Starting phenix.real_space_refine
on Fri Aug 22 14:48:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ex9_28655/08_2025/8ex9_28655.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ex9_28655/08_2025/8ex9_28655.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ex9_28655/08_2025/8ex9_28655.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ex9_28655/08_2025/8ex9_28655.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ex9_28655/08_2025/8ex9_28655.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ex9_28655/08_2025/8ex9_28655.cif"
  }
  resolution = 2.96
  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=   1.000
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     139      5.49       5
     S       1      5.16       5
     C    2136      2.51       5
     N     768      2.21       5
     O    1155      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4199
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1277
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 166, 1277
          Classifications: {'peptide': 166}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 3, 'TRANS': 162}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 74
          Unresolved non-hydrogen angles: 87
          Unresolved non-hydrogen dihedrals: 63
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 7, 'GLN:plan1': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 51
    Chain: "B"
      Number of atoms: 2179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 2179
          Classifications: {'RNA': 102}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p_pur': 50, 'rna3p_pyr': 44}
          Link IDs: {'rna2p': 8, 'rna3p': 93}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'  C%rna3p_pyr:plan': 1, '  C%rna3p_pyr:plan2': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "C"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 273
          Classifications: {'DNA': 14}
          Link IDs: {'rna3p': 13}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {' DT:plan': 1, ' DC:plan': 1, ' DC:plan2': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "D"
      Number of atoms: 470
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 470
          Classifications: {'DNA': 23}
          Link IDs: {'rna3p': 22}
  Time building chain proxies: 1.37, per 1000 atoms: 0.33
  Number of scatterers: 4199
  At special positions: 0
  Unit cell: (64.896, 83.2, 99.84, 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       1     16.00
     P     139     15.00
     O    1155      8.00
     N     768      7.00
     C    2136      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: 0.35
  Conformation dependent library (CDL) restraints added in 40.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  308

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 1 sheets defined
      45.2% alpha, 17.5% beta
      50 base pairs and 87 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 46
      removed outlier: 3.701A  pdb=" N   TYR A  43 " --> pdb=" O   ARG A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 64
    Processing helix  chain 'A' and resid 68 through 72
    Processing helix  chain 'A' and resid 75 through 97
      removed outlier: 3.542A  pdb=" N   LEU A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   THR A  96 " --> pdb=" O   ASN A  92 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 121
      removed outlier: 4.335A  pdb=" N   ASN A 156 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   THR A 158 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   TYR A 167 " --> pdb=" O   LEU A  11 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   VAL A 171 " --> pdb=" O   PHE A   7 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   LYS A 143 " --> pdb=" O   TYR A  12 " (cutoff:3.500A)

    78 hydrogen bonds defined for protein.
    222 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      127 hydrogen bonds
      222 hydrogen bond angles
      0 basepair planarities
      50 basepair parallelities
      87 stacking parallelities
  Total time for adding SS restraints: 0.77

