Starting phenix.real_space_refine
on Wed Sep 17 08:48:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y8v_39060/09_2025/8y8v_39060.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y8v_39060/09_2025/8y8v_39060.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y8v_39060/09_2025/8y8v_39060.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y8v_39060/09_2025/8y8v_39060.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y8v_39060/09_2025/8y8v_39060.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y8v_39060/09_2025/8y8v_39060.cif"
  }
  resolution = 2.49
  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=   0.188
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      52      5.16       5
     C    5072      2.51       5
     N    1212      2.21       5
     O    1276      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  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: 7616
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1876
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1876
          Classifications: {'peptide': 245}
          Link IDs: {'PTRANS': 11, 'TRANS': 233}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Classifications: {'peptide': 1}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'P5S:plan-1': 1, 'P5S:plan-3': 1}
          Unresolved non-hydrogen planarities: 8
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 1.51, per 1000 atoms: 0.20
  Number of scatterers: 7616
  At special positions: 0
  Unit cell: (85.425, 85.425, 65.325, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      52     16.00
     P       4     15.00
     O    1276      8.00
     N    1212      7.00
     C    5072      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 469.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1712

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      78.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 61
    Processing helix  chain 'A' and resid 66 through 86
      removed outlier: 3.603A  pdb=" N   THR A  79 " --> pdb=" O   GLY A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 104
    Processing helix  chain 'A' and resid 108 through 110
      No H-bonds generated for 'chain 'A' and resid 108 through 110'
    Processing helix  chain 'A' and resid 111 through 134
    Processing helix  chain 'A' and resid 134 through 143
    Processing helix  chain 'A' and resid 154 through 158
    Processing helix  chain 'A' and resid 167 through 190
    Processing helix  chain 'A' and resid 201 through 218
      removed outlier: 3.515A  pdb=" N   VAL A 205 " --> pdb=" O   THR A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 240
      Proline residue:  A 232  - end of helix
    Processing helix  chain 'A' and resid 244 through 253
      removed outlier: 6.752A  pdb=" N   GLY A 250 " --> pdb=" O   VAL A 246 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   GLU A 251 " --> pdb=" O   PHE A 247 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ASN A 252 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 276
      Proline residue:  A 261  - end of helix
    Processing helix  chain 'B' and resid 33 through 61
    Processing helix  chain 'B' and resid 66 through 86
      removed outlier: 3.603A  pdb=" N   THR B  79 " --> pdb=" O   GLY B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 104
    Processing helix  chain 'B' and resid 108 through 110
      No H-bonds generated for 'chain 'B' and resid 108 through 110'
    Processing helix  chain 'B' and resid 111 through 134
    Processing helix  chain 'B' and resid 134 through 143
    Processing helix  chain 'B' and resid 154 through 158
    Processing helix  chain 'B' and resid 167 through 190
    Processing helix  chain 'B' and resid 201 through 218
      removed outlier: 3.515A  pdb=" N   VAL B 205 " --> pdb=" O   THR B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 240
      Proline residue:  B 232  - end of helix
    Processing helix  chain 'B' and resid 244 through 253
      removed outlier: 6.752A  pdb=" N   GLY B 250 " --> pdb=" O   VAL B 246 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   GLU B 251 " --> pdb=" O   PHE B 247 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ASN B 252 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 276
      Proline residue:  B 261  - end of helix
    Processing helix  chain 'C' and resid 33 through 61
    Processing helix  chain 'C' and resid 66 through 86
      removed outlier: 3.603A  pdb=" N   THR C  79 " --> pdb=" O   GLY C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 94 through 104
    Processing helix  chain 'C' and resid 108 through 110
      No H-bonds generated for 'chain 'C' and resid 108 through 110'
    Processing helix  chain 'C' and resid 111 through 134
    Processing helix  chain 'C' and resid 134 through 143
    Processing helix  chain 'C' and resid 154 through 158
    Processing helix  chain 'C' and resid 167 through 190
    Processing helix  chain 'C' and resid 201 through 218
      removed outlier: 3.515A  pdb=" N   VAL C 205 " --> pdb=" O   THR C 201 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 226 through 240
      Proline residue:  C 232  - end of helix
    Processing helix  chain 'C' and resid 244 through 253
      removed outlier: 6.752A  pdb=" N   GLY C 250 " --> pdb=" O   VAL C 246 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   GLU C 251 " --> pdb=" O   PHE C 247 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ASN C 252 " --> pdb=" O   SER C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 255 through 276
      Proline residue:  C 261  - end of helix
    Processing helix  chain 'D' and resid 33 through 61
    Processing helix  chain 'D' and resid 66 through 86
      removed outlier: 3.603A  pdb=" N   THR D  79 " --> pdb=" O   GLY D  75 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 94 through 104
    Processing helix  chain 'D' and resid 108 through 110
      No H-bonds generated for 'chain 'D' and resid 108 through 110'
    Processing helix  chain 'D' and resid 111 through 134
    Processing helix  chain 'D' and resid 134 through 143
    Processing helix  chain 'D' and resid 154 through 158
    Processing helix  chain 'D' and resid 167 through 190
    Processing helix  chain 'D' and resid 201 through 218
      removed outlier: 3.515A  pdb=" N   VAL D 205 " --> pdb=" O   THR D 201 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 226 through 240
      Proline residue:  D 232  - end of helix
    Processing helix  chain 'D' and resid 244 through 253
      removed outlier: 6.752A  pdb=" N   GLY D 250 " --> pdb=" O   VAL D 246 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   GLU D 251 " --> pdb=" O   PHE D 247 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ASN D 252 " --> pdb=" O   SER D 248 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 255 through 276
      Proline residue:  D 261  - end of helix

    540 hydrogen bonds defined for protein.
