Starting phenix.real_space_refine
on Fri Aug 22 12:38:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zfb_60055/08_2025/8zfb_60055.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zfb_60055/08_2025/8zfb_60055.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zfb_60055/08_2025/8zfb_60055.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zfb_60055/08_2025/8zfb_60055.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zfb_60055/08_2025/8zfb_60055.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zfb_60055/08_2025/8zfb_60055.map"
  }
  resolution = 3.78
  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=   0.007
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: 4
    Type Number    sf(0)   Gaussians
     S      14      5.16       5
     C    1359      2.51       5
     N     363      2.21       5
     O     352      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  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: 2088
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "R"
      Number of atoms: 2088
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2088
          Classifications: {'peptide': 286}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 267}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 119
          Unresolved non-hydrogen angles: 151
          Unresolved non-hydrogen dihedrals: 96
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'ARG:plan': 7, 'GLU:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 69
  Time building chain proxies: 0.88, per 1000 atoms: 0.42
  Number of scatterers: 2088
  At special positions: 0
  Unit cell: (59.36, 71.02, 72.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      14     16.00
     O     352      8.00
     N     363      7.00
     C    1359      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  90 " - pdb=" SG  CYS R 168 " distance=2.03

  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: 0.22
  Conformation dependent library (CDL) restraints added in 80.9 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  526

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 0 sheets defined
      81.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'R' and resid 18 through 47
      Proline residue:  R  33  - end of helix
    Processing helix  chain 'R' and resid 50 through 79
      removed outlier: 4.143A  pdb=" N   VAL R  54 " --> pdb=" O   ARG R  50 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   TYR R  55 " --> pdb=" O   GLU R  51 " (cutoff:3.500A)
      Proline residue:  R  71  - end of helix
    Processing helix  chain 'R' and resid 89 through 121
      removed outlier: 4.137A  pdb=" N   PHE R  93 " --> pdb=" O   ALA R  89 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ALA R 105 " --> pdb=" O   LEU R 101 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   HIS R 121 " --> pdb=" O   LEU R 117 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 129 through 150
      removed outlier: 4.035A  pdb=" N   SER R 133 " --> pdb=" O   ARG R 129 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 180 through 191
      removed outlier: 4.224A  pdb=" N   VAL R 184 " --> pdb=" O   ALA R 180 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 191 through 209
    Processing helix  chain 'R' and resid 210 through 212
      No H-bonds generated for 'chain 'R' and resid 210 through 212'
    Processing helix  chain 'R' and resid 216 through 228
      removed outlier: 3.866A  pdb=" N   ARG R 222 " --> pdb=" O   ARG R 218 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 229 through 239
    Processing helix  chain 'R' and resid 239 through 254
    Processing helix  chain 'R' and resid 264 through 283
      Proline residue:  R 273  - end of helix
      removed outlier: 3.795A  pdb=" N   ALA R 277 " --> pdb=" O   PRO R 273 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU R 279 " --> pdb=" O   TYR R 275 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   ALA R 280 " --> pdb=" O   HIS R 276 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU R 281 " --> pdb=" O   ALA R 277 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 284 through 294
      Proline residue:  R 290  - end of helix
    Processing helix  chain 'R' and resid 297 through 308

    157 hydrogen bonds defined for protein.
    471 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.41

