Starting phenix.real_space_refine
on Mon Feb 10 19:56:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dwv_30887/02_2025/7dwv_30887.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dwv_30887/02_2025/7dwv_30887.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dwv_30887/02_2025/7dwv_30887.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dwv_30887/02_2025/7dwv_30887.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dwv_30887/02_2025/7dwv_30887.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dwv_30887/02_2025/7dwv_30887.cif"
  }
  resolution = 3.07
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      30      5.16       5
     C    1278      2.51       5
     N     354      2.21       5
     O     402      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 2064
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 344
          Classifications: {'peptide': 43}
          Link IDs: {'TRANS': 42}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 2.05, per 1000 atoms: 0.99
  Number of scatterers: 2064
  At special positions: 0
  Unit cell: (98.358, 84.162, 31.434, 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      30     16.00
     O     402      8.00
     N     354      7.00
     C    1278      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 179 " - pdb=" SG  CYS A 214 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.43
  Conformation dependent library (CDL) restraints added in 311.1 milliseconds
  

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  504

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 2 sheets defined
      0.0% alpha, 4.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 182
    Processing sheet with id=AA2, first strand: chain 'D' and resid 180 through 182

    8 hydrogen bonds defined for protein.
    24 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: 0.37

  Time building geometry restraints manager: 0.51 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 672
        1.34 -     1.45: 200
        1.45 -     1.57: 1162
        1.57 -     1.69: 0
        1.69 -     1.80: 48
  Bond restraints: 2082
  Sorted by residual:
  bond pdb=" CB  THR A 193 "
       pdb=" CG2 THR A 193 "
    ideal  model  delta    sigma   weight residual
    1.521  1.466  0.055 3.30e-02 9.18e+02 2.74e+00
  bond pdb=" CB  THR D 193 "
       pdb=" CG2 THR D 193 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.72e+00
  bond pdb=" CB  THR C 193 "
       pdb=" CG2 THR C 193 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.70e+00
  bond pdb=" CB  THR F 193 "
       pdb=" CG2 THR F 193 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.67e+00
  bond pdb=" CB  THR E 193 "
       pdb=" CG2 THR E 193 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.67e+00
  ... (remaining 2077 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.86: 2269
        0.86 -     1.72: 410
        1.72 -     2.58: 93
        2.58 -     3.45: 12
        3.45 -     4.31: 18
  Bond angle restraints: 2802
  Sorted by residual:
  angle pdb=" N   ASN C 181 "
        pdb=" CA  ASN C 181 "
        pdb=" C   ASN C 181 "
      ideal   model   delta    sigma   weight residual
     107.93  112.24   -4.31 1.65e+00 3.67e-01 6.82e+00
  angle pdb=" N   ASN D 181 "
        pdb=" CA  ASN D 181 "
        pdb=" C   ASN D 181 "
      ideal   model   delta    sigma   weight residual
     107.93  112.21   -4.28 1.65e+00 3.67e-01 6.74e+00
  angle pdb=" N   ASN F 181 "
        pdb=" CA  ASN F 181 "
        pdb=" C   ASN F 181 "
      ideal   model   delta    sigma   weight residual
     107.93  112.20   -4.27 1.65e+00 3.67e-01 6.71e+00
  angle pdb=" N   ASN A 181 "
        pdb=" CA  ASN A 181 "
        pdb=" C   ASN A 181 "
      ideal   model   delta    sigma   weight residual
     107.93  112.20   -4.27 1.65e+00 3.67e-01 6.70e+00
  angle pdb=" N   ASN B 181 "
        pdb=" CA  ASN B 181 "
        pdb=" C   ASN B 181 "
      ideal   model   delta    sigma   weight residual
     107.93  112.20   -4.27 1.65e+00 3.67e-01 6.69e+00
  ... (remaining 2797 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.64: 979
       11.64 -    23.29: 200
       23.29 -    34.93: 90
       34.93 -    46.57: 6
       46.57 -    58.21: 6
  Dihedral angle restraints: 1281
    sinusoidal: 525
      harmonic: 756
  Sorted by residual:
  dihedral pdb=" CA  MET C 206 "
           pdb=" C   MET C 206 "
           pdb=" N   GLU C 207 "
           pdb=" CA  GLU C 207 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.64  -14.36     0      5.00e+00 4.00e-02 8.25e+00
  dihedral pdb=" CA  MET E 206 "
           pdb=" C   MET E 206 "
           pdb=" N   GLU E 207 "
           pdb=" CA  GLU E 207 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.65  -14.35     0      5.00e+00 4.00e-02 8.24e+00
  dihedral pdb=" CA  MET A 206 "
           pdb=" C   MET A 206 "
           pdb=" N   GLU A 207 "
           pdb=" CA  GLU A 207 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.65  -14.35     0      5.00e+00 4.00e-02 8.24e+00
  ... (remaining 1278 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 115
       0.030 -    0.060: 127
       0.060 -    0.091: 62
       0.091 -    0.121: 32
       0.121 -    0.151: 24
  Chirality restraints: 360
  Sorted by residual:
  chirality pdb=" CB  THR C 183 "
            pdb=" CA  THR C 183 "
            pdb=" OG1 THR C 183 "
            pdb=" CG2 THR C 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.69e-01
  chirality pdb=" CB  THR A 183 "
            pdb=" CA  THR A 183 "
            pdb=" OG1 THR A 183 "
            pdb=" CG2 THR A 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.57e-01
  chirality pdb=" CB  THR D 183 "
            pdb=" CA  THR D 183 "
            pdb=" OG1 THR D 183 "
            pdb=" CG2 THR D 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.47e-01
  ... (remaining 357 not shown)