    1596 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: 1.33

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1380
        1.33 -     1.45: 2112
        1.45 -     1.57: 4244
        1.57 -     1.69: 8
        1.69 -     1.81: 96
  Bond restraints: 7840
  Sorted by residual:
  bond pdb=" N   MET A 219 "
       pdb=" CA  MET A 219 "
    ideal  model  delta    sigma   weight residual
    1.456  1.472 -0.016 1.33e-02 5.65e+03 1.51e+00
  bond pdb=" N   MET C 219 "
       pdb=" CA  MET C 219 "
    ideal  model  delta    sigma   weight residual
    1.456  1.472 -0.016 1.33e-02 5.65e+03 1.51e+00
  bond pdb=" N   MET B 219 "
       pdb=" CA  MET B 219 "
    ideal  model  delta    sigma   weight residual
    1.456  1.472 -0.016 1.33e-02 5.65e+03 1.51e+00
  bond pdb=" N   MET D 219 "
       pdb=" CA  MET D 219 "
    ideal  model  delta    sigma   weight residual
    1.456  1.472 -0.016 1.33e-02 5.65e+03 1.51e+00
  bond pdb=" C17 P5S B 500 "
       pdb=" O19 P5S B 500 "
    ideal  model  delta    sigma   weight residual
    1.351  1.327  0.024 2.00e-02 2.50e+03 1.45e+00
  ... (remaining 7835 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 10432
        1.44 -     2.87: 148
        2.87 -     4.31: 56
        4.31 -     5.74: 20
        5.74 -     7.17: 8
  Bond angle restraints: 10664
  Sorted by residual:
  angle pdb=" CA  TYR D 223 "
        pdb=" CB  TYR D 223 "
        pdb=" CG  TYR D 223 "
      ideal   model   delta    sigma   weight residual
     113.90  119.00   -5.10 1.80e+00 3.09e-01 8.02e+00
  angle pdb=" CA  TYR A 223 "
        pdb=" CB  TYR A 223 "
        pdb=" CG  TYR A 223 "
      ideal   model   delta    sigma   weight residual
     113.90  119.00   -5.10 1.80e+00 3.09e-01 8.02e+00
  angle pdb=" CA  TYR C 223 "
        pdb=" CB  TYR C 223 "
        pdb=" CG  TYR C 223 "
      ideal   model   delta    sigma   weight residual
     113.90  119.00   -5.10 1.80e+00 3.09e-01 8.02e+00
  angle pdb=" CA  TYR B 223 "
        pdb=" CB  TYR B 223 "
        pdb=" CG  TYR B 223 "
      ideal   model   delta    sigma   weight residual
     113.90  119.00   -5.10 1.80e+00 3.09e-01 8.02e+00
  angle pdb=" C   GLY A 218 "
        pdb=" N   MET A 219 "
        pdb=" CA  MET A 219 "
      ideal   model   delta    sigma   weight residual
     122.06  117.40    4.66 1.86e+00 2.89e-01 6.28e+00
  ... (remaining 10659 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.01: 4108
       27.01 -    54.01: 240
       54.01 -    81.02: 32
       81.02 -   108.02: 20
      108.02 -   135.03: 8
  Dihedral angle restraints: 4408
    sinusoidal: 1680
      harmonic: 2728
  Sorted by residual:
  dihedral pdb=" C27 P5S D 500 "
           pdb=" C28 P5S D 500 "
           pdb=" C29 P5S D 500 "
           pdb=" C30 P5S D 500 "
      ideal   model   delta sinusoidal    sigma   weight residual
     298.90  163.87  135.03     1      3.00e+01 1.11e-03 1.82e+01
  dihedral pdb=" C27 P5S A 500 "
           pdb=" C28 P5S A 500 "
           pdb=" C29 P5S A 500 "
           pdb=" C30 P5S A 500 "
      ideal   model   delta sinusoidal    sigma   weight residual
     298.90  163.87  135.03     1      3.00e+01 1.11e-03 1.82e+01
  dihedral pdb=" C27 P5S C 500 "
           pdb=" C28 P5S C 500 "
           pdb=" C29 P5S C 500 "
           pdb=" C30 P5S C 500 "
      ideal   model   delta sinusoidal    sigma   weight residual
     298.90  163.87  135.03     1      3.00e+01 1.11e-03 1.82e+01
  ... (remaining 4405 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 724
       0.029 -    0.058: 296
       0.058 -    0.086: 120
       0.086 -    0.115: 32
       0.115 -    0.144: 8
  Chirality restraints: 1180
  Sorted by residual:
  chirality pdb=" CA  TYR B 223 "
            pdb=" N   TYR B 223 "
            pdb=" C   TYR B 223 "
            pdb=" CB  TYR B 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.17e-01
  chirality pdb=" CA  TYR D 223 "
            pdb=" N   TYR D 223 "
            pdb=" C   TYR D 223 "
            pdb=" CB  TYR D 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.17e-01
  chirality pdb=" CA  TYR C 223 "
            pdb=" N   TYR C 223 "
            pdb=" C   TYR C 223 "
            pdb=" CB  TYR C 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.17e-01
  ... (remaining 1177 not shown)

  Planarity restraints: 1312
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 232 "   -0.020 5.00e-02 4.00e+02   3.03e-02 1.47e+00
        pdb=" N   PRO A 233 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 233 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 233 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 232 "    0.020 5.00e-02 4.00e+02   3.03e-02 1.47e+00
        pdb=" N   PRO C 233 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO C 233 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 233 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO D 232 "   -0.020 5.00e-02 4.00e+02   3.03e-02 1.47e+00
