Starting phenix.real_space_refine
on Wed Sep 17 03:32:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hh1_52168/09_2025/9hh1_52168.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hh1_52168/09_2025/9hh1_52168.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hh1_52168/09_2025/9hh1_52168.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hh1_52168/09_2025/9hh1_52168.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hh1_52168/09_2025/9hh1_52168.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hh1_52168/09_2025/9hh1_52168.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.112
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      16      5.16       5
     C    2092      2.51       5
     N     584      2.21       5
     O     608      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3300
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1650
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 194}
    Chain: "B"
      Number of atoms: 1650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1650
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 194}
  Time building chain proxies: 1.12, per 1000 atoms: 0.34
  Number of scatterers: 3300
  At special positions: 0
  Unit cell: (68.06, 74.62, 55.76, 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      16     16.00
     O     608      8.00
     N     584      7.00
     C    2092      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.39
  Conformation dependent library (CDL) restraints added in 120.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  780

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 2 sheets defined
      38.3% alpha, 20.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 102 through 109
    Processing helix  chain 'A' and resid 109 through 121
      removed outlier: 3.511A  pdb=" N   LEU A 120 " --> pdb=" O   GLU A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 179
      removed outlier: 3.922A  pdb=" N   ARG A 177 " --> pdb=" O   SER A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 190
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 3.546A  pdb=" N   ASN A 211 " --> pdb=" O   ASN A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 238
    Processing helix  chain 'A' and resid 247 through 251
    Processing helix  chain 'A' and resid 277 through 279
      No H-bonds generated for 'chain 'A' and resid 277 through 279'
    Processing helix  chain 'A' and resid 281 through 297
    Processing helix  chain 'B' and resid 102 through 109
    Processing helix  chain 'B' and resid 109 through 121
      removed outlier: 3.529A  pdb=" N   LEU B 120 " --> pdb=" O   GLU B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 179
      removed outlier: 3.956A  pdb=" N   ARG B 177 " --> pdb=" O   SER B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 190
    Processing helix  chain 'B' and resid 207 through 212
      removed outlier: 3.553A  pdb=" N   ASN B 211 " --> pdb=" O   ASN B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 238
    Processing helix  chain 'B' and resid 247 through 251
    Processing helix  chain 'B' and resid 277 through 279
      No H-bonds generated for 'chain 'B' and resid 277 through 279'
    Processing helix  chain 'B' and resid 281 through 297
    Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 164
      removed outlier: 5.301A  pdb=" N   GLN A 158 " --> pdb=" O   TYR A 274 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   TYR A 274 " --> pdb=" O   GLN A 158 " (cutoff:3.500A)
      removed outlier: 5.320A  pdb=" N   LYS A 160 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
      removed outlier: 5.800A  pdb=" N   PHE A 272 " --> pdb=" O   LYS A 160 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   PHE A 162 " --> pdb=" O   THR A 270 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ILE B 192 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
      removed outlier: 8.206A  pdb=" N   ILE B 226 " --> pdb=" O   ILE B 192 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   SER B 194 " --> pdb=" O   ILE B 226 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   CYS B 244 " --> pdb=" O   ILE B 193 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   VAL B 168 " --> pdb=" O   LEU B 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 259
      removed outlier: 4.715A  pdb=" N   VAL A 168 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   CYS A 244 " --> pdb=" O   ILE A 193 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   ILE A 192 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   ILE A 226 " --> pdb=" O   ILE A 192 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   SER A 194 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   GLN A 225 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
      removed outlier: 7.378A  pdb=" N   LEU B 130 " --> pdb=" O   GLN A 225 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   PHE B 162 " --> pdb=" O   THR B 270 " (cutoff:3.500A)
      removed outlier: 5.797A  pdb=" N   PHE B 272 " --> pdb=" O   LYS B 160 " (cutoff:3.500A)
      removed outlier: 5.311A  pdb=" N   LYS B 160 " --> pdb=" O   PHE B 272 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   TYR B 274 " --> pdb=" O   GLN B 158 " (cutoff:3.500A)
      removed outlier: 5.293A  pdb=" N   GLN B 158 " --> pdb=" O   TYR B 274 " (cutoff:3.500A)

    132 hydrogen bonds defined for protein.