  Time building geometry restraints manager: 0.28 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 320
        1.31 -     1.43: 597
        1.43 -     1.56: 1210
        1.56 -     1.68: 0
        1.68 -     1.81: 16
  Bond restraints: 2143
  Sorted by residual:
  bond pdb=" C   SER R 171 "
       pdb=" O   SER R 171 "
    ideal  model  delta    sigma   weight residual
    1.233  1.184  0.049 1.35e-02 5.49e+03 1.30e+01
  bond pdb=" C   THR R 166 "
       pdb=" O   THR R 166 "
    ideal  model  delta    sigma   weight residual
    1.232  1.194  0.038 1.44e-02 4.82e+03 7.12e+00
  bond pdb=" CA  THR R 166 "
       pdb=" C   THR R 166 "
    ideal  model  delta    sigma   weight residual
    1.531  1.502  0.030 1.46e-02 4.69e+03 4.12e+00
  bond pdb=" CA  ARG R  79 "
       pdb=" C   ARG R  79 "
    ideal  model  delta    sigma   weight residual
    1.524  1.554 -0.029 1.48e-02 4.57e+03 3.92e+00
  bond pdb=" CA  SER R 171 "
       pdb=" C   SER R 171 "
    ideal  model  delta    sigma   weight residual
    1.526  1.497  0.028 1.51e-02 4.39e+03 3.54e+00
  ... (remaining 2138 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.17: 2888
        3.17 -     6.34: 37
        6.34 -     9.51: 7
        9.51 -    12.68: 1
       12.68 -    15.84: 2
  Bond angle restraints: 2935
  Sorted by residual:
  angle pdb=" C   TYR R 169 "
        pdb=" CA  TYR R 169 "
        pdb=" CB  TYR R 169 "
      ideal   model   delta    sigma   weight residual
     111.48   95.64   15.84 1.59e+00 3.96e-01 9.93e+01
  angle pdb=" N   GLU R 170 "
        pdb=" CA  GLU R 170 "
        pdb=" C   GLU R 170 "
      ideal   model   delta    sigma   weight residual
     110.55  123.97  -13.42 1.35e+00 5.49e-01 9.88e+01
  angle pdb=" N   TYR R  85 "
        pdb=" CA  TYR R  85 "
        pdb=" C   TYR R  85 "
      ideal   model   delta    sigma   weight residual
     111.14  118.40   -7.26 1.08e+00 8.57e-01 4.52e+01
  angle pdb=" N   SER R 171 "
        pdb=" CA  SER R 171 "
        pdb=" C   SER R 171 "
      ideal   model   delta    sigma   weight residual
     107.71  119.35  -11.64 1.90e+00 2.77e-01 3.75e+01
  angle pdb=" N   ARG R  79 "
        pdb=" CA  ARG R  79 "
        pdb=" C   ARG R  79 "
      ideal   model   delta    sigma   weight residual
     112.72  106.12    6.60 1.14e+00 7.69e-01 3.35e+01
  ... (remaining 2930 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.10: 1061
       12.10 -    24.20: 121
       24.20 -    36.30: 52
       36.30 -    48.40: 10
       48.40 -    60.50: 5
  Dihedral angle restraints: 1249
    sinusoidal: 425
      harmonic: 824
  Sorted by residual:
  dihedral pdb=" C   ASP R  81 "
           pdb=" N   ASP R  81 "
           pdb=" CA  ASP R  81 "
           pdb=" CB  ASP R  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.86   14.26     0      2.50e+00 1.60e-01 3.25e+01
  dihedral pdb=" N   ASP R  81 "
           pdb=" C   ASP R  81 "
           pdb=" CA  ASP R  81 "
           pdb=" CB  ASP R  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  137.04  -14.24     0      2.50e+00 1.60e-01 3.24e+01
  dihedral pdb=" C   TYR R 169 "
           pdb=" N   TYR R 169 "
           pdb=" CA  TYR R 169 "
           pdb=" CB  TYR R 169 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -109.80  -12.80     0      2.50e+00 1.60e-01 2.62e+01
  ... (remaining 1246 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.115: 321
       0.115 -    0.229: 10
       0.229 -    0.343: 5
       0.343 -    0.458: 0
       0.458 -    0.572: 2
  Chirality restraints: 338
  Sorted by residual:
  chirality pdb=" CA  ASP R  81 "
            pdb=" N   ASP R  81 "
            pdb=" C   ASP R  81 "
            pdb=" CB  ASP R  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.94    0.57 2.00e-01 2.50e+01 8.17e+00
  chirality pdb=" CA  GLU R 170 "
            pdb=" N   GLU R 170 "
            pdb=" C   GLU R 170 "
            pdb=" CB  GLU R 170 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.99    0.52 2.00e-01 2.50e+01 6.86e+00
  chirality pdb=" CA  CYS R  90 "
            pdb=" N   CYS R  90 "
            pdb=" C   CYS R  90 "
            pdb=" CB  CYS R  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.89e+00
  ... (remaining 335 not shown)