        pdb=" N   PRO D 233 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO D 233 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO D 233 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1309 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1896
        2.79 -     3.32: 7424
        3.32 -     3.85: 13884
        3.85 -     4.37: 16452
        4.37 -     4.90: 28048
  Nonbonded interactions: 67704
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C  67 "
            pdb=" O   GLY C 214 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OH  TYR D  67 "
            pdb=" O   GLY D 214 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OH  TYR B  67 "
            pdb=" O   GLY B 214 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OH  TYR A  67 "
            pdb=" O   GLY A 214 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OE2 GLU D 175 "
            pdb=" OG1 THR D 221 "
     model   vdw
     2.343 3.040
  ... (remaining 67699 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.210
  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:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.780
  Find NCS groups from input model:        0.060
  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:10.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7840  Z= 0.127
  Angle     :  0.548   7.175  10664  Z= 0.281
  Chirality :  0.038   0.144   1180
  Planarity :  0.004   0.030   1312
  Dihedral  : 19.024 135.029   2696
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 20.42 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.26), residues: 972
  helix:  1.73 (0.19), residues: 672
  sheet:  None (None), residues: 0
  loop : -0.90 (0.38), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  35 
 TYR   0.019   0.001   TYR B 223 
 PHE   0.005   0.001   PHE C  76 
 TRP   0.007   0.001   TRP D 169 
 HIS   0.001   0.001   HIS C  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7840)
  covalent geometry    : angle       0.54832 (10664)
  hydrogen bonds       : bond        0.19071 (  540)
  hydrogen bonds       : angle       6.91910 ( 1596)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.279 
Fit side-chains
  outliers start: 20
  outliers final: 16
  residues processed: 124
  average time/residue: 0.6908
  time to fit residues: 89.7391
Evaluate side-chains
  132 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   36 GLU
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   36 GLU
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain B residue  219 MET
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   36 GLU
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  219 MET
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   36 GLU
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  219 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:   20.0000
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    6.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.142783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.126021 restraints weight = 7127.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 1.15
r_work: 0.3250 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   7840  Z= 0.265
  Angle     :  0.689   6.536  10664  Z= 0.369
  Chirality :  0.049   0.166   1180
  Planarity :  0.006   0.037   1312
  Dihedral  : 16.914 131.222   1180
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 17.80 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.79 (0.27), residues: 972
  helix:  2.00 (0.18), residues: 672
  sheet:  None (None), residues: 0
  loop : -0.70 (0.40), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D  35 
 TYR   0.024   0.003   TYR D 223 
 PHE   0.020   0.003   PHE B 236 
 TRP   0.015   0.003   TRP C 169 
 HIS   0.009   0.003   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00638 ( 7840)
  covalent geometry    : angle       0.68919 (10664)
  hydrogen bonds       : bond        0.05586 (  540)
  hydrogen bonds       : angle       4.96842 ( 1596)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A   36 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7729 (mt-10)
REVERT: A  219 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8285 (ptt)
REVERT: B   36 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7736 (mt-10)
REVERT: C   36 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7720 (mt-10)
REVERT: D   36 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7730 (mt-10)
REVERT: D  219 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8283 (ptt)
  outliers start: 20
  outliers final: 8
  residues processed: 128
  average time/residue: 0.6365
  time to fit residues: 85.9494
Evaluate side-chains
  134 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 GLU
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain B residue   36 GLU
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain C residue   36 GLU
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain D residue   36 GLU