  Planarity restraints: 342
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS C 187 "   -0.009 2.00e-02 2.50e+03   9.09e-03 1.24e+00
        pdb=" CG  HIS C 187 "    0.019 2.00e-02 2.50e+03
        pdb=" ND1 HIS C 187 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 HIS C 187 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 HIS C 187 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE2 HIS C 187 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS E 187 "   -0.010 2.00e-02 2.50e+03   9.07e-03 1.23e+00
        pdb=" CG  HIS E 187 "    0.019 2.00e-02 2.50e+03
        pdb=" ND1 HIS E 187 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 HIS E 187 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 HIS E 187 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE2 HIS E 187 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 187 "   -0.009 2.00e-02 2.50e+03   8.96e-03 1.20e+00
        pdb=" CG  HIS B 187 "    0.019 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 187 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 187 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 187 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 187 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 339 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 38
        2.60 -     3.17: 1904
        3.17 -     3.75: 2913
        3.75 -     4.32: 3792
        4.32 -     4.90: 7663
  Nonbonded interactions: 16310
  Sorted by model distance:
  nonbonded pdb=" SG  CYS C 179 "
            pdb=" SG  CYS C 214 "
     model   vdw
     2.024 3.760
  nonbonded pdb=" SG  CYS B 179 "
            pdb=" SG  CYS B 214 "
     model   vdw
     2.024 3.760
  nonbonded pdb=" SG  CYS D 179 "
            pdb=" SG  CYS D 214 "
     model   vdw
     2.024 3.760
  nonbonded pdb=" SG  CYS E 179 "
            pdb=" SG  CYS E 214 "
     model   vdw
     2.024 3.760
  nonbonded pdb=" SG  CYS F 179 "
            pdb=" SG  CYS F 214 "
     model   vdw
     2.025 3.760
  ... (remaining 16305 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 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

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:             3.500
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     10.660
  Find NCS groups from input model:        0.040
  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:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
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      :  0.007   0.055   2082  Z= 0.469
  Angle     :  0.799   4.308   2802  Z= 0.475
  Chirality :  0.062   0.151    360
  Planarity :  0.003   0.009    342
  Dihedral  : 14.691  58.214    774
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 16.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 26.83 %
    Favored  : 73.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 28.57 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -7.45 (0.29), residues: 246
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.67 (0.22), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS D 187 
 PHE   0.007   0.002   PHE D 175 
 ARG   0.001   0.000   ARG E 208 