  Planarity restraints: 373
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG R 129 "   -0.032 5.00e-02 4.00e+02   4.86e-02 3.77e+00
        pdb=" N   PRO R 130 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO R 130 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO R 130 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO R  71 "   -0.031 5.00e-02 4.00e+02   4.67e-02 3.49e+00
        pdb=" N   PRO R  72 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO R  72 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO R  72 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 239 "   -0.030 5.00e-02 4.00e+02   4.60e-02 3.39e+00
        pdb=" N   PRO R 240 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO R 240 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO R 240 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 370 not shown)

  Histogram of nonbonded interaction distances:
        1.79 -     2.41: 9
        2.41 -     3.03: 1227
        3.03 -     3.65: 3283
        3.65 -     4.28: 4382
        4.28 -     4.90: 7230
  Nonbonded interactions: 16131
  Sorted by model distance:
  nonbonded pdb=" O   TYR R 169 "
            pdb=" CG  TYR R 169 "
     model   vdw
     1.786 3.260
  nonbonded pdb=" O   TYR R 169 "
            pdb=" CD1 TYR R 169 "
     model   vdw
     1.841 3.340
  nonbonded pdb=" O   ASP R  81 "
            pdb=" OD1 ASP R  81 "
     model   vdw
     1.994 3.040
  nonbonded pdb=" C   ASP R  81 "
            pdb=" OD1 ASP R  81 "
     model   vdw
     2.208 3.270
  nonbonded pdb=" OD1 ASN R  58 "
            pdb=" OG  SER R 138 "
     model   vdw
     2.276 3.040
  ... (remaining 16126 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     5.570
  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:1.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5284
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   0.055   2144  Z= 0.255
  Angle     :  0.978  15.844   2937  Z= 0.608
  Chirality :  0.074   0.572    338
  Planarity :  0.007   0.049    373
  Dihedral  : 13.254  60.500    720
  Min Nonbonded Distance : 1.786

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.16 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  2.59 %
    Favored  : 96.89 %
  Cbeta Deviations :  0.76 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.06 (0.53), residues: 282
  helix:  0.83 (0.37), residues: 214
  sheet:  None (None), residues: 0
  loop : -2.47 (0.78), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R  80 
 TYR   0.014   0.002   TYR R 169 
 PHE   0.011   0.002   PHE R 107 
 TRP   0.021   0.002   TRP R  83 
 HIS   0.006   0.001   HIS R 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 2143)
  covalent geometry    : angle       0.97814 ( 2935)
  SS BOND              : bond        0.00444 (    1)
  SS BOND              : angle       1.16551 (    2)
  hydrogen bonds       : bond        0.11754 (  157)
  hydrogen bonds       : angle       5.67298 (  471)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 18
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 19
  average time/residue: 0.1343
  time to fit residues: 2.8431
Evaluate side-chains
  19 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 18
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   81 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 27 optimal weight:    0.3980
   chunk 12 optimal weight:    0.1980
   chunk 24 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0980
   chunk 1 optimal weight:    0.0470
   chunk 8 optimal weight:    0.0770
   chunk 16 optimal weight:    0.0370
   chunk 15 optimal weight:    9.9990
   chunk 25 optimal weight:    0.0970
   chunk 26 optimal weight:    0.7980
   chunk 9 optimal weight:    0.2980
   overall best weight:    0.0712