Chi-restraints excluded: chain D residue  136 THR
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  219 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 95 optimal weight:    7.9990
   chunk 62 optimal weight:    6.9990
   chunk 92 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 74 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 11 optimal weight:   20.0000
   chunk 73 optimal weight:    2.9990
   chunk 91 optimal weight:    7.9990
   chunk 75 optimal weight:    5.9990
   overall best weight:    3.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.144970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.128396 restraints weight = 7154.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 1.14
r_work: 0.3280 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7840  Z= 0.170
  Angle     :  0.574   6.055  10664  Z= 0.310
  Chirality :  0.043   0.159   1180
  Planarity :  0.005   0.036   1312
  Dihedral  : 16.373 131.125   1170
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 18.06 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.19 (0.27), residues: 972
  helix:  2.31 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop : -0.65 (0.40), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  35 
 TYR   0.023   0.002   TYR B 223 
 PHE   0.015   0.002   PHE A 236 
 TRP   0.014   0.002   TRP A 169 
 HIS   0.006   0.002   HIS B  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 7840)
  covalent geometry    : angle       0.57353 (10664)
  hydrogen bonds       : bond        0.04623 (  540)
  hydrogen bonds       : angle       4.67335 ( 1596)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A   36 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7700 (mt-10)
REVERT: A  245 GLN cc_start: 0.8077 (mt0) cc_final: 0.7863 (mt0)
REVERT: B   36 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7707 (mt-10)
REVERT: B  245 GLN cc_start: 0.8077 (mt0) cc_final: 0.7861 (mt0)
REVERT: C   36 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7697 (mt-10)
REVERT: C  245 GLN cc_start: 0.8085 (mt0) cc_final: 0.7867 (mt0)
REVERT: D   36 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7710 (mt-10)
REVERT: D  245 GLN cc_start: 0.8085 (mt0) cc_final: 0.7866 (mt0)
  outliers start: 16
  outliers final: 8
  residues processed: 128
  average time/residue: 0.6333
  time to fit residues: 85.4523
Evaluate side-chains
  132 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 GLU
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain B residue   36 GLU
Chi-restraints excluded: chain B residue   58 MET
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain C residue   36 GLU
Chi-restraints excluded: chain C residue   58 MET
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain D residue   36 GLU
Chi-restraints excluded: chain D residue   58 MET
Chi-restraints excluded: chain D residue  154 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 52 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9980
   chunk 35 optimal weight:   20.0000
   chunk 63 optimal weight:    6.9990
   chunk 5 optimal weight:   10.0000
   chunk 62 optimal weight:    5.9990
   chunk 54 optimal weight:    9.9990
   chunk 67 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   overall best weight:    4.1986

-------------------------------------------------------------------------------
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 = 0.3596 r_free = 0.3596 target = 0.144069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.127426 restraints weight = 7289.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 1.16
r_work: 0.3265 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.1361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7840  Z= 0.189
  Angle     :  0.601   6.131  10664  Z= 0.324
  Chirality :  0.044   0.162   1180
  Planarity :  0.005   0.037   1312
  Dihedral  : 16.244 128.213   1164
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 16.49 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.17 (0.27), residues: 972
  helix:  2.34 (0.19), residues: 676
  sheet:  None (None), residues: 0
  loop : -0.75 (0.40), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  35 
 TYR   0.023   0.002   TYR A 223 
 PHE   0.017   0.002   PHE C 236 
 TRP   0.015   0.002   TRP C 169 
 HIS   0.005   0.002   HIS B  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 7840)
  covalent geometry    : angle       0.60118 (10664)
  hydrogen bonds       : bond        0.04739 (  540)
  hydrogen bonds       : angle       4.64575 ( 1596)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A   36 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7782 (mt-10)
REVERT: A  245 GLN cc_start: 0.8096 (mt0) cc_final: 0.7872 (mt0)
REVERT: B   36 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7787 (mt-10)
REVERT: B  245 GLN cc_start: 0.8090 (mt0) cc_final: 0.7864 (mt0)
REVERT: C   36 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7785 (mt-10)