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

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

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  194 LYS cc_start: 0.8742 (mmmt) cc_final: 0.8526 (tppp)
REVERT: D  212 GLN cc_start: 0.8385 (mt0) cc_final: 0.8012 (mt0)
REVERT: E  217 GLN cc_start: 0.7454 (mt0) cc_final: 0.7237 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1317
  time to fit residues: 10.0485
Evaluate side-chains
  63 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 20 optimal weight:    0.4980
   chunk 18 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C 177 HIS
C 217 GLN
F 177 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.137361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.128478 restraints weight = 3453.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.4406 rms_B_bonded: 2.69
r_work: 0.4291 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.4291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2082  Z= 0.214
  Angle     :  0.636   5.113   2802  Z= 0.364
  Chirality :  0.052   0.137    360
  Planarity :  0.002   0.012    342
  Dihedral  :  5.148  11.740    258
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 25.61 %
    Favored  : 74.39 %
  Rotamer:
    Outliers :  9.92 %
    Allowed  : 25.40 %
    Favored  : 64.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.61 (0.35), residues: 246
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.03 (0.27), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS B 187 
 PHE   0.004   0.001   PHE F 175 
 ARG   0.000   0.000   ARG B 208 

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

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

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 65
  time to evaluate  : 0.360 
Fit side-chains
REVERT: A  194 LYS cc_start: 0.8755 (mmmt) cc_final: 0.8496 (tppp)
REVERT: D  212 GLN cc_start: 0.8613 (mt0) cc_final: 0.8229 (mt0)
REVERT: F  177 HIS cc_start: 0.6778 (m-70) cc_final: 0.6529 (m170)
  outliers start: 25
  outliers final: 20
  residues processed: 85
  average time/residue: 0.1123
  time to fit residues: 11.4147
Evaluate side-chains
  83 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  181 ASN
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  181 ASN
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  183 THR
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain E residue  176 VAL
Chi-restraints excluded: chain E residue  181 ASN
Chi-restraints excluded: chain E residue  183 THR
Chi-restraints excluded: chain E residue  189 VAL
Chi-restraints excluded: chain F residue  181 ASN
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  189 VAL
Chi-restraints excluded: chain F residue  192 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
E 217 GLN
F 217 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.135766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.126611 restraints weight = 3396.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.4299 rms_B_bonded: 2.72
r_work: 0.4201 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.4201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   2082  Z= 0.311
  Angle     :  0.705   4.541   2802  Z= 0.404
  Chirality :  0.056   0.142    360
  Planarity :  0.003   0.012    342
  Dihedral  :  5.759  13.153    258
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 14.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 28.46 %
    Favored  : 71.54 %
  Rotamer:
    Outliers : 20.24 %
    Allowed  : 22.22 %
    Favored  : 57.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.57 (0.35), residues: 246
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.00 (0.27), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS B 187 
 PHE   0.009   0.002   PHE F 175 
 ARG   0.000   0.000   ARG C 208 

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

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

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 62
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  194 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8546 (tppp)
REVERT: D  206 MET cc_start: 0.7436 (mtt) cc_final: 0.7040 (mtt)
REVERT: D  212 GLN cc_start: 0.8645 (mt0) cc_final: 0.8290 (mt0)
  outliers start: 51
  outliers final: 39
  residues processed: 102
  average time/residue: 0.0993
  time to fit residues: 12.3002
Evaluate side-chains
  99 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 60
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  181 ASN
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  181 ASN
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  193 THR
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  181 ASN
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  191 THR
Chi-restraints excluded: chain C residue  193 THR
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  183 THR
Chi-restraints excluded: chain D residue  191 THR
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  209 VAL
Chi-restraints excluded: chain E residue  176 VAL
Chi-restraints excluded: chain E residue  183 THR
Chi-restraints excluded: chain E residue  189 VAL
Chi-restraints excluded: chain E residue  191 THR
Chi-restraints excluded: chain E residue  193 THR
Chi-restraints excluded: chain E residue  209 VAL
Chi-restraints excluded: chain F residue  176 VAL
Chi-restraints excluded: chain F residue  181 ASN
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  189 VAL
Chi-restraints excluded: chain F residue  191 THR
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  193 THR
Chi-restraints excluded: chain F residue  206 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 3 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 11 optimal weight:    0.5980
   chunk 13 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C 177 HIS
F 217 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.139784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.130551 restraints weight = 3335.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.4355 rms_B_bonded: 2.74
r_work: 0.4256 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.4256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2082  Z= 0.204
  Angle     :  0.678   5.036   2802  Z= 0.384
  Chirality :  0.052   0.136    360
  Planarity :  0.003   0.014    342
  Dihedral  :  5.060  12.760    258
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 23.98 %
    Favored  : 76.02 %
  Rotamer:
    Outliers : 15.08 %
    Allowed  : 26.98 %
    Favored  : 57.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.33 (0.37), residues: 246
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.82 (0.29), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS B 187 
 PHE   0.004   0.001   PHE C 175 
 ARG   0.000   0.000   ARG C 208 