-------------------------------------------------------------------------------
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 = 0.3853 r_free = 0.3853 target = 0.151644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.145832 restraints weight = 2986.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.146216 restraints weight = 2983.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.146587 restraints weight = 2618.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.146989 restraints weight = 2115.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.147815 restraints weight = 1796.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5908
moved from start:          0.1060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2144  Z= 0.140
  Angle     :  0.670   6.614   2937  Z= 0.333
  Chirality :  0.041   0.195    338
  Planarity :  0.007   0.049    373
  Dihedral  :  5.164  49.903    317
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  :  7.77 %
    Favored  : 90.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  0.93 (0.54), residues: 282
  helix:  1.61 (0.37), residues: 215
  sheet:  None (None), residues: 0
  loop : -2.81 (0.76), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 210 
 TYR   0.010   0.001   TYR R 169 
 PHE   0.010   0.001   PHE R 107 
 TRP   0.013   0.001   TRP R  83 
 HIS   0.003   0.001   HIS R 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 2143)
  covalent geometry    : angle       0.67029 ( 2935)
  SS BOND              : bond        0.00072 (    1)
  SS BOND              : angle       0.89002 (    2)
  hydrogen bonds       : bond        0.04007 (  157)
  hydrogen bonds       : angle       4.54160 (  471)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 17
  time to evaluate  : 0.085 
Fit side-chains
REVERT: R  206 LEU cc_start: 0.7606 (mm) cc_final: 0.7027 (mp)
  outliers start: 4
  outliers final: 4
  residues processed: 19
  average time/residue: 0.1308
  time to fit residues: 2.7866
Evaluate side-chains
  20 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 16
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   81 ASP
Chi-restraints excluded: chain R residue  188 LEU
Chi-restraints excluded: chain R residue  199 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0270
   chunk 23 optimal weight:    0.2980
   chunk 15 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0970
   chunk 3 optimal weight:    0.0970
   chunk 21 optimal weight:    0.0570
   chunk 14 optimal weight:    0.9990
   chunk 18 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.1152

-------------------------------------------------------------------------------
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 = 0.3850 r_free = 0.3850 target = 0.151065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.145551 restraints weight = 3026.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.146206 restraints weight = 2388.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.146356 restraints weight = 2018.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.146599 restraints weight = 1871.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.146612 restraints weight = 1756.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5930
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2144  Z= 0.137
  Angle     :  0.619   6.143   2937  Z= 0.311
  Chirality :  0.041   0.130    338
  Planarity :  0.006   0.049    373
  Dihedral  :  5.268  53.237    317
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 10.36 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  1.43 (0.55), residues: 282
  helix:  2.00 (0.38), residues: 217
  sheet:  None (None), residues: 0
  loop : -2.90 (0.79), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 129 
 TYR   0.012   0.001   TYR R  76 
 PHE   0.012   0.001   PHE R 107 
 TRP   0.012   0.001   TRP R  43 
 HIS   0.004   0.001   HIS R 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 2143)
  covalent geometry    : angle       0.61923 ( 2935)
  SS BOND              : bond        0.00034 (    1)
  SS BOND              : angle       0.91159 (    2)
  hydrogen bonds       : bond        0.03771 (  157)
  hydrogen bonds       : angle       4.24346 (  471)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 18
  time to evaluate  : 0.085 
Fit side-chains
REVERT: R  206 LEU cc_start: 0.7641 (mm) cc_final: 0.7043 (mp)
  outliers start: 4
  outliers final: 1
  residues processed: 20
  average time/residue: 0.1275
  time to fit residues: 2.8701
Evaluate side-chains
  18 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 17
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  188 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 1 optimal weight:    0.2980
   chunk 4 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0770
   chunk 15 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 2 optimal weight:    0.3980
   chunk 18 optimal weight:    0.0980
   chunk 0 optimal weight:    0.3980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.2538

-------------------------------------------------------------------------------
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 = 0.3809 r_free = 0.3809 target = 0.147745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.141910 restraints weight = 2976.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.141910 restraints weight = 2494.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.141910 restraints weight = 2494.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.141910 restraints weight = 2494.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.141910 restraints weight = 2494.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6003
moved from start:          0.1512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   2144  Z= 0.192
  Angle     :  0.686   6.150   2937  Z= 0.344
  Chirality :  0.044   0.189    338
  Planarity :  0.007   0.046    373
  Dihedral  :  4.218  13.115    315
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 13.47 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  1.11 (0.54), residues: 282
  helix:  1.81 (0.37), residues: 216
  sheet:  None (None), residues: 0
  loop : -3.10 (0.78), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R  80 
 TYR   0.017   0.002   TYR R  76 
 PHE   0.015   0.002   PHE R 107 
 TRP   0.007   0.001   TRP R 195 
 HIS   0.004   0.001   HIS R 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 2143)
  covalent geometry    : angle       0.68582 ( 2935)
  SS BOND              : bond        0.00196 (    1)
  SS BOND              : angle       0.61440 (    2)
  hydrogen bonds       : bond        0.04605 (  157)
  hydrogen bonds       : angle       4.49686 (  471)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.071 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 18
  average time/residue: 0.1366
  time to fit residues: 2.7413
Evaluate side-chains
  19 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  188 LEU
Chi-restraints excluded: chain R residue  199 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 3 optimal weight:    0.0980
   chunk 13 optimal weight:    0.6980
   chunk 8 optimal weight:    0.4980
   chunk 25 optimal weight:    0.0770
   chunk 23 optimal weight:    0.0670
   chunk 1 optimal weight:    0.0980
   chunk 10 optimal weight:    0.5980
   chunk 11 optimal weight:    0.3980
   chunk 20 optimal weight:    0.0870
   chunk 21 optimal weight:    0.0980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.0854