REVERT: C  245 GLN cc_start: 0.8099 (mt0) cc_final: 0.7869 (mt0)
REVERT: D   36 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7792 (mt-10)
REVERT: D  245 GLN cc_start: 0.8110 (mt0) cc_final: 0.7877 (mt0)
  outliers start: 24
  outliers final: 16
  residues processed: 132
  average time/residue: 0.6090
  time to fit residues: 84.8472
Evaluate side-chains
  140 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 GLU
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain B residue   36 GLU
Chi-restraints excluded: chain B residue   58 MET
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain C residue   36 GLU
Chi-restraints excluded: chain C residue   58 MET
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  215 VAL
Chi-restraints excluded: chain D residue   36 GLU
Chi-restraints excluded: chain D residue   58 MET
Chi-restraints excluded: chain D residue  136 THR
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  215 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9990
   chunk 60 optimal weight:    5.9990
   chunk 55 optimal weight:    0.0050
   chunk 1 optimal weight:    6.9990
   chunk 11 optimal weight:   20.0000
   chunk 17 optimal weight:    8.9990
   chunk 86 optimal weight:   10.0000
   chunk 70 optimal weight:    0.0970
   chunk 42 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   overall best weight:    2.8198

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

Flipped N/Q/H residues before XYZ refinement:
A 165 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.145966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.129324 restraints weight = 7229.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 1.15
r_work: 0.3290 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7840  Z= 0.147
  Angle     :  0.553   6.003  10664  Z= 0.297
  Chirality :  0.042   0.155   1180
  Planarity :  0.005   0.035   1312
  Dihedral  : 15.560 126.000   1164
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 17.54 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.39 (0.27), residues: 972
  helix:  2.45 (0.19), residues: 684
  sheet:  None (None), residues: 0
  loop : -0.60 (0.41), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  35 
 TYR   0.022   0.002   TYR A 223 
 PHE   0.013   0.002   PHE B 236 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.005   0.001   HIS D  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7840)
  covalent geometry    : angle       0.55276 (10664)
  hydrogen bonds       : bond        0.04228 (  540)
  hydrogen bonds       : angle       4.51078 ( 1596)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A  245 GLN cc_start: 0.8089 (mt0) cc_final: 0.7868 (mt0)
REVERT: B  245 GLN cc_start: 0.8078 (mt0) cc_final: 0.7860 (mt0)
REVERT: C  245 GLN cc_start: 0.8076 (mt0) cc_final: 0.7856 (mt0)
REVERT: D  245 GLN cc_start: 0.8087 (mt0) cc_final: 0.7864 (mt0)
  outliers start: 16
  outliers final: 8
  residues processed: 128
  average time/residue: 0.5638
  time to fit residues: 76.2556
Evaluate side-chains
  128 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain B residue   58 MET
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain C residue   58 MET
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain D residue   58 MET
Chi-restraints excluded: chain D residue  136 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 22 optimal weight:    0.3980
   chunk 83 optimal weight:    6.9990
   chunk 67 optimal weight:    8.9990
   chunk 75 optimal weight:    8.9990
   chunk 30 optimal weight:    9.9990
   chunk 77 optimal weight:   20.0000
   chunk 24 optimal weight:   10.0000
   chunk 78 optimal weight:    0.9980
   chunk 27 optimal weight:    9.9990
   chunk 87 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    3.4786

-------------------------------------------------------------------------------
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 = 0.3612 r_free = 0.3612 target = 0.145196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.128365 restraints weight = 7189.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 1.15
r_work: 0.3279 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7840  Z= 0.168
  Angle     :  0.583   6.419  10664  Z= 0.311
  Chirality :  0.043   0.159   1180
  Planarity :  0.005   0.036   1312
  Dihedral  : 14.872 120.217   1148
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 16.10 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.31 (0.27), residues: 972
  helix:  2.46 (0.19), residues: 676
  sheet:  None (None), residues: 0
  loop : -0.74 (0.40), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  35 
 TYR   0.023   0.002   TYR D 223 
 PHE   0.015   0.002   PHE D 236 
 TRP   0.014   0.002   TRP A 169 
 HIS   0.004   0.001   HIS B  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 7840)
  covalent geometry    : angle       0.58349 (10664)
  hydrogen bonds       : bond        0.04450 (  540)