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

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

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 61
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  194 LYS cc_start: 0.8766 (mmmt) cc_final: 0.8450 (tppp)
REVERT: B  181 ASN cc_start: 0.7483 (OUTLIER) cc_final: 0.7280 (p0)
REVERT: D  206 MET cc_start: 0.7280 (mtt) cc_final: 0.6907 (mtt)
REVERT: D  212 GLN cc_start: 0.8551 (mt0) cc_final: 0.8179 (mt0)
REVERT: F  177 HIS cc_start: 0.6884 (m-70) cc_final: 0.6501 (m170)
  outliers start: 38
  outliers final: 31
  residues processed: 94
  average time/residue: 0.1058
  time to fit residues: 11.9851
Evaluate side-chains
  93 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 61
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 ASN
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  181 ASN
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  191 THR
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  183 THR
Chi-restraints excluded: chain D residue  190 THR
Chi-restraints excluded: chain D residue  191 THR
Chi-restraints excluded: chain D residue  209 VAL
Chi-restraints excluded: chain E residue  176 VAL
Chi-restraints excluded: chain E residue  183 THR
Chi-restraints excluded: chain E residue  189 VAL
Chi-restraints excluded: chain E residue  191 THR
Chi-restraints excluded: chain E residue  193 THR
Chi-restraints excluded: chain F residue  176 VAL
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  189 VAL
Chi-restraints excluded: chain F residue  191 THR
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  203 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 1 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C 177 HIS
F 217 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.141114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.131352 restraints weight = 3385.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.4374 rms_B_bonded: 2.79
r_work: 0.4269 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.4269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
moved from start:          0.2638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2082  Z= 0.184
  Angle     :  0.637   5.749   2802  Z= 0.359
  Chirality :  0.051   0.133    360
  Planarity :  0.002   0.014    342
  Dihedral  :  4.771  11.016    258
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 25.20 %
    Favored  : 74.80 %
  Rotamer:
    Outliers : 13.89 %
    Allowed  : 28.57 %
    Favored  : 57.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.18 (0.39), residues: 246
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.70 (0.29), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS E 187 
 PHE   0.004   0.001   PHE C 175 
 ARG   0.000   0.000   ARG C 208 

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

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

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 62
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  194 LYS cc_start: 0.8746 (mmmt) cc_final: 0.8438 (tppp)
REVERT: B  181 ASN cc_start: 0.7525 (OUTLIER) cc_final: 0.7317 (p0)
REVERT: D  206 MET cc_start: 0.7262 (mtt) cc_final: 0.6916 (mtt)
REVERT: D  212 GLN cc_start: 0.8584 (mt0) cc_final: 0.8227 (mt0)
REVERT: F  177 HIS cc_start: 0.6799 (m-70) cc_final: 0.6436 (m-70)
  outliers start: 35
  outliers final: 31
  residues processed: 95
  average time/residue: 0.1057
  time to fit residues: 12.0577
Evaluate side-chains
  93 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 61
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  181 ASN
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  181 ASN
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  191 THR
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  183 THR
Chi-restraints excluded: chain D residue  190 THR
Chi-restraints excluded: chain D residue  209 VAL
Chi-restraints excluded: chain E residue  181 ASN
Chi-restraints excluded: chain E residue  183 THR
Chi-restraints excluded: chain E residue  189 VAL
Chi-restraints excluded: chain E residue  190 THR
Chi-restraints excluded: chain E residue  191 THR
Chi-restraints excluded: chain F residue  176 VAL
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  189 VAL
Chi-restraints excluded: chain F residue  191 THR
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  203 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 22 optimal weight:    0.4980
   chunk 7 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
C 177 HIS
F 217 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.138201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.128811 restraints weight = 3362.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.4340 rms_B_bonded: 2.72
r_work: 0.4236 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.4236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2082  Z= 0.251
  Angle     :  0.697   6.275   2802  Z= 0.391
  Chirality :  0.053   0.136    360
  Planarity :  0.003   0.012    342
  Dihedral  :  5.210  11.985    258
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 15.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 24.80 %
    Favored  : 75.20 %
  Rotamer:
    Outliers : 17.46 %
    Allowed  : 25.00 %
    Favored  : 57.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.21 (0.38), residues: 246
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.73 (0.29), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS B 187 
 PHE   0.006   0.001   PHE C 175 
 ARG   0.000   0.000   ARG F 208 