-------------------------------------------------------------------------------
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 = 0.3853 r_free = 0.3853 target = 0.151273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.145663 restraints weight = 2934.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.146191 restraints weight = 2322.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.146423 restraints weight = 2003.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.147306 restraints weight = 1830.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.147417 restraints weight = 1611.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5899
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2144  Z= 0.127
  Angle     :  0.597   6.215   2937  Z= 0.299
  Chirality :  0.040   0.190    338
  Planarity :  0.006   0.049    373
  Dihedral  :  3.793  11.808    315
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 12.95 %
    Favored  : 84.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  1.68 (0.56), residues: 282
  helix:  2.19 (0.37), residues: 217
  sheet:  None (None), residues: 0
  loop : -2.86 (0.81), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 270 
 TYR   0.010   0.001   TYR R  76 
 PHE   0.010   0.001   PHE R 107 
 TRP   0.007   0.001   TRP R  43 
 HIS   0.002   0.001   HIS R 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 2143)
  covalent geometry    : angle       0.59701 ( 2935)
  SS BOND              : bond        0.00026 (    1)
  SS BOND              : angle       0.25933 (    2)
  hydrogen bonds       : bond        0.03561 (  157)
  hydrogen bonds       : angle       4.14187 (  471)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 15
  time to evaluate  : 0.071 
Fit side-chains
REVERT: R  225 ARG cc_start: 0.6079 (mmt180) cc_final: 0.5781 (mmt180)
  outliers start: 5
  outliers final: 3
  residues processed: 17
  average time/residue: 0.1368
  time to fit residues: 2.5769
Evaluate side-chains
  18 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 15
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  188 LEU
Chi-restraints excluded: chain R residue  199 MET
Chi-restraints excluded: chain R residue  206 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 24 optimal weight:    0.0970
   chunk 15 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0970
   chunk 10 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0870
   chunk 2 optimal weight:    0.0980
   chunk 20 optimal weight:    0.0980
   chunk 12 optimal weight:    0.0870
   chunk 22 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0570
   overall best weight:    0.0850

-------------------------------------------------------------------------------
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 = 0.3860 r_free = 0.3860 target = 0.151702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.146156 restraints weight = 2899.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.146644 restraints weight = 2442.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.146937 restraints weight = 2038.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.146975 restraints weight = 1856.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.146992 restraints weight = 1815.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5908
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2144  Z= 0.125
  Angle     :  0.605   7.383   2937  Z= 0.296
  Chirality :  0.040   0.236    338
  Planarity :  0.006   0.048    373
  Dihedral  :  3.638  11.649    315
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.03 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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:  1.88 (0.56), residues: 282
  helix:  2.36 (0.37), residues: 217
  sheet:  None (None), residues: 0
  loop : -2.92 (0.80), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 221 
 TYR   0.011   0.001   TYR R  76 
 PHE   0.010   0.001   PHE R 107 
 TRP   0.008   0.001   TRP R  43 
 HIS   0.002   0.001   HIS R 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 2143)
  covalent geometry    : angle       0.60502 ( 2935)
  SS BOND              : bond        0.00008 (    1)
  SS BOND              : angle       0.25652 (    2)
  hydrogen bonds       : bond        0.03458 (  157)
  hydrogen bonds       : angle       4.03891 (  471)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.074 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 22
  average time/residue: 0.1038
  time to fit residues: 2.5862
Evaluate side-chains
  23 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  188 LEU
Chi-restraints excluded: chain R residue  199 MET
Chi-restraints excluded: chain R residue  206 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 22 optimal weight:    0.0970
   chunk 14 optimal weight:    0.0050
   chunk 16 optimal weight:    0.0670
   chunk 12 optimal weight:    0.1980
   chunk 8 optimal weight:    0.4980
   chunk 25 optimal weight:    0.0970
   chunk 0 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.0728