  Time building geometry restraints manager: 0.38 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 710
        1.33 -     1.45: 1878
        1.45 -     1.57: 1705
        1.57 -     1.69: 273
        1.69 -     1.81: 1
  Bond restraints: 4567
  Sorted by residual:
  bond pdb=" N   GLY A 130 "
       pdb=" CA  GLY A 130 "
    ideal  model  delta    sigma   weight residual
    1.442  1.449 -0.007 7.70e-03 1.69e+04 9.04e-01
  bond pdb=" O4'  DT C   0 "
       pdb=" C1'  DT C   0 "
    ideal  model  delta    sigma   weight residual
    1.414  1.398  0.016 2.00e-02 2.50e+03 6.78e-01
  bond pdb=" C3'  DT C   0 "
       pdb=" C2'  DT C   0 "
    ideal  model  delta    sigma   weight residual
    1.525  1.541 -0.016 2.00e-02 2.50e+03 6.65e-01
  bond pdb=" O4'  DA D   4 "
       pdb=" C1'  DA D   4 "
    ideal  model  delta    sigma   weight residual
    1.414  1.398  0.016 2.00e-02 2.50e+03 6.28e-01
  bond pdb=" C2'  DC C   1 "
       pdb=" C1'  DC C   1 "
    ideal  model  delta    sigma   weight residual
    1.525  1.540 -0.015 2.00e-02 2.50e+03 5.57e-01
  ... (remaining 4562 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.79: 6268
        0.79 -     1.59: 433
        1.59 -     2.38: 96
        2.38 -     3.17: 27
        3.17 -     3.96: 6
  Bond angle restraints: 6830
  Sorted by residual:
  angle pdb=" C2'   U B -34 "
        pdb=" C1'   U B -34 "
        pdb=" N1    U B -34 "
      ideal   model   delta    sigma   weight residual
     112.00  115.67   -3.67 1.50e+00 4.44e-01 5.98e+00
  angle pdb=" CA  GLY A 130 "
        pdb=" C   GLY A 130 "
        pdb=" N   GLU A 131 "
      ideal   model   delta    sigma   weight residual
     114.65  116.66   -2.01 9.20e-01 1.18e+00 4.78e+00
  angle pdb=" C4'  DA D  -8 "
        pdb=" C3'  DA D  -8 "
        pdb=" C2'  DA D  -8 "
      ideal   model   delta    sigma   weight residual
     102.40  105.07   -2.67 1.50e+00 4.44e-01 3.17e+00
  angle pdb=" C2'   G B   3 "
        pdb=" C1'   G B   3 "
        pdb=" N9    G B   3 "
      ideal   model   delta    sigma   weight residual
     112.00  114.58   -2.58 1.50e+00 4.44e-01 2.97e+00
  angle pdb=" C4'  DT C   0 "
        pdb=" O4'  DT C   0 "
        pdb=" C1'  DT C   0 "
      ideal   model   delta    sigma   weight residual
     109.70  107.21    2.49 1.50e+00 4.44e-01 2.75e+00
  ... (remaining 6825 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.38: 2128
       20.38 -    40.75: 300
       40.75 -    61.13: 238
       61.13 -    81.50: 95
       81.50 -   101.88: 3
  Dihedral angle restraints: 2764
    sinusoidal: 2285
      harmonic: 479
  Sorted by residual:
  dihedral pdb=" O4'   U B -89 "
           pdb=" C1'   U B -89 "
           pdb=" N1    U B -89 "
           pdb=" C2    U B -89 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -65.40  -94.60     1      1.50e+01 4.44e-03 4.61e+01
  dihedral pdb=" O5'   A B -95 "
           pdb=" C5'   A B -95 "
           pdb=" C4'   A B -95 "
           pdb=" C3'   A B -95 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -65.00 -123.14   58.14     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" O5'   A B   2 "
           pdb=" C5'   A B   2 "
           pdb=" C4'   A B   2 "
           pdb=" C3'   A B   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.00  117.25   57.75     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 2761 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 727
       0.036 -    0.071: 99
       0.071 -    0.107: 28
       0.107 -    0.143: 5
       0.143 -    0.178: 1
  Chirality restraints: 860
  Sorted by residual:
  chirality pdb=" C1'   U B -34 "
            pdb=" O4'   U B -34 "
            pdb=" C2'   U B -34 "
            pdb=" N1    U B -34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.29    0.18 2.00e-01 2.50e+01 7.93e-01
  chirality pdb=" CA  PHE A  35 "
            pdb=" N   PHE A  35 "
            pdb=" C   PHE A  35 "
            pdb=" CB  PHE A  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.83e-01
  chirality pdb=" C1'   G B   3 "
            pdb=" O4'   G B   3 "
            pdb=" C2'   G B   3 "
            pdb=" N9    G B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.34    0.12 2.00e-01 2.50e+01 3.61e-01
  ... (remaining 857 not shown)