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

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

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 61
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A  194 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8458 (tppp)
REVERT: D  206 MET cc_start: 0.7445 (mtt) cc_final: 0.7140 (mtt)
REVERT: D  212 GLN cc_start: 0.8525 (mt0) cc_final: 0.8180 (mt0)
REVERT: F  177 HIS cc_start: 0.6967 (m-70) cc_final: 0.6638 (m-70)
REVERT: F  190 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7791 (m)
  outliers start: 44
  outliers final: 40
  residues processed: 102
  average time/residue: 0.0885
  time to fit residues: 10.9834
Evaluate side-chains
  102 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 61
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  181 ASN
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  212 GLN
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  191 THR
Chi-restraints excluded: chain C residue  193 THR
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  183 THR
Chi-restraints excluded: chain D residue  190 THR
Chi-restraints excluded: chain D residue  191 THR
Chi-restraints excluded: chain D residue  209 VAL
Chi-restraints excluded: chain E residue  176 VAL
Chi-restraints excluded: chain E residue  181 ASN
Chi-restraints excluded: chain E residue  183 THR
Chi-restraints excluded: chain E residue  189 VAL
Chi-restraints excluded: chain E residue  190 THR
Chi-restraints excluded: chain E residue  191 THR
Chi-restraints excluded: chain E residue  203 VAL
Chi-restraints excluded: chain E residue  209 VAL
Chi-restraints excluded: chain F residue  176 VAL
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  189 VAL
Chi-restraints excluded: chain F residue  190 THR
Chi-restraints excluded: chain F residue  191 THR
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  203 VAL
Chi-restraints excluded: chain F residue  209 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
C 177 HIS
F 217 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.137211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.128019 restraints weight = 3474.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.4307 rms_B_bonded: 2.83
r_work: 0.4196 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.4196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.2723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   2082  Z= 0.299
  Angle     :  0.723   6.736   2802  Z= 0.406
  Chirality :  0.054   0.138    360
  Planarity :  0.003   0.013    342
  Dihedral  :  5.598  12.948    258
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 15.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 28.46 %
    Favored  : 71.54 %
  Rotamer:
    Outliers : 22.22 %
    Allowed  : 22.62 %
    Favored  : 55.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.23 (0.38), residues: 246
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.75 (0.29), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.003   HIS B 187 
 PHE   0.008   0.002   PHE E 175 
 ARG   0.000   0.000   ARG C 208 

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

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

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 61
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  194 LYS cc_start: 0.8731 (mmmt) cc_final: 0.8451 (tppp)
REVERT: D  206 MET cc_start: 0.7531 (mtt) cc_final: 0.7246 (mtt)
REVERT: D  212 GLN cc_start: 0.8551 (mt0) cc_final: 0.8194 (mt0)
REVERT: F  177 HIS cc_start: 0.6786 (m-70) cc_final: 0.6424 (m-70)
REVERT: F  190 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7781 (m)
  outliers start: 56
  outliers final: 52
  residues processed: 107
  average time/residue: 0.0959
  time to fit residues: 12.5561
Evaluate side-chains
  114 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 61
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  181 ASN
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  181 ASN
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  193 THR
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  206 MET
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  212 GLN
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  181 ASN
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  191 THR
Chi-restraints excluded: chain C residue  193 THR
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  183 THR
Chi-restraints excluded: chain D residue  190 THR
Chi-restraints excluded: chain D residue  191 THR
Chi-restraints excluded: chain D residue  209 VAL
Chi-restraints excluded: chain E residue  176 VAL
Chi-restraints excluded: chain E residue  183 THR
Chi-restraints excluded: chain E residue  187 HIS
Chi-restraints excluded: chain E residue  189 VAL
Chi-restraints excluded: chain E residue  190 THR
Chi-restraints excluded: chain E residue  191 THR
Chi-restraints excluded: chain E residue  193 THR
Chi-restraints excluded: chain E residue  203 VAL
Chi-restraints excluded: chain E residue  206 MET
Chi-restraints excluded: chain E residue  209 VAL
Chi-restraints excluded: chain F residue  176 VAL
Chi-restraints excluded: chain F residue  181 ASN
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  189 VAL
Chi-restraints excluded: chain F residue  190 THR
Chi-restraints excluded: chain F residue  191 THR
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  193 THR
Chi-restraints excluded: chain F residue  203 VAL
Chi-restraints excluded: chain F residue  209 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 217 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.136089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.127063 restraints weight = 3525.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.4293 rms_B_bonded: 2.79
r_work: 0.4183 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.4183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   2082  Z= 0.329
  Angle     :  0.746   6.942   2802  Z= 0.419
  Chirality :  0.055   0.139    360
  Planarity :  0.003   0.013    342
  Dihedral  :  5.848  13.360    258
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 15.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 25.61 %
    Favored  : 74.39 %
  Rotamer:
    Outliers : 22.62 %
    Allowed  : 23.41 %
    Favored  : 53.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.27 (0.38), residues: 246
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.78 (0.29), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.003   HIS E 187 
 PHE   0.009   0.002   PHE D 198 
 ARG   0.000   0.000   ARG B 208 