-------------------------------------------------------------------------------
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 = 0.3879 r_free = 0.3879 target = 0.153080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.147374 restraints weight = 2929.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.147400 restraints weight = 3532.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.148170 restraints weight = 3190.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.148430 restraints weight = 2234.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.149100 restraints weight = 1745.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5870
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2144  Z= 0.120
  Angle     :  0.600   7.629   2937  Z= 0.290
  Chirality :  0.040   0.242    338
  Planarity :  0.006   0.048    373
  Dihedral  :  3.558  11.734    315
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.54 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.00 (0.55), residues: 282
  helix:  2.47 (0.37), residues: 217
  sheet:  None (None), residues: 0
  loop : -2.95 (0.78), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 270 
 TYR   0.009   0.001   TYR R  76 
 PHE   0.010   0.001   PHE R 107 
 TRP   0.007   0.001   TRP R  43 
 HIS   0.002   0.001   HIS R 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 2143)
  covalent geometry    : angle       0.60012 ( 2935)
  SS BOND              : bond        0.00030 (    1)
  SS BOND              : angle       0.18903 (    2)
  hydrogen bonds       : bond        0.03238 (  157)
  hydrogen bonds       : angle       3.93230 (  471)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 18
  time to evaluate  : 0.044 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 20
  average time/residue: 0.1208
  time to fit residues: 2.7151
Evaluate side-chains
  22 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 18
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  199 MET
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  207 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 52.6872 > 50:
  distance: 10 - 15:  11.427
  distance: 15 - 16:  16.955
  distance: 16 - 17:  14.453
  distance: 16 - 19:  12.207
  distance: 17 - 18:  19.549
  distance: 17 - 23:  17.425
  distance: 19 - 20:  50.537
  distance: 20 - 21:  25.988
  distance: 20 - 22:  24.593
  distance: 23 - 24:  15.790
  distance: 24 - 25:  18.375
  distance: 24 - 27:  32.790
  distance: 25 - 26:  14.280
  distance: 25 - 29:  15.258
  distance: 27 - 28:  25.446
  distance: 29 - 30:  11.537
  distance: 30 - 31:  13.203
  distance: 31 - 32:  10.490
  distance: 31 - 33:  28.830
  distance: 33 - 34:   9.198
  distance: 34 - 35:  31.350
  distance: 34 - 37:  30.934
  distance: 35 - 36:   9.935
  distance: 35 - 38:  23.437
  distance: 38 - 39:   6.545
  distance: 39 - 40:  11.112
  distance: 40 - 41:   3.412
  distance: 40 - 42:   7.609
  distance: 42 - 43:   3.993
  distance: 43 - 44:   7.692
  distance: 43 - 46:   9.850
  distance: 44 - 45:   4.870
  distance: 44 - 47:   5.032
  distance: 47 - 48:   7.558
  distance: 48 - 49:   5.875
  distance: 48 - 51:   6.246
  distance: 49 - 50:  11.564
  distance: 49 - 52:   4.795
  distance: 52 - 53:   4.581
  distance: 53 - 54:   7.587
  distance: 53 - 56:   8.038
  distance: 54 - 55:   8.062
  distance: 55 - 80:  13.735
  distance: 57 - 58:  18.974
  distance: 57 - 59:  16.401
  distance: 60 - 61:   8.454
  distance: 61 - 62:  13.723
  distance: 61 - 64:   4.873
  distance: 62 - 63:  10.320
  distance: 62 - 65:  20.156
  distance: 63 - 84:  16.813
  distance: 65 - 66:  15.619
  distance: 66 - 67:  15.677
  distance: 66 - 69:   8.912
  distance: 67 - 68:  12.291
  distance: 67 - 73:  12.566
  distance: 68 - 88:   6.283
  distance: 69 - 70:   9.776
  distance: 70 - 71:   4.623
  distance: 70 - 72:   7.144
  distance: 76 - 92:   3.213