    354 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: 0.45

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 890
        1.33 -     1.46: 626
        1.46 -     1.58: 1834
        1.58 -     1.71: 0
        1.71 -     1.83: 24
  Bond restraints: 3374
  Sorted by residual:
  bond pdb=" CZ  ARG A 147 "
       pdb=" NH2 ARG A 147 "
    ideal  model  delta    sigma   weight residual
    1.330  1.285  0.045 1.30e-02 5.92e+03 1.18e+01
  bond pdb=" CZ  ARG A 234 "
       pdb=" NH2 ARG A 234 "
    ideal  model  delta    sigma   weight residual
    1.330  1.288  0.042 1.30e-02 5.92e+03 1.03e+01
  bond pdb=" CZ  ARG B 191 "
       pdb=" NH2 ARG B 191 "
    ideal  model  delta    sigma   weight residual
    1.330  1.289  0.041 1.30e-02 5.92e+03 1.02e+01
  bond pdb=" CZ  ARG B  98 "
       pdb=" NH2 ARG B  98 "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.37e+00
  bond pdb=" ND1 HIS A 167 "
       pdb=" CE1 HIS A 167 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 9.14e+00
  ... (remaining 3369 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.02: 2577
        1.02 -     2.05: 1245
        2.05 -     3.07: 568
        3.07 -     4.10: 177
        4.10 -     5.12: 13
  Bond angle restraints: 4580
  Sorted by residual:
  angle pdb=" OE1 GLN B 107 "
        pdb=" CD  GLN B 107 "
        pdb=" NE2 GLN B 107 "
      ideal   model   delta    sigma   weight residual
     122.60  118.76    3.84 1.00e+00 1.00e+00 1.48e+01
  angle pdb=" OE1 GLN A 225 "
        pdb=" CD  GLN A 225 "
        pdb=" NE2 GLN A 225 "
      ideal   model   delta    sigma   weight residual
     122.60  118.84    3.76 1.00e+00 1.00e+00 1.42e+01
  angle pdb=" OE1 GLN B 119 "
        pdb=" CD  GLN B 119 "
        pdb=" NE2 GLN B 119 "
      ideal   model   delta    sigma   weight residual
     122.60  118.85    3.75 1.00e+00 1.00e+00 1.40e+01
  angle pdb=" OE1 GLN B 115 "
        pdb=" CD  GLN B 115 "
        pdb=" NE2 GLN B 115 "
      ideal   model   delta    sigma   weight residual
     122.60  118.92    3.68 1.00e+00 1.00e+00 1.35e+01
  angle pdb=" OE1 GLN A 127 "
        pdb=" CD  GLN A 127 "
        pdb=" NE2 GLN A 127 "
      ideal   model   delta    sigma   weight residual
     122.60  119.04    3.56 1.00e+00 1.00e+00 1.27e+01
  ... (remaining 4575 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.91: 1895
       13.91 -    27.81: 109
       27.81 -    41.71: 20
       41.71 -    55.62: 14
       55.62 -    69.52: 2
  Dihedral angle restraints: 2040
    sinusoidal: 836
      harmonic: 1204
  Sorted by residual:
  dihedral pdb=" CA  ALA A 145 "
           pdb=" C   ALA A 145 "
           pdb=" N   ILE A 146 "
           pdb=" CA  ILE A 146 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.84   20.16     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  ALA B 145 "
           pdb=" C   ALA B 145 "
           pdb=" N   ILE B 146 "
           pdb=" CA  ILE B 146 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.88   20.12     0      5.00e+00 4.00e-02 1.62e+01
  dihedral pdb=" CA  ILE B 126 "
           pdb=" C   ILE B 126 "
           pdb=" N   GLN B 127 "
           pdb=" CA  GLN B 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.67   19.33     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 2037 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 278
       0.062 -    0.124: 161
       0.124 -    0.186: 62
       0.186 -    0.248: 1
       0.248 -    0.310: 2
  Chirality restraints: 504
  Sorted by residual:
  chirality pdb=" CA  ASP B 205 "
            pdb=" N   ASP B 205 "
            pdb=" C   ASP B 205 "
            pdb=" CB  ASP B 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.40e+00
  chirality pdb=" CA  ASP A 205 "
            pdb=" N   ASP A 205 "
            pdb=" C   ASP A 205 "
            pdb=" CB  ASP A 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.22e+00
  chirality pdb=" CA  ARG A 140 "
            pdb=" N   ARG A 140 "
            pdb=" C   ARG A 140 "
            pdb=" CB  ARG A 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.33e-01
  ... (remaining 501 not shown)

  Planarity restraints: 602
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 202 "    0.066 2.00e-02 2.50e+03   3.63e-02 2.63e+01
        pdb=" CG  TYR A 202 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 202 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 202 "   -0.029 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 202 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 202 "   -0.022 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 202 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 202 "    0.055 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 174 "   -0.060 2.00e-02 2.50e+03   3.22e-02 2.07e+01