  hydrogen bonds       : angle       4.53477 ( 1596)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.304 
Fit side-chains
REVERT: A  245 GLN cc_start: 0.8086 (mt0) cc_final: 0.7860 (mt0)
REVERT: B  245 GLN cc_start: 0.8077 (mt0) cc_final: 0.7851 (mt0)
REVERT: C  245 GLN cc_start: 0.8080 (mt0) cc_final: 0.7850 (mt0)
REVERT: D  245 GLN cc_start: 0.8082 (mt0) cc_final: 0.7853 (mt0)
  outliers start: 23
  outliers final: 19
  residues processed: 135
  average time/residue: 0.5516
  time to fit residues: 78.8898
Evaluate side-chains
  139 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   58 MET
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   58 MET
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  215 VAL
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   58 MET
Chi-restraints excluded: chain D residue  136 THR
Chi-restraints excluded: chain D residue  154 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 54 optimal weight:    9.9990
   chunk 20 optimal weight:    4.9990
   chunk 86 optimal weight:    8.9990
   chunk 52 optimal weight:    9.9990
   chunk 37 optimal weight:    9.9990
   chunk 59 optimal weight:    6.9990
   chunk 69 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9990
   chunk 82 optimal weight:   10.0000
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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 = 0.3609 r_free = 0.3609 target = 0.144975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.128154 restraints weight = 7213.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 1.15
r_work: 0.3270 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7840  Z= 0.176
  Angle     :  0.592   6.756  10664  Z= 0.315
  Chirality :  0.043   0.161   1180
  Planarity :  0.005   0.037   1312
  Dihedral  : 14.677 119.361   1148
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 15.05 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.30 (0.27), residues: 972
  helix:  2.42 (0.19), residues: 676
  sheet:  None (None), residues: 0
  loop : -0.65 (0.40), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  35 
 TYR   0.022   0.002   TYR D 223 
 PHE   0.015   0.002   PHE D 236 
 TRP   0.014   0.002   TRP A 169 
 HIS   0.004   0.001   HIS C  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 7840)
  covalent geometry    : angle       0.59225 (10664)
  hydrogen bonds       : bond        0.04493 (  540)
  hydrogen bonds       : angle       4.55154 ( 1596)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 124
  time to evaluate  : 0.300 
Fit side-chains
REVERT: A   36 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7799 (mt-10)
REVERT: A  245 GLN cc_start: 0.8094 (mt0) cc_final: 0.7864 (mt0)
REVERT: A  275 PHE cc_start: 0.7726 (m-10) cc_final: 0.7494 (m-80)
REVERT: B   36 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7807 (mt-10)
REVERT: B  245 GLN cc_start: 0.8090 (mt0) cc_final: 0.7860 (mt0)
REVERT: B  275 PHE cc_start: 0.7721 (m-10) cc_final: 0.7488 (m-80)
REVERT: C   36 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7808 (mt-10)
REVERT: C  245 GLN cc_start: 0.8089 (mt0) cc_final: 0.7858 (mt0)
REVERT: C  275 PHE cc_start: 0.7719 (m-10) cc_final: 0.7488 (m-80)
REVERT: D   36 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7818 (mt-10)
REVERT: D  245 GLN cc_start: 0.8095 (mt0) cc_final: 0.7865 (mt0)
REVERT: D  275 PHE cc_start: 0.7727 (m-10) cc_final: 0.7498 (m-80)
  outliers start: 31
  outliers final: 20
  residues processed: 140
  average time/residue: 0.5129
  time to fit residues: 76.3147
Evaluate side-chains
  144 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   36 GLU
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   36 GLU
Chi-restraints excluded: chain B residue   58 MET
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   36 GLU
Chi-restraints excluded: chain C residue   58 MET
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  215 VAL
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   36 GLU
Chi-restraints excluded: chain D residue   58 MET
Chi-restraints excluded: chain D residue  136 THR
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  215 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 53 optimal weight:    6.9990
   chunk 11 optimal weight:   10.0000
   chunk 39 optimal weight:    9.9990
   chunk 91 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   chunk 46 optimal weight:    0.8980
   chunk 18 optimal weight:    6.9990
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
B 165 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.144692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.127812 restraints weight = 7269.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 1.16
r_work: 0.3269 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.1474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7840  Z= 0.182
  Angle     :  0.600   7.057  10664  Z= 0.319
  Chirality :  0.043   0.161   1180