  Planarity restraints: 359
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B   3 "   -0.027 2.00e-02 2.50e+03   1.11e-02 3.68e+00
        pdb=" N9    G B   3 "    0.023 2.00e-02 2.50e+03
        pdb=" C8    G B   3 "    0.006 2.00e-02 2.50e+03
        pdb=" N7    G B   3 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    G B   3 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G B   3 "   -0.004 2.00e-02 2.50e+03
        pdb=" O6    G B   3 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1    G B   3 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2    G B   3 "    0.003 2.00e-02 2.50e+03
        pdb=" N2    G B   3 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    G B   3 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    G B   3 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B -34 "    0.023 2.00e-02 2.50e+03   1.25e-02 3.52e+00
        pdb=" N1    U B -34 "   -0.028 2.00e-02 2.50e+03
        pdb=" C2    U B -34 "   -0.001 2.00e-02 2.50e+03
        pdb=" O2    U B -34 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    U B -34 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    U B -34 "   -0.001 2.00e-02 2.50e+03
        pdb=" O4    U B -34 "    0.009 2.00e-02 2.50e+03
        pdb=" C5    U B -34 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    U B -34 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B-114 "   -0.020 2.00e-02 2.50e+03   9.23e-03 2.56e+00
        pdb=" N9    G B-114 "    0.021 2.00e-02 2.50e+03
        pdb=" C8    G B-114 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    G B-114 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    G B-114 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    G B-114 "   -0.002 2.00e-02 2.50e+03
        pdb=" O6    G B-114 "   -0.004 2.00e-02 2.50e+03
        pdb=" N1    G B-114 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2    G B-114 "   -0.005 2.00e-02 2.50e+03
        pdb=" N2    G B-114 "    0.008 2.00e-02 2.50e+03
        pdb=" N3    G B-114 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    G B-114 "    0.001 2.00e-02 2.50e+03
  ... (remaining 356 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 464
        2.74 -     3.28: 3804
        3.28 -     3.82: 8592
        3.82 -     4.36: 10535
        4.36 -     4.90: 13713
  Nonbonded interactions: 37108
  Sorted by model distance:
  nonbonded pdb=" N2    G B-106 "
            pdb=" O6    G B  -5 "
     model   vdw
     2.200 3.120
  nonbonded pdb=" OH  TYR A  12 "
            pdb=" OP1   G B-106 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OG  SER A 170 "
            pdb=" O2'   A B   2 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OG  SER A 117 "
            pdb=" OP1   U B   4 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O2'   C B -92 "
            pdb=" N1    A B -88 "
     model   vdw
     2.282 3.120
  ... (remaining 37103 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:             1.680
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.420
  Find NCS groups from input model:        0.010
  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:6.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6874
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      :  0.003   0.024   4567  Z= 0.143
  Angle     :  0.491   3.964   6830  Z= 0.270
  Chirality :  0.029   0.178    860
  Planarity :  0.004   0.038    359
  Dihedral  : 24.066 101.879   2456
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  3.97 %
    Favored  : 95.24 %
  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: -1.52 (0.62), residues: 162
  helix:  0.89 (0.60), residues: 73
  sheet: -5.10 (0.72), residues: 19
  loop : -1.83 (0.61), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 133 
 TYR   0.011   0.001   TYR A 118 
 PHE   0.015   0.001   PHE A  35 
 TRP   0.004   0.001   TRP A  70 
 HIS   0.003   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 4567)
  covalent geometry    : angle       0.49100 ( 6830)
  hydrogen bonds       : bond        0.12893 (  205)
  hydrogen bonds       : angle       5.48072 (  444)

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

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

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.088 
Fit side-chains
REVERT: A   52 TYR cc_start: 0.7894 (t80) cc_final: 0.7558 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 20
  average time/residue: 0.7996
  time to fit residues: 16.4222
Evaluate side-chains
  17 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 16
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 15 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 128 GLN
A 156 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.234619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.184790 restraints weight = 4738.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.4250 rms_B_bonded: 1.15
r_work: 0.4085 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3940 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
moved from start:          0.0840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4567  Z= 0.204
  Angle     :  0.570  10.819   6830  Z= 0.299
  Chirality :  0.033   0.160    860
  Planarity :  0.004   0.042    359
  Dihedral  : 24.820 101.358   2182
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 12.70 %
    Favored  : 84.92 %
  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: -0.94 (0.64), residues: 162
  helix:  1.20 (0.61), residues: 67
  sheet: -4.89 (0.71), residues: 19
  loop : -1.08 (0.66), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 133 
 TYR   0.012   0.002   TYR A 118 
 PHE   0.018   0.002   PHE A  35 
 TRP   0.004   0.001   TRP A  70 
 HIS   0.004   0.002   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 4567)
  covalent geometry    : angle       0.57045 ( 6830)
  hydrogen bonds       : bond        0.05931 (  205)
  hydrogen bonds       : angle       3.88111 (  444)