        pdb=" CG  TYR B 174 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 174 "    0.027 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 174 "    0.027 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 174 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 174 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 174 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 174 "   -0.047 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 174 "   -0.060 2.00e-02 2.50e+03   3.17e-02 2.01e+01
        pdb=" CG  TYR A 174 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 174 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 174 "    0.025 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 174 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 174 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 174 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 174 "   -0.046 2.00e-02 2.50e+03
  ... (remaining 599 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.49: 18
        2.49 -     3.09: 2077
        3.09 -     3.70: 4949
        3.70 -     4.30: 7687
        4.30 -     4.90: 12363
  Nonbonded interactions: 27094
  Sorted by model distance:
  nonbonded pdb=" CE2 TRP A 298 "
            pdb=" CE2 PHE A 300 "
     model   vdw
     1.889 3.560
  nonbonded pdb=" NE1 TRP A 298 "
            pdb=" CE2 PHE A 300 "
     model   vdw
     1.925 3.420
  nonbonded pdb=" CZ2 TRP A 298 "
            pdb=" CE2 PHE A 300 "
     model   vdw
     2.219 3.640
  nonbonded pdb=" OE1 GLN A 225 "
            pdb=" NZ  LYS B  96 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" NZ  LYS A  96 "
            pdb=" OE1 GLN B 225 "
     model   vdw
     2.297 3.120
  ... (remaining 27089 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.310
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4610
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      :  0.015   0.456   3375  Z= 1.077
  Angle     :  1.448   5.120   4580  Z= 0.958
  Chirality :  0.080   0.310    504
  Planarity :  0.010   0.068    602
  Dihedral  : 10.772  69.520   1260
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  2.22 %
    Favored  : 97.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.27 (0.35), residues: 408
  helix: -1.72 (0.32), residues: 138
  sheet:  0.34 (0.64), residues: 56
  loop : -0.43 (0.37), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 234 
 TYR   0.066   0.013   TYR A 202 
 PHE   0.027   0.006   PHE B 195 
 TRP   0.023   0.006   TRP B 109 
 HIS   0.004   0.002   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.01276 ( 3374)
  covalent geometry    : angle       1.44785 ( 4580)
  hydrogen bonds       : bond        0.16259 (  132)
  hydrogen bonds       : angle       6.61137 (  354)
  Misc. bond           : bond        0.45643 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 169
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 LEU cc_start: 0.6950 (tp) cc_final: 0.6701 (tp)
REVERT: A  128 LEU cc_start: 0.6873 (mt) cc_final: 0.6350 (mp)
REVERT: A  136 ASP cc_start: 0.4341 (t0) cc_final: 0.3766 (m-30)
REVERT: A  280 ASN cc_start: 0.6861 (m-40) cc_final: 0.6452 (m110)
REVERT: B  136 ASP cc_start: 0.4450 (t0) cc_final: 0.4035 (m-30)
REVERT: B  280 ASN cc_start: 0.6870 (m-40) cc_final: 0.6534 (m110)
  outliers start: 2
  outliers final: 0
  residues processed: 169
  average time/residue: 0.0863
  time to fit residues: 16.9154
Evaluate side-chains
  111 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0070
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 22 optimal weight:    0.0670
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN
B 141 HIS
B 158 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4924 r_free = 0.4924 target = 0.212780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4584 r_free = 0.4584 target = 0.174121 restraints weight = 6027.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.181718 restraints weight = 3914.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4703 r_free = 0.4703 target = 0.187611 restraints weight = 2773.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4737 r_free = 0.4737 target = 0.192035 restraints weight = 2080.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4768 r_free = 0.4768 target = 0.195417 restraints weight = 1634.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.4739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5903
moved from start:          0.4479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3375  Z= 0.137
  Angle     :  0.654   5.902   4580  Z= 0.335
  Chirality :  0.046   0.148    504
  Planarity :  0.004   0.031    602