  Planarity :  0.005   0.037   1312
  Dihedral  : 14.645 118.743   1148
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 15.97 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.31 (0.27), residues: 972
  helix:  2.39 (0.19), residues: 676
  sheet:  None (None), residues: 0
  loop : -0.54 (0.41), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  35 
 TYR   0.022   0.002   TYR D 223 
 PHE   0.016   0.002   PHE D 236 
 TRP   0.015   0.002   TRP A 169 
 HIS   0.004   0.001   HIS C  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 7840)
  covalent geometry    : angle       0.60048 (10664)
  hydrogen bonds       : bond        0.04543 (  540)
  hydrogen bonds       : angle       4.55017 ( 1596)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 120
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A   36 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7773 (mt-10)
REVERT: A  245 GLN cc_start: 0.8089 (mt0) cc_final: 0.7860 (mt0)
REVERT: A  275 PHE cc_start: 0.7734 (m-10) cc_final: 0.7521 (m-80)
REVERT: B   36 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7783 (mt-10)
REVERT: B  245 GLN cc_start: 0.8089 (mt0) cc_final: 0.7862 (mt0)
REVERT: B  275 PHE cc_start: 0.7731 (m-10) cc_final: 0.7519 (m-80)
REVERT: C   36 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7784 (mt-10)
REVERT: C  245 GLN cc_start: 0.8090 (mt0) cc_final: 0.7859 (mt0)
REVERT: C  275 PHE cc_start: 0.7725 (m-10) cc_final: 0.7513 (m-80)
REVERT: D   36 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7791 (mt-10)
REVERT: D  245 GLN cc_start: 0.8096 (mt0) cc_final: 0.7867 (mt0)
REVERT: D  275 PHE cc_start: 0.7736 (m-10) cc_final: 0.7527 (m-80)
  outliers start: 28
  outliers final: 20
  residues processed: 136
  average time/residue: 0.5515
  time to fit residues: 79.4893
Evaluate side-chains
  144 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   36 GLU
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   36 GLU
Chi-restraints excluded: chain B residue   58 MET
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   36 GLU
Chi-restraints excluded: chain C residue   58 MET
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  215 VAL
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   36 GLU
Chi-restraints excluded: chain D residue   58 MET
Chi-restraints excluded: chain D residue  136 THR
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  215 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 20 optimal weight:    7.9990
   chunk 59 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   chunk 31 optimal weight:    7.9990
   chunk 89 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 4 optimal weight:    9.9990
   chunk 9 optimal weight:    7.9990
   chunk 26 optimal weight:    6.9990
   chunk 7 optimal weight:    8.9990
   overall best weight:    6.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.142651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.125786 restraints weight = 7234.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.15
r_work: 0.3247 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.1537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   7840  Z= 0.249
  Angle     :  0.674   7.414  10664  Z= 0.358
  Chirality :  0.048   0.170   1180
  Planarity :  0.006   0.039   1312
  Dihedral  : 15.024 121.297   1148
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 15.97 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.98 (0.27), residues: 972
  helix:  2.06 (0.19), residues: 676
  sheet:  None (None), residues: 0
  loop : -0.43 (0.41), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C  35 
 TYR   0.023   0.003   TYR D 223 
 PHE   0.019   0.003   PHE D 236 
 TRP   0.015   0.002   TRP A 169 
 HIS   0.004   0.002   HIS C  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00600 ( 7840)
  covalent geometry    : angle       0.67361 (10664)
  hydrogen bonds       : bond        0.05154 (  540)
  hydrogen bonds       : angle       4.70906 ( 1596)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 112
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A   36 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7823 (mt-10)
REVERT: A  245 GLN cc_start: 0.8121 (mt0) cc_final: 0.7867 (mt0)
REVERT: B   36 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7817 (mt-10)
REVERT: B  245 GLN cc_start: 0.8107 (mt0) cc_final: 0.7854 (mt0)
REVERT: C   36 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7821 (mt-10)
REVERT: C  245 GLN cc_start: 0.8113 (mt0) cc_final: 0.7860 (mt0)
REVERT: D   36 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7821 (mt-10)
REVERT: D  245 GLN cc_start: 0.8124 (mt0) cc_final: 0.7866 (mt0)
  outliers start: 28
  outliers final: 24
  residues processed: 128
  average time/residue: 0.5771
  time to fit residues: 78.1618
Evaluate side-chains
  140 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 112
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   36 GLU
