Starting phenix.real_space_refine
on Wed Feb  4 23:52:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dmb_27533/02_2026/8dmb_27533.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dmb_27533/02_2026/8dmb_27533.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dmb_27533/02_2026/8dmb_27533.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dmb_27533/02_2026/8dmb_27533.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dmb_27533/02_2026/8dmb_27533.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dmb_27533/02_2026/8dmb_27533.map"
  }
  resolution = 3.1
  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=   0.006
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: 7
    Type Number    sf(0)   Gaussians
     P     274      5.49       5
     Mg      2      5.21       5
     S       9      5.16       5
     C    4303      2.51       5
     N    1586      2.21       5
     O    2323      1.98       5
     H    5728      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14225
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "P"
      Number of atoms: 5376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 5376
          Classifications: {'peptide': 328}
          Link IDs: {'PTRANS': 20, 'TRANS': 307}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "W"
      Number of atoms: 7634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 7634
          Classifications: {'RNA': 237}
          Modifications used: {'3*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 14, 'rna3p_pur': 109, 'rna3p_pyr': 103}
          Link IDs: {'rna2p': 25, 'rna3p': 211}
          Chain breaks: 4
    Chain: "X"
      Number of atoms: 893
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 893
          Classifications: {'DNA': 28}
          Link IDs: {'rna3p': 27}
    Chain: "Y"
      Number of atoms: 320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 320
          Classifications: {'DNA': 10}
          Modifications used: {'3*END': 1, '5*END': 1}
          Link IDs: {'rna3p': 9}
    Chain: "W"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.63, per 1000 atoms: 0.18
  Number of scatterers: 14225
  At special positions: 0
  Unit cell: (108.68, 128.128, 102.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S       9     16.00
     P     274     15.00
     Mg      2     11.99
     O    2323      8.00
     N    1586      7.00
     C    4303      6.00
     H    5728      1.00
    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: 1.03
  Conformation dependent library (CDL) restraints added in 267.9 milliseconds
  

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  604

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 3 sheets defined
      34.5% alpha, 21.3% beta
      108 base pairs and 159 stacking pairs defined.
    Time for finding SS restraints: 2.24
  Creating SS restraints...
    Processing helix  chain 'P' and resid 22 through 32
    Processing helix  chain 'P' and resid 92 through 112
    Processing helix  chain 'P' and resid 130 through 151
      removed outlier: 4.105A  pdb=" N   ILE P 150 " --> pdb=" O   GLU P 146 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 164 through 168
    Processing helix  chain 'P' and resid 171 through 179
      removed outlier: 4.974A  pdb=" N   VAL P 177 " --> pdb=" O   TYR P 173 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 180 through 192
      removed outlier: 3.668A  pdb=" N   LYS P 190 " --> pdb=" O   ARG P 186 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LEU P 191 " --> pdb=" O   GLU P 187 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 198 through 210
    Processing helix  chain 'P' and resid 226 through 239
    Processing helix  chain 'P' and resid 267 through 271
      removed outlier: 3.581A  pdb=" N   VAL P 271 " --> pdb=" O   LYS P 268 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'P' and resid 10 through 11
      removed outlier: 7.201A  pdb=" N   VAL P  11 " --> pdb=" O   MET P  49 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'P' and resid 193 through 197
      removed outlier: 3.640A  pdb=" N   LEU P 155 " --> pdb=" O   VAL P  60 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   GLU P 159 " --> pdb=" O   VAL P  64 " (cutoff:3.500A)
      removed outlier: 5.980A  pdb=" N   SER P  77 " --> pdb=" O   VAL P  81 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   VAL P  81 " --> pdb=" O   SER P  77 " (cutoff:3.500A)
      removed outlier: 8.956A  pdb=" N   PHE P 249 " --> pdb=" O   GLU P  82 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   ARG P  84 " --> pdb=" O   PHE P 249 " (cutoff:3.500A)
      removed outlier: 8.231A  pdb=" N   TRP P 251 " --> pdb=" O   ARG P  84 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   MET P  86 " --> pdb=" O   TRP P 251 " (cutoff:3.500A)
      removed outlier: 8.073A  pdb=" N   ARG P 253 " --> pdb=" O   MET P  86 " (cutoff:3.500A)
      removed outlier: 7.547A  pdb=" N   PHE P  88 " --> pdb=" O   ARG P 253 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   PHE P 248 " --> pdb=" O   VAL P 346 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ARG P 252 " --> pdb=" O   SER P 342 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'P' and resid 323 through 327
      removed outlier: 6.074A  pdb=" N   GLY P 315 " --> pdb=" O   CYS P 304 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   GLU P 291 " --> pdb=" O   LEU P 334 " (cutoff:3.500A)
      removed outlier: 5.287A  pdb=" N   LEU P 334 " --> pdb=" O   GLU P 291 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   GLU P 293 " --> pdb=" O   VAL P 332 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   VAL P 332 " --> pdb=" O   GLU P 293 " (cutoff:3.500A)