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

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

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 61
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  194 LYS cc_start: 0.8754 (mmmt) cc_final: 0.8489 (tppp)
REVERT: C  177 HIS cc_start: 0.6762 (m170) cc_final: 0.6558 (m-70)
REVERT: D  206 MET cc_start: 0.7540 (mtt) cc_final: 0.7279 (mtt)
REVERT: D  212 GLN cc_start: 0.8513 (mt0) cc_final: 0.8169 (mt0)
REVERT: F  177 HIS cc_start: 0.6822 (m-70) cc_final: 0.6445 (m-70)
REVERT: F  190 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7739 (m)
  outliers start: 57
  outliers final: 53
  residues processed: 108
  average time/residue: 0.0924
  time to fit residues: 12.2058
Evaluate side-chains
  115 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 61
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  181 ASN
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  181 ASN
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  193 THR
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  206 MET
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  212 GLN
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  181 ASN
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  191 THR
Chi-restraints excluded: chain C residue  193 THR
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  183 THR
Chi-restraints excluded: chain D residue  190 THR
Chi-restraints excluded: chain D residue  191 THR
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  209 VAL
Chi-restraints excluded: chain E residue  176 VAL
Chi-restraints excluded: chain E residue  183 THR
Chi-restraints excluded: chain E residue  187 HIS
Chi-restraints excluded: chain E residue  189 VAL
Chi-restraints excluded: chain E residue  190 THR
Chi-restraints excluded: chain E residue  191 THR
Chi-restraints excluded: chain E residue  193 THR
Chi-restraints excluded: chain E residue  203 VAL
Chi-restraints excluded: chain E residue  206 MET
Chi-restraints excluded: chain E residue  209 VAL
Chi-restraints excluded: chain F residue  176 VAL
Chi-restraints excluded: chain F residue  181 ASN
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  189 VAL
Chi-restraints excluded: chain F residue  190 THR
Chi-restraints excluded: chain F residue  191 THR
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  193 THR
Chi-restraints excluded: chain F residue  203 VAL
Chi-restraints excluded: chain F residue  209 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 21 optimal weight:    0.1980
   chunk 12 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.143081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.133628 restraints weight = 3442.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.4396 rms_B_bonded: 2.82
r_work: 0.4287 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.4287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.2891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2082  Z= 0.195
  Angle     :  0.675   6.367   2802  Z= 0.376
  Chirality :  0.051   0.135    360
  Planarity :  0.003   0.014    342
  Dihedral  :  4.937  12.306    258
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.95 %
    Favored  : 78.05 %
  Rotamer:
    Outliers : 17.06 %
    Allowed  : 28.97 %
    Favored  : 53.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.08 (0.40), residues: 246
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.63 (0.30), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS E 187 
 PHE   0.004   0.001   PHE B 175 
 ARG   0.000   0.000   ARG C 208 