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue   61 ASN
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   36 GLU
Chi-restraints excluded: chain B residue   58 MET
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   36 GLU
Chi-restraints excluded: chain C residue   58 MET
Chi-restraints excluded: chain C residue   61 ASN
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  215 VAL
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   36 GLU
Chi-restraints excluded: chain D residue   58 MET
Chi-restraints excluded: chain D residue   61 ASN
Chi-restraints excluded: chain D residue  136 THR
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  215 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 77 optimal weight:    6.9990
   chunk 30 optimal weight:    6.9990
   chunk 42 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   chunk 37 optimal weight:    8.9990
   chunk 82 optimal weight:   10.0000
   chunk 4 optimal weight:    8.9990
   chunk 70 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   overall best weight:    3.5988

-------------------------------------------------------------------------------
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 = 0.3605 r_free = 0.3605 target = 0.144713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.127965 restraints weight = 7181.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 1.14
r_work: 0.3277 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7840  Z= 0.172
  Angle     :  0.596   7.446  10664  Z= 0.316
  Chirality :  0.043   0.163   1180
  Planarity :  0.005   0.037   1312
  Dihedral  : 14.717 120.419   1148
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 17.15 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.28 (0.27), residues: 972
  helix:  2.33 (0.19), residues: 676
  sheet:  None (None), residues: 0
  loop : -0.44 (0.41), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  35 
 TYR   0.022   0.002   TYR A 223 
 PHE   0.015   0.002   PHE A 236 
 TRP   0.015   0.002   TRP A 169 
 HIS   0.004   0.001   HIS C  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 7840)
  covalent geometry    : angle       0.59608 (10664)
  hydrogen bonds       : bond        0.04439 (  540)
  hydrogen bonds       : angle       4.55939 ( 1596)

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A   36 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7784 (mt-10)
REVERT: A  245 GLN cc_start: 0.8078 (mt0) cc_final: 0.7855 (mt0)
REVERT: B   36 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7784 (mt-10)
REVERT: B  245 GLN cc_start: 0.8066 (mt0) cc_final: 0.7847 (mt0)
REVERT: C   36 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7791 (mt-10)
REVERT: C  245 GLN cc_start: 0.8072 (mt0) cc_final: 0.7848 (mt0)
REVERT: D   36 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7791 (mt-10)
REVERT: D  245 GLN cc_start: 0.8079 (mt0) cc_final: 0.7855 (mt0)
  outliers start: 19
  outliers final: 15
  residues processed: 127
  average time/residue: 0.5770
  time to fit residues: 77.3950
Evaluate side-chains
  135 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 GLU
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain B residue   36 GLU
Chi-restraints excluded: chain B residue   58 MET
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain C residue   36 GLU
Chi-restraints excluded: chain C residue   58 MET
Chi-restraints excluded: chain C residue  136 THR
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  215 VAL
Chi-restraints excluded: chain D residue   36 GLU
Chi-restraints excluded: chain D residue   58 MET
Chi-restraints excluded: chain D residue  136 THR
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  215 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
C 165 HIS
D 165 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.148371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.131862 restraints weight = 7131.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 1.13
r_work: 0.3328 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7840  Z= 0.117
  Angle     :  0.515   5.907  10664  Z= 0.274
  Chirality :  0.039   0.147   1180
  Planarity :  0.004   0.034   1312
  Dihedral  : 14.111 112.215   1148
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 18.32 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.72 (0.28), residues: 972
  helix:  2.65 (0.19), residues: 684
  sheet:  None (None), residues: 0
  loop : -0.32 (0.41), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  35 
 TYR   0.020   0.001   TYR C 223 
 PHE   0.009   0.001   PHE D 236 
 TRP   0.013   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7840)
  covalent geometry    : angle       0.51520 (10664)
  hydrogen bonds       : bond        0.03628 (  540)
  hydrogen bonds       : angle       4.34212 ( 1596)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2398.75 seconds
wall clock time: 41 minutes 43.01 seconds (2503.01 seconds total)