    116 hydrogen bonds defined for protein.
    330 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      285 hydrogen bonds
      526 hydrogen bond angles
      0 basepair planarities
      108 basepair parallelities
      159 stacking parallelities
  Total time for adding SS restraints: 2.98

  Time building geometry restraints manager: 1.52 seconds

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

  Histogram of bond lengths:
        0.82 -     1.02: 5725
        1.02 -     1.22: 5
        1.22 -     1.41: 3882
        1.41 -     1.61: 5326
        1.61 -     1.81: 29
  Bond restraints: 14967
  Sorted by residual:
  bond pdb=" C   ALA P 130 "
       pdb=" N   PRO P 131 "
    ideal  model  delta    sigma   weight residual
    1.334  1.373 -0.039 1.51e-02 4.39e+03 6.50e+00
  bond pdb=" C3'  DT Y   2 "
       pdb=" O3'  DT Y   2 "
    ideal  model  delta    sigma   weight residual
    1.422  1.498 -0.076 3.00e-02 1.11e+03 6.34e+00
  bond pdb=" C   TYR P 151 "
       pdb=" N   PRO P 152 "
    ideal  model  delta    sigma   weight residual
    1.334  1.389 -0.055 2.34e-02 1.83e+03 5.47e+00
  bond pdb=" C1'  DT Y   2 "
       pdb=" N1   DT Y   2 "
    ideal  model  delta    sigma   weight residual
    1.490  1.552 -0.062 3.00e-02 1.11e+03 4.30e+00
  bond pdb=" C4'   U W  19 "
       pdb=" C3'   U W  19 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 1.50e-02 4.44e+03 3.97e+00
  ... (remaining 14962 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 24434
        1.60 -     3.20: 2143
        3.20 -     4.79: 239
        4.79 -     6.39: 52
        6.39 -     7.99: 4
  Bond angle restraints: 26872
  Sorted by residual:
  angle pdb=" O3'  DT Y   2 "
        pdb=" C3'  DT Y   2 "
        pdb=" C2'  DT Y   2 "
      ideal   model   delta    sigma   weight residual
     111.50  119.49   -7.99 1.50e+00 4.44e-01 2.84e+01
  angle pdb=" C3'  DT Y   2 "
        pdb=" O3'  DT Y   2 "
        pdb=" P    DG Y   3 "
      ideal   model   delta    sigma   weight residual
     120.20  127.04   -6.84 1.50e+00 4.44e-01 2.08e+01
  angle pdb=" C2'   A W  11 "
        pdb=" C1'   A W  11 "
        pdb=" N9    A W  11 "
      ideal   model   delta    sigma   weight residual
     112.00  118.06   -6.06 1.50e+00 4.44e-01 1.63e+01
  angle pdb=" C2'   A W 251 "
        pdb=" C1'   A W 251 "
        pdb=" N9    A W 251 "
      ideal   model   delta    sigma   weight residual
     112.00  117.64   -5.64 1.50e+00 4.44e-01 1.41e+01
  angle pdb=" C5'   U W  19 "
        pdb=" C4'   U W  19 "
        pdb=" O4'   U W  19 "
      ideal   model   delta    sigma   weight residual
     109.80  115.42   -5.62 1.50e+00 4.44e-01 1.40e+01
  ... (remaining 26867 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.61: 6434
       35.61 -    71.23: 784
       71.23 -   106.84: 142
      106.84 -   142.46: 1
      142.46 -   178.07: 2
  Dihedral angle restraints: 7363
    sinusoidal: 6260
      harmonic: 1103
  Sorted by residual:
  dihedral pdb=" O4'   U W 255 "
           pdb=" C1'   U W 255 "
           pdb=" N1    U W 255 "
           pdb=" C2    U W 255 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   53.93  178.07     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   C W 146 "
           pdb=" C1'   C W 146 "
           pdb=" N1    C W 146 "
           pdb=" C2    C W 146 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   44.32 -172.32     1      1.70e+01 3.46e-03 6.61e+01
  dihedral pdb=" O4'   C W 147 "
           pdb=" C1'   C W 147 "
           pdb=" N1    C W 147 "
           pdb=" C2    C W 147 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -86.23  -73.77     1      1.50e+01 4.44e-03 3.07e+01
  ... (remaining 7360 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1316
       0.052 -    0.104: 319
       0.104 -    0.157: 70
       0.157 -    0.209: 10
       0.209 -    0.261: 7
  Chirality restraints: 1722
  Sorted by residual:
  chirality pdb=" C1'   A W  11 "
            pdb=" O4'   A W  11 "
            pdb=" C2'   A W  11 "
            pdb=" N9    A W  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.20    0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" C1'   A W 251 "
            pdb=" O4'   A W 251 "
            pdb=" C2'   A W 251 "
            pdb=" N9    A W 251 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.20    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" C1'   A W 189 "
            pdb=" O4'   A W 189 "
            pdb=" C2'   A W 189 "
            pdb=" N9    A W 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.21    0.25 2.00e-01 2.50e+01 1.54e+00
  ... (remaining 1719 not shown)

