Starting phenix.real_space_refine
on Fri Aug 22 16:48:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pds_17620/08_2025/8pds_17620.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pds_17620/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pds_17620/08_2025/8pds_17620.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pds_17620/08_2025/8pds_17620.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pds_17620/08_2025/8pds_17620.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pds_17620/08_2025/8pds_17620.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.025
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.41, per 1000 atoms: 0.23
  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: 0.42
  Conformation dependent library (CDL) restraints added in 312.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.72
  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: 0.97

  Time building geometry restraints manager: 0.56 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:             5.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.760
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.670
-------------------------------------------------------------------------------
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 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: -0.16 (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
 ARG   0.007   0.000   ARG A  78 
 TYR   0.025   0.002   TYR C  53 
 PHE   0.016   0.002   PHE C 169 
 TRP   0.007   0.001   TRP C 123 
 HIS   0.004   0.001   HIS C  56 

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

*********************** 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  : 0.222 
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: 0.7549
  time to fit residues: 76.6395
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  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0970
   chunk 38 optimal weight:    0.3980
   chunk 61 optimal weight:    0.3980
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
C  81 GLN
C 150 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.144337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.117426 restraints weight = 7010.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 1.56
r_work: 0.3095 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1031

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= 0.170
  Angle     :  0.536   5.817   8384  Z= 0.287
  Chirality :  0.041   0.146    986
  Planarity :  0.004   0.032   1018
  Dihedral  : 11.625  74.570   1031
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  8.04 %
    Favored  : 90.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.30), residues: 736
  helix:  0.86 (0.24), residues: 478
  sheet: -1.05 (0.63), residues: 42
  loop : -0.43 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  96 
 TYR   0.015   0.002   TYR C  69 
 PHE   0.014   0.002   PHE C 169 
 TRP   0.005   0.001   TRP C 123 
 HIS   0.003   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 6171)
  covalent geometry    : angle       0.53645 ( 8384)
  hydrogen bonds       : bond        0.04575 (  338)
  hydrogen bonds       : angle       4.59004 (  987)

*********************** 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
  97 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A   26 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7869 (mtmm)
REVERT: A  105 ASN cc_start: 0.7605 (OUTLIER) cc_final: 0.7111 (p0)
REVERT: A  208 ARG cc_start: 0.8279 (tpt-90) cc_final: 0.7537 (tpm-80)
REVERT: A  339 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7821 (mmt180)
REVERT: C  283 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7444 (mmpt)
REVERT: C  341 ARG cc_start: 0.8078 (ptt-90) cc_final: 0.7671 (ptm-80)
  outliers start: 10
  outliers final: 6
  residues processed: 91
  average time/residue: 0.7363
  time to fit residues: 69.3852
Evaluate side-chains
  87 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
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  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 36 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 7 optimal weight:    0.4980
   chunk 35 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0070
   chunk 13 optimal weight:    0.6980
   chunk 52 optimal weight:    0.2980
   chunk 33 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0970
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.3196

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

Flipped N/Q/H residues before XYZ refinement:
A 284 GLN
C  81 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 = 0.3532 r_free = 0.3532 target = 0.145769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.118586 restraints weight = 6956.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 1.63
r_work: 0.3091 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.1253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6171  Z= 0.134
  Angle     :  0.490   6.749   8384  Z= 0.261
  Chirality :  0.039   0.138    986
  Planarity :  0.003   0.032   1018
  Dihedral  : 11.551  74.284   1031
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  9.46 %
    Favored  : 88.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.31), residues: 736
  helix:  1.16 (0.24), residues: 478
  sheet: -0.91 (0.66), residues: 42
  loop : -0.36 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  96 
 TYR   0.013   0.002   TYR C  69 
 PHE   0.011   0.002   PHE C 169 
 TRP   0.005   0.001   TRP C 123 
 HIS   0.002   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 6171)
  covalent geometry    : angle       0.49029 ( 8384)
  hydrogen bonds       : bond        0.04099 (  338)
  hydrogen bonds       : angle       4.32877 (  987)