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

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

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 61
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A  194 LYS cc_start: 0.8722 (mmmt) cc_final: 0.8435 (tppp)
REVERT: D  206 MET cc_start: 0.7235 (mtt) cc_final: 0.6944 (mtt)
REVERT: D  212 GLN cc_start: 0.8540 (mt0) cc_final: 0.8191 (mt0)
REVERT: F  177 HIS cc_start: 0.6742 (m-70) cc_final: 0.6291 (m170)
  outliers start: 43
  outliers final: 42
  residues processed: 100
  average time/residue: 0.0991
  time to fit residues: 11.9671
Evaluate side-chains
  103 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 61
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  181 ASN
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  181 ASN
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  206 MET
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  212 GLN
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  181 ASN
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  191 THR
Chi-restraints excluded: chain C residue  193 THR
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  183 THR
Chi-restraints excluded: chain D residue  187 HIS
Chi-restraints excluded: chain D residue  190 THR
Chi-restraints excluded: chain D residue  191 THR
Chi-restraints excluded: chain D residue  209 VAL
Chi-restraints excluded: chain E residue  176 VAL
Chi-restraints excluded: chain E residue  183 THR
Chi-restraints excluded: chain E residue  189 VAL
Chi-restraints excluded: chain E residue  190 THR
Chi-restraints excluded: chain E residue  191 THR
Chi-restraints excluded: chain E residue  209 VAL
Chi-restraints excluded: chain F residue  176 VAL
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  189 VAL
Chi-restraints excluded: chain F residue  191 THR
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  203 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.137685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.128767 restraints weight = 3418.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.4323 rms_B_bonded: 2.69
r_work: 0.4215 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.4215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   2082  Z= 0.307
  Angle     :  0.767   7.264   2802  Z= 0.427
  Chirality :  0.054   0.138    360
  Planarity :  0.003   0.013    342
  Dihedral  :  5.684  14.968    258
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 16.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 27.64 %
    Favored  : 72.36 %
  Rotamer:
    Outliers : 18.65 %
    Allowed  : 27.38 %
    Favored  : 53.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.17 (0.39), residues: 246
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.69 (0.30), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS F 187 
 PHE   0.008   0.002   PHE E 175 
 ARG   0.001   0.000   ARG B 208 

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

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

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 61
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A  194 LYS cc_start: 0.8717 (mmmt) cc_final: 0.8441 (tppp)
REVERT: A  213 MET cc_start: 0.7194 (ttt) cc_final: 0.6786 (ttt)
REVERT: D  206 MET cc_start: 0.7511 (mtt) cc_final: 0.7239 (mtt)
REVERT: D  212 GLN cc_start: 0.8470 (mt0) cc_final: 0.8145 (mt0)
REVERT: F  177 HIS cc_start: 0.6761 (m-70) cc_final: 0.6320 (m-70)
  outliers start: 47
  outliers final: 46
  residues processed: 102
  average time/residue: 0.0959
  time to fit residues: 11.9228
Evaluate side-chains
  107 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 61
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  181 ASN
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  181 ASN
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  206 MET
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  212 GLN
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  181 ASN
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  191 THR
Chi-restraints excluded: chain C residue  193 THR
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  183 THR
Chi-restraints excluded: chain D residue  187 HIS
Chi-restraints excluded: chain D residue  190 THR
Chi-restraints excluded: chain D residue  191 THR
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  209 VAL
Chi-restraints excluded: chain E residue  176 VAL
Chi-restraints excluded: chain E residue  183 THR
Chi-restraints excluded: chain E residue  189 VAL
Chi-restraints excluded: chain E residue  190 THR
Chi-restraints excluded: chain E residue  191 THR
Chi-restraints excluded: chain E residue  193 THR
Chi-restraints excluded: chain E residue  209 VAL
Chi-restraints excluded: chain F residue  176 VAL
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  189 VAL
Chi-restraints excluded: chain F residue  191 THR
Chi-restraints excluded: chain F residue  192 THR
Chi-restraints excluded: chain F residue  203 VAL
Chi-restraints excluded: chain F residue  209 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.138947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.129547 restraints weight = 3441.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.4346 rms_B_bonded: 2.86
r_work: 0.4234 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.4234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2082  Z= 0.268
  Angle     :  0.744   7.058   2802  Z= 0.414
  Chirality :  0.053   0.137    360
  Planarity :  0.003   0.013    342
  Dihedral  :  5.469  15.410    258
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 15.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 23.58 %
    Favored  : 76.42 %
  Rotamer:
    Outliers : 19.44 %
    Allowed  : 26.98 %
    Favored  : 53.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.15 (0.39), residues: 246
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.68 (0.30), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS C 187 
 PHE   0.008   0.002   PHE E 175 
 ARG   0.000   0.000   ARG B 208 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1803.95 seconds
wall clock time: 32 minutes 52.96 seconds (1972.96 seconds total)