  Dihedral  :  5.117  19.544    450
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 16.39 %
    Favored  : 81.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  0.85 (0.39), residues: 408
  helix:  0.22 (0.44), residues: 124
  sheet:  1.46 (0.49), residues: 84
  loop :  0.56 (0.42), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  98 
 TYR   0.017   0.003   TYR A 169 
 PHE   0.015   0.002   PHE B 300 
 TRP   0.012   0.002   TRP A 109 
 HIS   0.003   0.001   HIS B 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 3374)
  covalent geometry    : angle       0.65380 ( 4580)
  hydrogen bonds       : bond        0.04825 (  132)
  hydrogen bonds       : angle       4.73230 (  354)
  Misc. bond           : bond        0.00044 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 123
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 LYS cc_start: 0.6373 (OUTLIER) cc_final: 0.6118 (tptp)
REVERT: A  188 ASP cc_start: 0.8962 (m-30) cc_final: 0.8365 (p0)
REVERT: A  280 ASN cc_start: 0.8139 (m-40) cc_final: 0.7848 (m-40)
REVERT: B  188 ASP cc_start: 0.8996 (m-30) cc_final: 0.8425 (p0)
REVERT: B  280 ASN cc_start: 0.7927 (m-40) cc_final: 0.7589 (m-40)
REVERT: B  297 ASN cc_start: 0.8700 (t0) cc_final: 0.8389 (m110)
  outliers start: 8
  outliers final: 3
  residues processed: 130
  average time/residue: 0.0787
  time to fit residues: 12.0337
Evaluate side-chains
  108 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain B residue  173 SER
Chi-restraints excluded: chain B residue  204 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 38 optimal weight:    9.9990
   chunk 7 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0370
   chunk 30 optimal weight:    0.1980
   chunk 13 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 5 optimal weight:    9.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    0.8260

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN
B 158 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4852 r_free = 0.4852 target = 0.195823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.157356 restraints weight = 5586.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.165302 restraints weight = 3152.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4632 r_free = 0.4632 target = 0.171282 restraints weight = 2062.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.175458 restraints weight = 1470.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4707 r_free = 0.4707 target = 0.179156 restraints weight = 1121.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.4692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6090
moved from start:          0.5868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3375  Z= 0.136
  Angle     :  0.673   7.208   4580  Z= 0.337
  Chirality :  0.047   0.157    504
  Planarity :  0.004   0.030    602
  Dihedral  :  5.222  18.885    450
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 17.50 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.39), residues: 408
  helix:  0.10 (0.45), residues: 112
  sheet:  1.33 (0.56), residues: 72
  loop :  0.69 (0.41), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 296 
 TYR   0.010   0.002   TYR B 169 
 PHE   0.023   0.003   PHE B 117 
 TRP   0.003   0.001   TRP B 109 
 HIS   0.004   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 3374)
  covalent geometry    : angle       0.67252 ( 4580)
  hydrogen bonds       : bond        0.04433 (  132)
  hydrogen bonds       : angle       4.94684 (  354)
  Misc. bond           : bond        0.00046 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8152 (ttpt)
REVERT: A   98 ARG cc_start: 0.7873 (mtp180) cc_final: 0.7550 (mtp-110)
REVERT: A  188 ASP cc_start: 0.8986 (m-30) cc_final: 0.8426 (p0)
REVERT: B   98 ARG cc_start: 0.8185 (mtp180) cc_final: 0.7777 (mtp-110)
REVERT: B  297 ASN cc_start: 0.8699 (t0) cc_final: 0.8163 (m110)
  outliers start: 13
  outliers final: 11
  residues processed: 120
  average time/residue: 0.0883
  time to fit residues: 12.2890
Evaluate side-chains
  113 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  227 ASN
Chi-restraints excluded: chain B residue  173 SER
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  227 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 36 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 20 optimal weight:    4.9990
   chunk 38 optimal weight:    8.9990
   chunk 12 optimal weight:    0.1980
   chunk 35 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
B 153 GLN