*********************** 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
  98 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A   26 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7870 (mtmm)
REVERT: A  208 ARG cc_start: 0.8248 (tpt-90) cc_final: 0.7514 (tpm-80)
REVERT: C  283 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7392 (mmpt)
REVERT: C  341 ARG cc_start: 0.8058 (ptt-90) cc_final: 0.7638 (ptm-80)
  outliers start: 16
  outliers final: 8
  residues processed: 89
  average time/residue: 0.6622
  time to fit residues: 61.2134
Evaluate side-chains
  87 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LYS
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   92 VAL
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 68 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 14 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3483 r_free = 0.3483 target = 0.141399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.114853 restraints weight = 6967.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 1.36
r_work: 0.3051 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.1341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   6171  Z= 0.249
  Angle     :  0.601   6.515   8384  Z= 0.316
  Chirality :  0.044   0.141    986
  Planarity :  0.004   0.033   1018
  Dihedral  : 11.540  75.083   1031
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 11.51 %
    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 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:  0.38 (0.30), residues: 736
  helix:  0.80 (0.24), residues: 478
  sheet: -1.13 (0.65), residues: 42
  loop : -0.49 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  96 
 TYR   0.019   0.002   TYR C  69 
 PHE   0.019   0.002   PHE C 169 
 TRP   0.007   0.001   TRP C 123 
 HIS   0.003   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 ( 6171)
  covalent geometry    : angle       0.60057 ( 8384)
  hydrogen bonds       : bond        0.05007 (  338)
  hydrogen bonds       : angle       4.55952 (  987)

*********************** 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
  99 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A   26 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7958 (mtmm)
REVERT: A  208 ARG cc_start: 0.8272 (tpt-90) cc_final: 0.7516 (tpm-80)
REVERT: A  339 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7852 (mmt180)
REVERT: C  216 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7914 (mt0)
REVERT: C  272 MET cc_start: 0.8399 (mmm) cc_final: 0.8159 (mmm)
REVERT: C  283 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7806 (pptt)
REVERT: C  341 ARG cc_start: 0.8086 (ptt-90) cc_final: 0.7701 (ptm-80)
  outliers start: 20
  outliers final: 14
  residues processed: 88
  average time/residue: 0.6271
  time to fit residues: 57.4521
Evaluate side-chains
  93 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
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  135 MET
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  216 GLN
Chi-restraints excluded: chain C residue  283 LYS
Chi-restraints excluded: chain C residue  286 THR
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 37 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 43 optimal weight:    0.2980
   chunk 27 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 11 optimal weight:    0.3980
   chunk 4 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 69 optimal weight:    0.0980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.143872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.117068 restraints weight = 7032.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 1.62
r_work: 0.3071 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.1403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6171  Z= 0.155
  Angle     :  0.517   6.638   8384  Z= 0.274
  Chirality :  0.040   0.139    986
  Planarity :  0.004   0.040   1018
  Dihedral  : 11.530  74.517   1031
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 12.93 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.30), residues: 736
  helix:  1.06 (0.24), residues: 478
  sheet: -1.05 (0.65), residues: 42
  loop : -0.42 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  96 
 TYR   0.014   0.002   TYR C  69 
 PHE   0.013   0.002   PHE C 169 
 TRP   0.006   0.001   TRP C 123 
 HIS   0.002   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6171)
  covalent geometry    : angle       0.51691 ( 8384)
  hydrogen bonds       : bond        0.04229 (  338)
  hydrogen bonds       : angle       4.33606 (  987)

*********************** 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
  97 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A  208 ARG cc_start: 0.8266 (tpt-90) cc_final: 0.7524 (tpm-80)
REVERT: A  339 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7808 (mmt180)
REVERT: C  341 ARG cc_start: 0.8068 (ptt-90) cc_final: 0.7648 (ptm-80)
REVERT: C  363 LYS cc_start: 0.7629 (mmtt) cc_final: 0.6924 (mtpm)
  outliers start: 19
  outliers final: 13
  residues processed: 88
  average time/residue: 0.6027
  time to fit residues: 55.2928
Evaluate side-chains
  92 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
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  135 MET
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  358 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 10 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0770
   chunk 5 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0670
   chunk 57 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.4076

-------------------------------------------------------------------------------
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 = 0.3519 r_free = 0.3519 target = 0.144590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.117642 restraints weight = 6951.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 1.43
r_work: 0.3076 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.1483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6171  Z= 0.153
  Angle     :  0.516   6.914   8384  Z= 0.274
  Chirality :  0.040   0.138    986
  Planarity :  0.004   0.042   1018
  Dihedral  : 11.482  74.497   1031
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 12.93 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.30), residues: 736
  helix:  1.15 (0.24), residues: 480
  sheet: -1.01 (0.65), residues: 42
  loop : -0.38 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C  96 
 TYR   0.014   0.002   TYR C  69 
 PHE   0.013   0.002   PHE C 169 
 TRP   0.006   0.001   TRP C 123 
 HIS   0.002   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 6171)
  covalent geometry    : angle       0.51636 ( 8384)
  hydrogen bonds       : bond        0.04162 (  338)
  hydrogen bonds       : angle       4.26688 (  987)