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

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

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 11
  time to evaluate  : 0.070 
Fit side-chains
REVERT: A   52 TYR cc_start: 0.8173 (t80) cc_final: 0.7929 (t80)
  outliers start: 3
  outliers final: 1
  residues processed: 13
  average time/residue: 0.8682
  time to fit residues: 11.6532
Evaluate side-chains
  11 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 10
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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 = 0.4639 r_free = 0.4639 target = 0.227911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.176748 restraints weight = 4752.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.4173 rms_B_bonded: 1.38
r_work: 0.3992 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3850 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
moved from start:          0.1498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.050   4567  Z= 0.358
  Angle     :  0.747  10.187   6830  Z= 0.386
  Chirality :  0.043   0.218    860
  Planarity :  0.006   0.047    359
  Dihedral  : 24.945  97.500   2182
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 12.70 %
    Favored  : 80.95 %
  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: -1.80 (0.62), residues: 162
  helix: -0.00 (0.57), residues: 67
  sheet: -2.91 (0.83), residues: 33
  loop : -1.32 (0.74), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 160 
 TYR   0.014   0.003   TYR A 118 
 PHE   0.023   0.003   PHE A  35 
 TRP   0.002   0.001   TRP A  70 
 HIS   0.007   0.003   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00753 ( 4567)
  covalent geometry    : angle       0.74725 ( 6830)
  hydrogen bonds       : bond        0.07765 (  205)
  hydrogen bonds       : angle       4.30879 (  444)

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

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

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 10
  time to evaluate  : 0.050 
Fit side-chains
REVERT: A   23 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6880 (ttp-110)
  outliers start: 8
  outliers final: 4
  residues processed: 16
  average time/residue: 0.5160
  time to fit residues: 8.5311
Evaluate side-chains
  13 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 8
  time to evaluate  : 0.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   72 SER
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  158 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 21 optimal weight:    8.9990
   chunk 0 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   overall best weight:    1.0582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4757 r_free = 0.4757 target = 0.236685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.189598 restraints weight = 4695.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.4329 rms_B_bonded: 1.16
r_work: 0.4119 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.4119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7003
moved from start:          0.1293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4567  Z= 0.190
  Angle     :  0.574  11.098   6830  Z= 0.301
  Chirality :  0.032   0.157    860
  Planarity :  0.005   0.049    359
  Dihedral  : 24.650  99.760   2182
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 13.49 %
    Favored  : 80.95 %
  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: -1.06 (0.64), residues: 162
  helix:  0.77 (0.59), residues: 67
  sheet: -2.75 (0.82), residues: 33
  loop : -0.99 (0.76), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 110 
 TYR   0.013   0.002   TYR A  52 
 PHE   0.019   0.002   PHE A  35 
 TRP   0.005   0.001   TRP A  70 
 HIS   0.003   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 4567)
  covalent geometry    : angle       0.57353 ( 6830)
  hydrogen bonds       : bond        0.05942 (  205)
  hydrogen bonds       : angle       3.78393 (  444)

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

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

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 9
  time to evaluate  : 0.054 
Fit side-chains
REVERT: A   52 TYR cc_start: 0.8006 (t80) cc_final: 0.7352 (t80)
REVERT: A  138 LYS cc_start: 0.7504 (tppp) cc_final: 0.7260 (tppt)
  outliers start: 7
  outliers final: 4
  residues processed: 15
  average time/residue: 0.2857
  time to fit residues: 4.5429
Evaluate side-chains
  12 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 8
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   72 SER
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  158 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 24 optimal weight:    4.9990
   chunk 15 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 20 optimal weight:   10.0000
   chunk 10 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4809 r_free = 0.4809 target = 0.242677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.195633 restraints weight = 4679.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.4384 rms_B_bonded: 1.15
r_work: 0.4183 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.4183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6875
moved from start:          0.1510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4567  Z= 0.140
  Angle     :  0.512  11.262   6830  Z= 0.269
  Chirality :  0.029   0.144    860
  Planarity :  0.004   0.046    359
  Dihedral  : 24.314  99.293   2182
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 15.87 %
    Favored  : 80.16 %
  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: -0.43 (0.66), residues: 162
  helix:  1.59 (0.59), residues: 69
  sheet: -2.63 (0.81), residues: 33
  loop : -1.00 (0.80), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 110 
 TYR   0.010   0.002   TYR A 118 
 PHE   0.019   0.001   PHE A  35 
 TRP   0.005   0.001   TRP A  70 
 HIS   0.002   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4567)
  covalent geometry    : angle       0.51182 ( 6830)
  hydrogen bonds       : bond        0.05442 (  205)
  hydrogen bonds       : angle       3.33686 (  444)

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

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

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 13
  time to evaluate  : 0.086 
Fit side-chains
  outliers start: 5
  outliers final: 3
  residues processed: 16
  average time/residue: 0.4552
  time to fit residues: 7.6294
Evaluate side-chains
  17 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 14
  time to evaluate  : 0.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 SER
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  158 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 9 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 20 optimal weight:   10.0000
   chunk 13 optimal weight:    0.0870
   overall best weight:    1.7364