  Planarity restraints: 1284
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG P 108 "    0.369 9.50e-02 1.11e+02   1.25e-01 2.38e+01
        pdb=" NE  ARG P 108 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  ARG P 108 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG P 108 "   -0.036 2.00e-02 2.50e+03
        pdb=" NH2 ARG P 108 "   -0.028 2.00e-02 2.50e+03
        pdb="HH11 ARG P 108 "   -0.000 2.00e-02 2.50e+03
        pdb="HH12 ARG P 108 "    0.024 2.00e-02 2.50e+03
        pdb="HH21 ARG P 108 "    0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG P 108 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG P 253 "    0.295 9.50e-02 1.11e+02   1.00e-01 1.75e+01
        pdb=" NE  ARG P 253 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  ARG P 253 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG P 253 "   -0.036 2.00e-02 2.50e+03
        pdb=" NH2 ARG P 253 "   -0.024 2.00e-02 2.50e+03
        pdb="HH11 ARG P 253 "   -0.001 2.00e-02 2.50e+03
        pdb="HH12 ARG P 253 "    0.025 2.00e-02 2.50e+03
        pdb="HH21 ARG P 253 "   -0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG P 253 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN P 170 "    0.025 2.00e-02 2.50e+03   3.26e-02 1.59e+01
        pdb=" CG  ASN P 170 "   -0.020 2.00e-02 2.50e+03
        pdb=" OD1 ASN P 170 "   -0.001 2.00e-02 2.50e+03
        pdb=" ND2 ASN P 170 "   -0.054 2.00e-02 2.50e+03
        pdb="HD21 ASN P 170 "    0.000 2.00e-02 2.50e+03
        pdb="HD22 ASN P 170 "    0.049 2.00e-02 2.50e+03
  ... (remaining 1281 not shown)