*********************** 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
  102 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A  208 ARG cc_start: 0.8248 (tpt-90) cc_final: 0.7516 (tpm-80)
REVERT: C  341 ARG cc_start: 0.8050 (ptt-90) cc_final: 0.7643 (ptm-80)
REVERT: C  363 LYS cc_start: 0.7667 (mmtt) cc_final: 0.6965 (mtpm)
  outliers start: 20
  outliers final: 15
  residues processed: 93
  average time/residue: 0.6183
  time to fit residues: 59.9753
Evaluate side-chains
  94 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
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  135 MET
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 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   92 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue   97 THR
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 2 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 25 optimal weight:    0.4980
   chunk 32 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3494 r_free = 0.3494 target = 0.142331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.116093 restraints weight = 6965.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 1.35
r_work: 0.3045 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6171  Z= 0.218
  Angle     :  0.584   7.065   8384  Z= 0.307
  Chirality :  0.043   0.139    986
  Planarity :  0.004   0.046   1018
  Dihedral  : 11.492  74.881   1031
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 13.72 %
    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 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:  0.53 (0.30), residues: 736
  helix:  0.94 (0.24), residues: 478
  sheet: -1.05 (0.67), residues: 42
  loop : -0.49 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C  96 
 TYR   0.017   0.002   TYR C  69 
 PHE   0.017   0.002   PHE C 169 
 TRP   0.008   0.001   TRP C 123 
 HIS   0.003   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 6171)
  covalent geometry    : angle       0.58391 ( 8384)
  hydrogen bonds       : bond        0.04685 (  338)
  hydrogen bonds       : angle       4.44445 (  987)

*********************** 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
  100 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A   53 TYR cc_start: 0.6753 (OUTLIER) cc_final: 0.5213 (p90)
REVERT: A  208 ARG cc_start: 0.8272 (tpt-90) cc_final: 0.7522 (tpm-80)
REVERT: A  282 LEU cc_start: 0.8578 (mm) cc_final: 0.8289 (mp)
REVERT: C  283 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7939 (pptt)
REVERT: C  341 ARG cc_start: 0.8083 (ptt-90) cc_final: 0.7665 (ptm-80)
REVERT: C  363 LYS cc_start: 0.7690 (mmtt) cc_final: 0.6997 (mtpt)
  outliers start: 21
  outliers final: 16
  residues processed: 90
  average time/residue: 0.7274
  time to fit residues: 68.2962
Evaluate side-chains
  97 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
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  135 MET
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   67 ILE
Chi-restraints excluded: chain C residue   94 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 53 optimal weight:    0.1980
   chunk 46 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 19 optimal weight:    0.4980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.143104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.116776 restraints weight = 7003.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 1.43
r_work: 0.3059 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.1505

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= 0.179
  Angle     :  0.547   7.038   8384  Z= 0.290
  Chirality :  0.041   0.139    986
  Planarity :  0.004   0.052   1018
  Dihedral  : 11.508  74.646   1031
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 14.04 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.30), residues: 736
  helix:  1.06 (0.24), residues: 478
  sheet: -1.08 (0.67), residues: 42
  loop : -0.45 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C  96 
 TYR   0.015   0.002   TYR C  69 
 PHE   0.015   0.002   PHE C 169 
 TRP   0.007   0.001   TRP C 123 
 HIS   0.002   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 6171)
  covalent geometry    : angle       0.54743 ( 8384)
  hydrogen bonds       : bond        0.04369 (  338)
  hydrogen bonds       : angle       4.35186 (  987)

*********************** 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
  102 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A  208 ARG cc_start: 0.8275 (tpt-90) cc_final: 0.7531 (tpm-80)
REVERT: C    1 MET cc_start: 0.6207 (pmm) cc_final: 0.6002 (ppp)
REVERT: C  277 SER cc_start: 0.8464 (m) cc_final: 0.8196 (m)
REVERT: C  283 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7965 (pptt)
REVERT: C  341 ARG cc_start: 0.8068 (ptt-90) cc_final: 0.7645 (ptm-80)
REVERT: C  363 LYS cc_start: 0.7702 (mmtt) cc_final: 0.7023 (mtpm)
  outliers start: 22
  outliers final: 15
  residues processed: 90
  average time/residue: 0.7086
  time to fit residues: 66.4931
Evaluate side-chains
  93 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
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  135 MET
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 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   94 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 68 optimal weight:    0.5980
   chunk 24 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9990
   chunk 64 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0980
   chunk 56 optimal weight:    0.8980
   chunk 20 optimal weight:    0.2980
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.3514 r_free = 0.3514 target = 0.144033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.117660 restraints weight = 6998.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.40
r_work: 0.3088 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6171  Z= 0.166
  Angle     :  0.540   7.213   8384  Z= 0.285
  Chirality :  0.041   0.139    986
  Planarity :  0.004   0.055   1018
  Dihedral  : 11.492  74.565   1031
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 15.14 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.30), residues: 736
  helix:  1.09 (0.24), residues: 480
  sheet: -1.05 (0.67), residues: 42
  loop : -0.38 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C  96 
 TYR   0.015   0.002   TYR C  69 
 PHE   0.014   0.002   PHE C 169 
 TRP   0.007   0.001   TRP C 123 
 HIS   0.002   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 6171)
  covalent geometry    : angle       0.54005 ( 8384)
  hydrogen bonds       : bond        0.04267 (  338)
  hydrogen bonds       : angle       4.30039 (  987)