B 225 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4780 r_free = 0.4780 target = 0.189753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.152073 restraints weight = 6266.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.158565 restraints weight = 4214.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.163459 restraints weight = 3092.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.167067 restraints weight = 2407.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.170103 restraints weight = 1962.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.4547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6400
moved from start:          0.7210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3375  Z= 0.162
  Angle     :  0.691   7.407   4580  Z= 0.351
  Chirality :  0.048   0.163    504
  Planarity :  0.005   0.068    602
  Dihedral  :  5.231  18.469    450
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 17.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 18.89 %
    Favored  : 76.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  0.37 (0.40), residues: 408
  helix: -0.44 (0.43), residues: 124
  sheet:  1.15 (0.64), residues: 72
  loop :  0.54 (0.42), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 159 
 TYR   0.016   0.003   TYR B 248 
 PHE   0.028   0.003   PHE A 117 
 TRP   0.005   0.001   TRP A 298 
 HIS   0.003   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 3374)
  covalent geometry    : angle       0.69143 ( 4580)
  hydrogen bonds       : bond        0.04699 (  132)
  hydrogen bonds       : angle       5.27788 (  354)
  Misc. bond           : bond        0.00021 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 ARG cc_start: 0.7872 (mtp180) cc_final: 0.7553 (mtp180)
REVERT: B   98 ARG cc_start: 0.8205 (mtp180) cc_final: 0.7663 (mtp180)
REVERT: B  234 ARG cc_start: 0.8849 (mtm180) cc_final: 0.8629 (mtm180)
REVERT: B  297 ASN cc_start: 0.8805 (t0) cc_final: 0.8398 (m110)
  outliers start: 18
  outliers final: 16
  residues processed: 128
  average time/residue: 0.0871
  time to fit residues: 12.9977
Evaluate side-chains
  112 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  227 ASN
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  173 SER
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  227 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 17 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 32 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 31 optimal weight:    0.3980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 225 GLN
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4743 r_free = 0.4743 target = 0.189280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.151527 restraints weight = 6025.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.157694 restraints weight = 4110.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.162342 restraints weight = 3064.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.165666 restraints weight = 2444.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.168009 restraints weight = 2041.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.4483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6453
moved from start:          0.7741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3375  Z= 0.125
  Angle     :  0.664   7.091   4580  Z= 0.334
  Chirality :  0.045   0.148    504
  Planarity :  0.004   0.033    602
  Dihedral  :  4.873  17.920    450
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 18.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 22.22 %
    Favored  : 72.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.16 (0.40), residues: 408
  helix: -0.69 (0.43), residues: 128
  sheet:  0.87 (0.64), residues: 72
  loop :  0.57 (0.42), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  98 
 TYR   0.016   0.002   TYR A 121 
 PHE   0.024   0.003   PHE B 117 
 TRP   0.005   0.001   TRP B 109 
 HIS   0.002   0.001   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 3374)
  covalent geometry    : angle       0.66412 ( 4580)
  hydrogen bonds       : bond        0.04293 (  132)
  hydrogen bonds       : angle       5.27604 (  354)
  Misc. bond           : bond        0.00152 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  234 ARG cc_start: 0.8783 (mtm180) cc_final: 0.8506 (ttt180)
REVERT: B  234 ARG cc_start: 0.8840 (mtm180) cc_final: 0.8601 (ttt180)
  outliers start: 18
  outliers final: 15
  residues processed: 114
  average time/residue: 0.0969
  time to fit residues: 12.8064
Evaluate side-chains
  114 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  227 ASN
Chi-restraints excluded: chain B residue  107 GLN
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  227 ASN
Chi-restraints excluded: chain B residue  247 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0060
   chunk 30 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    2.6004