  Histogram of nonbonded interaction distances:
        1.68 -     2.26: 1437
        2.26 -     2.85: 24223
        2.85 -     3.43: 33487
        3.43 -     4.02: 52883
        4.02 -     4.60: 74867
  Nonbonded interactions: 186897
  Sorted by model distance:
  nonbonded pdb="HO2'   A W 152 "
            pdb=" OP2   U W 154 "
     model   vdw
     1.677 2.450
  nonbonded pdb="HO2'   G W  72 "
            pdb=" O2    C W  98 "
     model   vdw
     1.688 2.450
  nonbonded pdb=" HZ1 LYS P 142 "
            pdb=" OP1   G W 250 "
     model   vdw
     1.717 2.450
  nonbonded pdb=" O   ARG P 108 "
            pdb=" HG1 THR P 112 "
     model   vdw
     1.718 2.450
  nonbonded pdb=" OD1 ASP P  91 "
            pdb=" HZ1 LYS P 136 "
     model   vdw
     1.728 2.450
  ... (remaining 186892 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.370
  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:             0.070
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     15.190
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076   9239  Z= 0.250
  Angle     :  0.905   7.989  13808  Z= 0.533
  Chirality :  0.051   0.261   1722
  Planarity :  0.014   0.143    751
  Dihedral  : 23.251 178.072   5273
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 0.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  3.70 %
    Favored  : 95.56 %
  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 are not related in a simple way.
  whole:  0.39 (0.46), residues: 324
  helix:  0.05 (0.48), residues: 95
  sheet:  0.92 (0.62), residues: 76
  loop :  0.21 (0.51), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.003   ARG P 263 
 TYR   0.018   0.004   TYR P 127 
 PHE   0.010   0.002   PHE P 135 
 TRP   0.011   0.003   TRP P 251 
 HIS   0.003   0.002   HIS P  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 ( 9239)
  covalent geometry    : angle       0.90519 (13808)
  hydrogen bonds       : bond        0.10658 (  401)
  hydrogen bonds       : angle       4.91605 (  856)

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

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

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 41
  average time/residue: 0.4062
  time to fit residues: 19.1636
Evaluate side-chains
  30 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 29
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  226 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    9.9990
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:   10.0000
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
P 226 HIS
P 264 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.147744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.115527 restraints weight = 28035.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 1.21
r_work: 0.3118 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9239  Z= 0.154
  Angle     :  0.603   6.448  13808  Z= 0.332
  Chirality :  0.037   0.195   1722
  Planarity :  0.006   0.049    751
  Dihedral  : 24.096 178.201   4611
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 1.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  6.30 %
    Favored  : 92.96 %
  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 are not related in a simple way.
  whole:  0.93 (0.48), residues: 324
  helix:  1.36 (0.51), residues: 98
  sheet:  0.32 (0.52), residues: 100
  loop :  0.47 (0.60), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG P  79 
 TYR   0.010   0.002   TYR P 127 
 PHE   0.008   0.001   PHE P 135 
 TRP   0.006   0.001   TRP P 343 
 HIS   0.004   0.002   HIS P 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9239)
  covalent geometry    : angle       0.60305 (13808)
  hydrogen bonds       : bond        0.05095 (  401)
  hydrogen bonds       : angle       3.51341 (  856)

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

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

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 29
  time to evaluate  : 0.246 
Fit side-chains
REVERT: P   24 ARG cc_start: 0.8263 (tmt90) cc_final: 0.7999 (tmt90)
REVERT: P  269 ASP cc_start: 0.7024 (t0) cc_final: 0.6799 (t70)
  outliers start: 2
  outliers final: 1
  residues processed: 30
  average time/residue: 0.3851
  time to fit residues: 13.6932
Evaluate side-chains
  27 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   71 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 56 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 20 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    1.5588

-------------------------------------------------------------------------------
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 = 0.3848 r_free = 0.3848 target = 0.148394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.116052 restraints weight = 28046.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.27
r_work: 0.3125 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9239  Z= 0.136
  Angle     :  0.545   4.699  13808  Z= 0.301
  Chirality :  0.034   0.156   1722
  Planarity :  0.005   0.037    751
  Dihedral  : 24.039 176.418   4609
  Min Nonbonded Distance : 1.778

Molprobity Statistics.
  All-atom Clashscore : 1.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  5.93 %
    Favored  : 93.33 %
  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 are not related in a simple way.
  whole:  1.08 (0.48), residues: 324
  helix:  1.75 (0.51), residues: 98
  sheet:  0.11 (0.51), residues: 100
  loop :  0.61 (0.61), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG P  79 
 TYR   0.010   0.001   TYR P 127 
 PHE   0.009   0.001   PHE P 135 
 TRP   0.006   0.001   TRP P 289 
 HIS   0.004   0.002   HIS P 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 9239)
  covalent geometry    : angle       0.54452 (13808)
  hydrogen bonds       : bond        0.04705 (  401)
  hydrogen bonds       : angle       3.22122 (  856)

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

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

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 26
  average time/residue: 0.3915
  time to fit residues: 12.0813
Evaluate side-chains
  25 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   71 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 56 optimal weight:    5.9990
   chunk 38 optimal weight:   20.0000
   chunk 49 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 42 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 46 optimal weight:    7.9990
   chunk 32 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   chunk 11 optimal weight:    0.5980
   chunk 47 optimal weight:    7.9990
   overall best weight:    4.9188