*********************** 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
  94 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A   53 TYR cc_start: 0.6709 (OUTLIER) cc_final: 0.5437 (p90)
REVERT: A  208 ARG cc_start: 0.8259 (tpt-90) cc_final: 0.7516 (tpm-80)
REVERT: C  277 SER cc_start: 0.8415 (m) cc_final: 0.8152 (m)
REVERT: C  283 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7909 (pptt)
REVERT: C  341 ARG cc_start: 0.8024 (ptt-90) cc_final: 0.7633 (ptm-80)
REVERT: C  363 LYS cc_start: 0.7718 (mmtt) cc_final: 0.7068 (mtpm)
  outliers start: 18
  outliers final: 15
  residues processed: 85
  average time/residue: 0.7110
  time to fit residues: 62.9096
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  : 0.269 
-------------------------------------------------------------------------------
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  135 MET
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   92 VAL
Chi-restraints excluded: chain C residue   94 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 57 optimal weight:    0.2980
   chunk 33 optimal weight:    0.0050
   chunk 54 optimal weight:    0.0270
   chunk 20 optimal weight:    0.4980
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 61 optimal weight:    0.4980
   chunk 5 optimal weight:    0.5980
   chunk 49 optimal weight:    0.5980
   overall best weight:    0.2652

-------------------------------------------------------------------------------
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 = 0.3539 r_free = 0.3539 target = 0.146492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.119793 restraints weight = 6937.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 1.43
r_work: 0.3107 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6171  Z= 0.124
  Angle     :  0.511   8.894   8384  Z= 0.268
  Chirality :  0.039   0.135    986
  Planarity :  0.004   0.056   1018
  Dihedral  : 11.454  74.229   1031
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 15.77 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.05 (0.31), residues: 736
  helix:  1.35 (0.24), residues: 480
  sheet: -0.98 (0.66), residues: 42
  loop : -0.28 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG C  96 
 TYR   0.013   0.001   TYR A 354 
 PHE   0.010   0.001   PHE C 169 
 TRP   0.006   0.001   TRP C 123 
 HIS   0.002   0.001   HIS A  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6171)
  covalent geometry    : angle       0.51115 ( 8384)
  hydrogen bonds       : bond        0.03787 (  338)
  hydrogen bonds       : angle       4.11951 (  987)

********************** 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
  91 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A  208 ARG cc_start: 0.8246 (tpt-90) cc_final: 0.7519 (tpm-80)
REVERT: C  283 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7940 (pptt)
REVERT: C  341 ARG cc_start: 0.7931 (ptt-90) cc_final: 0.7555 (ptm-80)
REVERT: C  363 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7092 (mtpm)
  outliers start: 15
  outliers final: 11
  residues processed: 82
  average time/residue: 0.6554
  time to fit residues: 55.8226
Evaluate side-chains
  86 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
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 C residue   25 ILE
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue   94 LEU
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 13 optimal weight:    2.9990
   chunk 31 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0060
   chunk 1 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 67 optimal weight:    0.2980
   chunk 20 optimal weight:    0.4980
   chunk 57 optimal weight:    0.6980
   chunk 47 optimal weight:    0.1980
   overall best weight:    0.2796

-------------------------------------------------------------------------------
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 = 0.3535 r_free = 0.3535 target = 0.146191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.119933 restraints weight = 6944.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 1.65
r_work: 0.3113 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6171  Z= 0.128
  Angle     :  0.519   8.090   8384  Z= 0.272
  Chirality :  0.039   0.129    986
  Planarity :  0.004   0.061   1018
  Dihedral  : 11.438  74.201   1031
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.62 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.15 (0.31), residues: 736
  helix:  1.42 (0.24), residues: 480
  sheet: -0.89 (0.67), residues: 42
  loop : -0.26 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A  96 
 TYR   0.014   0.001   TYR A 354 
 PHE   0.011   0.001   PHE C 169 
 TRP   0.006   0.001   TRP C 123 
 HIS   0.002   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6171)
  covalent geometry    : angle       0.51882 ( 8384)
  hydrogen bonds       : bond        0.03818 (  338)
  hydrogen bonds       : angle       4.09682 (  987)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2324.25 seconds
wall clock time: 40 minutes 22.15 seconds (2422.15 seconds total)