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

Flipped N/Q/H residues before XYZ refinement:
A 211 ASN
B 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.167628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.127203 restraints weight = 5792.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.132264 restraints weight = 4002.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.136379 restraints weight = 3041.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.139422 restraints weight = 2433.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.142054 restraints weight = 2042.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.4304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6752
moved from start:          0.9356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   3375  Z= 0.219
  Angle     :  0.808   7.247   4580  Z= 0.410
  Chirality :  0.050   0.168    504
  Planarity :  0.006   0.053    602
  Dihedral  :  5.512  19.642    450
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 24.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  6.94 %
    Allowed  : 21.94 %
    Favored  : 71.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.39), residues: 408
  helix: -1.10 (0.40), residues: 128
  sheet:  0.08 (0.60), residues: 74
  loop :  0.28 (0.41), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 288 
 TYR   0.013   0.002   TYR B 274 
 PHE   0.030   0.003   PHE A 117 
 TRP   0.008   0.002   TRP A 208 
 HIS   0.003   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 ( 3374)
  covalent geometry    : angle       0.80813 ( 4580)
  hydrogen bonds       : bond        0.05386 (  132)
  hydrogen bonds       : angle       5.86488 (  354)
  Misc. bond           : bond        0.00101 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  234 ARG cc_start: 0.8741 (mtm180) cc_final: 0.8534 (mtm180)
REVERT: B  269 ASP cc_start: 0.8085 (t0) cc_final: 0.7661 (t0)
REVERT: B  297 ASN cc_start: 0.8760 (t0) cc_final: 0.8450 (m110)
  outliers start: 25
  outliers final: 18
  residues processed: 120
  average time/residue: 0.0828
  time to fit residues: 11.6753
Evaluate side-chains
  111 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  169 TYR
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  107 GLN
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  169 TYR
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  247 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 69.7031 > 50:
  distance: 4 - 9:  34.032
  distance: 9 - 10:  55.742
  distance: 9 - 248:  32.369
  distance: 10 - 11:  33.067
  distance: 10 - 13:  56.873
  distance: 11 - 12:  37.269
  distance: 11 - 16:  35.837
  distance: 12 - 245:  30.547
  distance: 13 - 14:  55.968
  distance: 13 - 15:  39.197
  distance: 17 - 20:  35.986
  distance: 18 - 19:  21.749
  distance: 18 - 26:  39.770
  distance: 20 - 21:  38.532
  distance: 21 - 22:  36.002
  distance: 21 - 23:  38.958
  distance: 22 - 24:  37.922
  distance: 23 - 25:  39.734
  distance: 24 - 25:  22.594
  distance: 26 - 27:  33.993
  distance: 27 - 28:   5.104
  distance: 27 - 30:  19.433
  distance: 28 - 29:  20.434
  distance: 28 - 34:  41.060
  distance: 30 - 31:  20.433
  distance: 31 - 32:  65.309
  distance: 32 - 33:  31.182
  distance: 34 - 35:  40.177
  distance: 34 - 165:  24.207
  distance: 35 - 38:  36.581
  distance: 36 - 44:  12.721
  distance: 37 - 162:  35.114
  distance: 38 - 39:  43.183
  distance: 39 - 40:  38.689
  distance: 39 - 41:  13.743
  distance: 40 - 42:  42.996
  distance: 44 - 45:  42.528
  distance: 45 - 46:  38.804
  distance: 45 - 48:  39.312
  distance: 46 - 47:  28.087
  distance: 46 - 51:  40.836
  distance: 47 - 218:  28.853
  distance: 48 - 49:  57.522
  distance: 51 - 52:  26.394
  distance: 51 - 154:  36.949
  distance: 52 - 53:  27.371
  distance: 52 - 55:  42.261
  distance: 53 - 54:  57.003
  distance: 53 - 63:  56.817
  distance: 54 - 151:  35.410
  distance: 56 - 58:  39.901
  distance: 58 - 60:  10.585
  distance: 59 - 61:  20.298
  distance: 60 - 61:  21.707
  distance: 61 - 62:  33.892
  distance: 63 - 64:  17.474
  distance: 63 - 205:  27.106
  distance: 64 - 65:  41.373
  distance: 64 - 67:  38.978
  distance: 65 - 66:  40.874
  distance: 66 - 202:  33.167
  distance: 68 - 69:  21.969
  distance: 69 - 70:  45.374
  distance: 69 - 72:  42.453
  distance: 70 - 71:  38.834
  distance: 70 - 73:  30.395
  distance: 71 - 95:  36.484
  distance: 73 - 74:  49.839
  distance: 73 - 79:  41.827
  distance: 74 - 75:  40.816
  distance: 74 - 77:  40.544
  distance: 76 - 103:  32.932
  distance: 78 - 79:  57.223
  distance: 81 - 82:  38.585
  distance: 82 - 83:  16.015
  distance: 82 - 86:  27.319