-------------------------------------------------------------------------------
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 = 0.3779 r_free = 0.3779 target = 0.142791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.109484 restraints weight = 27911.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 1.40
r_work: 0.3030 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   9239  Z= 0.306
  Angle     :  0.669   6.588  13808  Z= 0.359
  Chirality :  0.042   0.206   1722
  Planarity :  0.007   0.054    751
  Dihedral  : 24.334 179.142   4609
  Min Nonbonded Distance : 1.754

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  9.26 %
    Favored  : 90.00 %
  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 are not related in a simple way.
  whole:  0.56 (0.46), residues: 324
  helix:  1.21 (0.48), residues: 98
  sheet: -0.04 (0.52), residues: 96
  loop :  0.23 (0.57), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG P 124 
 TYR   0.013   0.002   TYR P 127 
 PHE   0.018   0.002   PHE P 135 
 TRP   0.012   0.002   TRP P 289 
 HIS   0.007   0.002   HIS P 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00630 ( 9239)
  covalent geometry    : angle       0.66935 (13808)
  hydrogen bonds       : bond        0.06097 (  401)
  hydrogen bonds       : angle       3.36269 (  856)

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

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

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.243 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 25
  average time/residue: 0.3867
  time to fit residues: 11.4978
Evaluate side-chains
  23 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   71 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 56 optimal weight:    4.9990
   chunk 42 optimal weight:    8.9990
   chunk 47 optimal weight:    7.9990
   chunk 41 optimal weight:    8.9990
   chunk 48 optimal weight:    7.9990
   chunk 30 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 36 optimal weight:   10.0000
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.3789 r_free = 0.3789 target = 0.143513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.111420 restraints weight = 27838.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 1.23
r_work: 0.3056 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9239  Z= 0.239
  Angle     :  0.598   5.742  13808  Z= 0.323
  Chirality :  0.038   0.188   1722
  Planarity :  0.006   0.048    751
  Dihedral  : 24.281 179.361   4609
  Min Nonbonded Distance : 1.802

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.63 %
    Favored  : 89.26 %
  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 are not related in a simple way.
  whole:  0.42 (0.46), residues: 324
  helix:  1.42 (0.49), residues: 98
  sheet: -0.17 (0.51), residues: 100
  loop : -0.09 (0.56), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG P  79 
 TYR   0.011   0.002   TYR P 127 
 PHE   0.012   0.001   PHE P 135 
 TRP   0.008   0.002   TRP P 343 
 HIS   0.005   0.002   HIS P 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 ( 9239)
  covalent geometry    : angle       0.59768 (13808)
  hydrogen bonds       : bond        0.05510 (  401)
  hydrogen bonds       : angle       3.18344 (  856)

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

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

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.259 
Fit side-chains
REVERT: P   47 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8554 (mt)
  outliers start: 3
  outliers final: 2
  residues processed: 26
  average time/residue: 0.4563
  time to fit residues: 13.8281
Evaluate side-chains
  27 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   47 ILE
Chi-restraints excluded: chain P residue   65 ASP
Chi-restraints excluded: chain P residue   71 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 49 optimal weight:   10.0000
   chunk 42 optimal weight:   10.0000
   chunk 40 optimal weight:    8.9990
   chunk 32 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 39 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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 = 0.3775 r_free = 0.3775 target = 0.142381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.110461 restraints weight = 27671.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 1.20
r_work: 0.3044 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.3157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9239  Z= 0.263
  Angle     :  0.626   4.952  13808  Z= 0.337
  Chirality :  0.039   0.178   1722
  Planarity :  0.007   0.050    751
  Dihedral  : 24.307 177.535   4609
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.63 %
    Favored  : 89.26 %
  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 are not related in a simple way.
  whole:  0.20 (0.46), residues: 324
  helix:  1.30 (0.49), residues: 98
  sheet: -0.21 (0.52), residues: 100
  loop : -0.35 (0.55), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG P  79 
 TYR   0.011   0.002   TYR P 127 
 PHE   0.015   0.002   PHE P 135 
 TRP   0.008   0.002   TRP P 343 
 HIS   0.005   0.002   HIS P 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00545 ( 9239)
  covalent geometry    : angle       0.62635 (13808)
  hydrogen bonds       : bond        0.05946 (  401)
  hydrogen bonds       : angle       3.22622 (  856)

