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   53 TYR
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  104 LYS
Chi-restraints excluded: chain C residue  283 LYS
Chi-restraints excluded: chain C residue  358 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 68 optimal weight:    0.4980
   chunk 46 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0970
   chunk 5 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN
C 365 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.143152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.116091 restraints weight = 7057.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.44
r_work: 0.3064 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6171  Z= 0.181
  Angle     :  0.563   8.695   8384  Z= 0.294
  Chirality :  0.041   0.139    986
  Planarity :  0.004   0.059   1018
  Dihedral  : 11.503  74.646   1031
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 14.20 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.30), residues: 736
  helix:  1.09 (0.24), residues: 478
  sheet: -1.02 (0.68), residues: 42
  loop : -0.44 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 123 
 HIS   0.002   0.001   HIS C  56 
 PHE   0.015   0.002   PHE C 169 
 TYR   0.015   0.002   TYR C  69 
 ARG   0.014   0.001   ARG C  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04363 (  338)
  hydrogen bonds       : angle       4.32804 (  987)
  covalent geometry    : bond        0.00428 ( 6171)
  covalent geometry    : angle       0.56261 ( 8384)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4823.79 seconds
wall clock time: 83 minutes 52.98 seconds (5032.98 seconds total)