-------------------------------------------------------------------------------
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 = 0.4732 r_free = 0.4732 target = 0.234088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.185498 restraints weight = 4808.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.4281 rms_B_bonded: 1.18
r_work: 0.4065 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   4567  Z= 0.273
  Angle     :  0.639  10.337   6830  Z= 0.333
  Chirality :  0.037   0.182    860
  Planarity :  0.005   0.045    359
  Dihedral  : 24.534  96.533   2182
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 18.25 %
    Favored  : 76.98 %
  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: -1.07 (0.64), residues: 162
  helix:  0.76 (0.59), residues: 67
  sheet: -2.78 (0.83), residues: 33
  loop : -0.98 (0.77), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 110 
 TYR   0.015   0.002   TYR A  52 
 PHE   0.020   0.002   PHE A  35 
 TRP   0.002   0.001   TRP A 141 
 HIS   0.005   0.002   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 ( 4567)
  covalent geometry    : angle       0.63898 ( 6830)
  hydrogen bonds       : bond        0.06862 (  205)
  hydrogen bonds       : angle       3.90462 (  444)

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

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

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 11
  time to evaluate  : 0.052 
Fit side-chains
REVERT: A   52 TYR cc_start: 0.8118 (t80) cc_final: 0.7619 (t80)
  outliers start: 6
  outliers final: 4
  residues processed: 16
  average time/residue: 0.4719
  time to fit residues: 7.8795
Evaluate side-chains
  14 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 10
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   72 SER
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  158 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4787 r_free = 0.4787 target = 0.240319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.193539 restraints weight = 4768.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.4365 rms_B_bonded: 1.19
r_work: 0.4163 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.4163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6908
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4567  Z= 0.148
  Angle     :  0.524  11.259   6830  Z= 0.276
  Chirality :  0.030   0.145    860
  Planarity :  0.004   0.047    359
  Dihedral  : 24.333  99.142   2182
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 18.25 %
    Favored  : 76.98 %
  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: -0.46 (0.66), residues: 162
  helix:  1.47 (0.61), residues: 67
  sheet: -2.65 (0.81), residues: 33
  loop : -0.81 (0.78), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 110 
 TYR   0.009   0.002   TYR A  52 
 PHE   0.018   0.001   PHE A  35 
 TRP   0.005   0.001   TRP A  70 
 HIS   0.001   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 4567)
  covalent geometry    : angle       0.52401 ( 6830)
  hydrogen bonds       : bond        0.05519 (  205)
  hydrogen bonds       : angle       3.48416 (  444)

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

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

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 11
  time to evaluate  : 0.048 
Fit side-chains
REVERT: A   52 TYR cc_start: 0.7844 (t80) cc_final: 0.7132 (t80)
  outliers start: 6
  outliers final: 4
  residues processed: 16
  average time/residue: 0.4283
  time to fit residues: 7.1743
Evaluate side-chains
  15 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 11
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   72 SER
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  158 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 16 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 27 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.4771 r_free = 0.4771 target = 0.238444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.191164 restraints weight = 4751.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.4337 rms_B_bonded: 1.14
r_work: 0.4143 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4567  Z= 0.182
  Angle     :  0.548  10.890   6830  Z= 0.288
  Chirality :  0.031   0.161    860
  Planarity :  0.004   0.046    359
  Dihedral  : 24.351  95.717   2182
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 19.05 %
    Favored  : 76.98 %
  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: -0.49 (0.65), residues: 162
  helix:  1.42 (0.61), residues: 67
  sheet: -2.61 (0.82), residues: 33
  loop : -0.83 (0.77), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 110 
 TYR   0.011   0.002   TYR A  52 
 PHE   0.019   0.002   PHE A  35 
 TRP   0.003   0.001   TRP A  70 
 HIS   0.003   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 4567)
  covalent geometry    : angle       0.54811 ( 6830)
  hydrogen bonds       : bond        0.05897 (  205)
  hydrogen bonds       : angle       3.56476 (  444)

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

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

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 11
  time to evaluate  : 0.084 
Fit side-chains
REVERT: A   52 TYR cc_start: 0.7934 (t80) cc_final: 0.7314 (t80)
  outliers start: 5
  outliers final: 4
  residues processed: 15
  average time/residue: 0.6323
  time to fit residues: 9.8560
Evaluate side-chains
  15 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 11
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   72 SER
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  158 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 20 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 24 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    1.6384