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

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

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
REVERT: P   47 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8537 (mt)
  outliers start: 3
  outliers final: 2
  residues processed: 24
  average time/residue: 0.4496
  time to fit residues: 12.4951
Evaluate side-chains
  25 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   47 ILE
Chi-restraints excluded: chain P residue   65 ASP
Chi-restraints excluded: chain P residue   71 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 36 optimal weight:   10.0000
   chunk 22 optimal weight:    7.9990
   chunk 37 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   chunk 41 optimal weight:    9.9990
   chunk 0 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.3792 r_free = 0.3792 target = 0.143805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.112098 restraints weight = 27619.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 1.21
r_work: 0.3064 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9239  Z= 0.179
  Angle     :  0.568   4.801  13808  Z= 0.310
  Chirality :  0.036   0.177   1722
  Planarity :  0.006   0.052    751
  Dihedral  : 24.257 178.148   4609
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 10.00 %
    Favored  : 88.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.46), residues: 324
  helix:  1.51 (0.50), residues: 98
  sheet: -0.07 (0.51), residues: 98
  loop : -0.31 (0.55), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG P  80 
 TYR   0.010   0.001   TYR P 127 
 PHE   0.013   0.001   PHE P 135 
 TRP   0.009   0.001   TRP P 343 
 HIS   0.004   0.001   HIS P 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 9239)
  covalent geometry    : angle       0.56848 (13808)
  hydrogen bonds       : bond        0.05159 (  401)
  hydrogen bonds       : angle       3.10258 (  856)

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

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

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.243 
Fit side-chains
REVERT: P   47 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8550 (mt)
  outliers start: 4
  outliers final: 3
  residues processed: 28
  average time/residue: 0.3827
  time to fit residues: 12.4894
Evaluate side-chains
  28 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   47 ILE
Chi-restraints excluded: chain P residue   65 ASP
Chi-restraints excluded: chain P residue   71 ASP
Chi-restraints excluded: chain P residue  310 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 35 optimal weight:   20.0000
   chunk 8 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 53 optimal weight:    8.9990
   chunk 9 optimal weight:    0.7980
   chunk 45 optimal weight:    5.9990
   overall best weight:    2.1386

-------------------------------------------------------------------------------
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 = 0.3800 r_free = 0.3800 target = 0.144391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.112392 restraints weight = 27688.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.24
r_work: 0.3076 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9239  Z= 0.162
  Angle     :  0.551   4.494  13808  Z= 0.301
  Chirality :  0.035   0.177   1722
  Planarity :  0.006   0.060    751
  Dihedral  : 24.186 178.205   4609
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 10.74 %
    Favored  : 88.15 %
  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 are not related in a simple way.
  whole:  0.48 (0.46), residues: 324
  helix:  1.63 (0.51), residues: 98
  sheet: -0.03 (0.51), residues: 98
  loop : -0.31 (0.55), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG P  16 
 TYR   0.009   0.001   TYR P  46 
 PHE   0.009   0.001   PHE P 135 
 TRP   0.009   0.001   TRP P 343 
 HIS   0.002   0.001   HIS P 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9239)
  covalent geometry    : angle       0.55069 (13808)
  hydrogen bonds       : bond        0.04978 (  401)
  hydrogen bonds       : angle       3.05090 (  856)

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

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

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   47 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8531 (mt)
  outliers start: 3
  outliers final: 2
  residues processed: 27
  average time/residue: 0.4916
  time to fit residues: 15.2969
Evaluate side-chains
  27 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   47 ILE
Chi-restraints excluded: chain P residue   65 ASP
Chi-restraints excluded: chain P residue   71 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 28 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   chunk 56 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   chunk 19 optimal weight:    7.9990
   chunk 5 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 48 optimal weight:   10.0000
   overall best weight:    3.5788