-------------------------------------------------------------------------------
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 = 0.4733 r_free = 0.4733 target = 0.234192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.185772 restraints weight = 4767.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.4286 rms_B_bonded: 1.13
r_work: 0.4072 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7085
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   4567  Z= 0.260
  Angle     :  0.637  10.287   6830  Z= 0.332
  Chirality :  0.036   0.177    860
  Planarity :  0.005   0.045    359
  Dihedral  : 24.537  95.936   2182
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 19.84 %
    Favored  : 76.19 %
  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: -1.10 (0.63), residues: 162
  helix:  0.71 (0.58), residues: 67
  sheet: -2.71 (0.83), residues: 33
  loop : -1.00 (0.75), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 110 
 TYR   0.013   0.002   TYR A  52 
 PHE   0.021   0.002   PHE A  35 
 TRP   0.002   0.001   TRP A  70 
 HIS   0.005   0.002   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00544 ( 4567)
  covalent geometry    : angle       0.63730 ( 6830)
  hydrogen bonds       : bond        0.06920 (  205)
  hydrogen bonds       : angle       3.92884 (  444)

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

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

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 11
  time to evaluate  : 0.089 
Fit side-chains
REVERT: A   52 TYR cc_start: 0.8147 (t80) cc_final: 0.7754 (t80)
  outliers start: 5
  outliers final: 4
  residues processed: 15
  average time/residue: 0.5040
  time to fit residues: 7.8995
Evaluate side-chains
  13 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 9
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   72 SER
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  158 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 20 optimal weight:   10.0000
   chunk 24 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 7 optimal weight:    0.4980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.4768 r_free = 0.4768 target = 0.237951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.190918 restraints weight = 4708.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.4329 rms_B_bonded: 1.12
r_work: 0.4135 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.4135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6960
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4567  Z= 0.180
  Angle     :  0.555  11.341   6830  Z= 0.292
  Chirality :  0.032   0.154    860
  Planarity :  0.004   0.047    359
  Dihedral  : 24.397  95.539   2182
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 19.84 %
    Favored  : 76.19 %
  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: -0.64 (0.65), residues: 162
  helix:  1.18 (0.60), residues: 67
  sheet: -2.64 (0.82), residues: 33
  loop : -0.78 (0.78), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 110 
 TYR   0.011   0.002   TYR A  52 
 PHE   0.018   0.002   PHE A  35 
 TRP   0.004   0.001   TRP A  70 
 HIS   0.003   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 4567)
  covalent geometry    : angle       0.55496 ( 6830)
  hydrogen bonds       : bond        0.05882 (  205)
  hydrogen bonds       : angle       3.65036 (  444)

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

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

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  324 Ramachandran restraints generated.
    162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 11
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A   52 TYR cc_start: 0.7993 (t80) cc_final: 0.7430 (t80)
  outliers start: 5
  outliers final: 4
  residues processed: 15
  average time/residue: 0.5471
  time to fit residues: 8.5756
Evaluate side-chains
  14 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 10
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   72 SER
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  158 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0570
   chunk 28 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 7 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 10 optimal weight:    0.1980
   overall best weight:    0.9500

-------------------------------------------------------------------------------
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 = 0.4776 r_free = 0.4776 target = 0.238957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.191865 restraints weight = 4732.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.4338 rms_B_bonded: 1.13
r_work: 0.4144 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6938
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4567  Z= 0.175
  Angle     :  0.545  11.290   6830  Z= 0.286
  Chirality :  0.031   0.154    860
  Planarity :  0.004   0.046    359
  Dihedral  : 24.320  96.110   2182
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 19.84 %
    Favored  : 76.19 %
  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: -0.48 (0.66), residues: 162
  helix:  1.37 (0.61), residues: 67
  sheet: -2.56 (0.82), residues: 33
  loop : -0.76 (0.80), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 110 
 TYR   0.010   0.002   TYR A  52 
 PHE   0.018   0.002   PHE A  35 
 TRP   0.003   0.001   TRP A  70 
 HIS   0.003   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 4567)
  covalent geometry    : angle       0.54495 ( 6830)
  hydrogen bonds       : bond        0.05834 (  205)
  hydrogen bonds       : angle       3.56143 (  444)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1154.60 seconds
wall clock time: 20 minutes 25.33 seconds (1225.33 seconds total)