-------------------------------------------------------------------------------
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 = 0.3784 r_free = 0.3784 target = 0.142975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.111137 restraints weight = 27739.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 1.20
r_work: 0.3054 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.3342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   9239  Z= 0.226
  Angle     :  0.589   4.904  13808  Z= 0.319
  Chirality :  0.038   0.176   1722
  Planarity :  0.007   0.068    751
  Dihedral  : 24.191 177.510   4609
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 10.74 %
    Favored  : 87.78 %
  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 are not related in a simple way.
  whole:  0.25 (0.46), residues: 324
  helix:  1.47 (0.50), residues: 98
  sheet: -0.11 (0.51), residues: 98
  loop : -0.52 (0.54), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG P  80 
 TYR   0.011   0.002   TYR P 127 
 PHE   0.014   0.001   PHE P 135 
 TRP   0.009   0.002   TRP P 343 
 HIS   0.004   0.001   HIS P 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 9239)
  covalent geometry    : angle       0.58941 (13808)
  hydrogen bonds       : bond        0.05465 (  401)
  hydrogen bonds       : angle       3.10431 (  856)

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

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

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
REVERT: P   47 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8573 (mt)
  outliers start: 4
  outliers final: 3
  residues processed: 27
  average time/residue: 0.4127
  time to fit residues: 12.9928
Evaluate side-chains
  28 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   47 ILE
Chi-restraints excluded: chain P residue   65 ASP
Chi-restraints excluded: chain P residue   71 ASP
Chi-restraints excluded: chain P residue  310 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 55 optimal weight:    7.9990
   chunk 33 optimal weight:    5.9990
   chunk 43 optimal weight:    7.9990
   chunk 15 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 47 optimal weight:    8.9990
   chunk 54 optimal weight:   10.0000
   chunk 49 optimal weight:    9.9990
   chunk 52 optimal weight:    5.9990
   overall best weight:    4.5388

-------------------------------------------------------------------------------
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 = 0.3768 r_free = 0.3768 target = 0.141615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.109584 restraints weight = 27657.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 1.26
r_work: 0.3027 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.3508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   9239  Z= 0.276
  Angle     :  0.637   5.120  13808  Z= 0.342
  Chirality :  0.040   0.186   1722
  Planarity :  0.007   0.061    751
  Dihedral  : 24.268 176.713   4609
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 10.37 %
    Favored  : 88.15 %
  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 are not related in a simple way.
  whole: -0.01 (0.45), residues: 324
  helix:  1.26 (0.50), residues: 98
  sheet: -0.16 (0.51), residues: 98
  loop : -0.79 (0.53), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG P  80 
 TYR   0.011   0.002   TYR P 127 
 PHE   0.014   0.002   PHE P 135 
 TRP   0.008   0.002   TRP P 289 
 HIS   0.005   0.002   HIS P 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 ( 9239)
  covalent geometry    : angle       0.63689 (13808)
  hydrogen bonds       : bond        0.06050 (  401)
  hydrogen bonds       : angle       3.18524 (  856)

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

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

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: P   47 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8542 (mt)
  outliers start: 4
  outliers final: 3
  residues processed: 27
  average time/residue: 0.4720
  time to fit residues: 14.5800
Evaluate side-chains
  28 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   47 ILE
Chi-restraints excluded: chain P residue   65 ASP
Chi-restraints excluded: chain P residue   71 ASP
Chi-restraints excluded: chain P residue  310 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 49 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 46 optimal weight:    7.9990
   chunk 16 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 = 0.3798 r_free = 0.3798 target = 0.144038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.112459 restraints weight = 27771.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 1.22
r_work: 0.3078 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.3517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9239  Z= 0.161
  Angle     :  0.550   4.555  13808  Z= 0.300
  Chirality :  0.035   0.163   1722
  Planarity :  0.006   0.062    751
  Dihedral  : 24.062 177.910   4609
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 2.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 10.00 %
    Favored  : 88.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.46), residues: 324
  helix:  1.71 (0.51), residues: 98
  sheet: -0.02 (0.52), residues: 98
  loop : -0.56 (0.55), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG P  80 
 TYR   0.010   0.001   TYR P  46 
 PHE   0.009   0.001   PHE P 135 
 TRP   0.008   0.001   TRP P 343 
 HIS   0.002   0.001   HIS P 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9239)
  covalent geometry    : angle       0.55029 (13808)
  hydrogen bonds       : bond        0.04914 (  401)
  hydrogen bonds       : angle       3.02829 (  856)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3171.69 seconds
wall clock time: 54 minutes 29.85 seconds (3269.85 seconds total)