Starting phenix.real_space_refine
on Fri May  9 13:01:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8spa_40677/05_2025/8spa_40677.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8spa_40677/05_2025/8spa_40677.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8spa_40677/05_2025/8spa_40677.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8spa_40677/05_2025/8spa_40677.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8spa_40677/05_2025/8spa_40677.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8spa_40677/05_2025/8spa_40677.cif"
  }
  resolution = 3.0
  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
-------------------------------------------------------------------------------
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=   0.002
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       5      5.16       5
     C    1210      2.51       5
     N     300      2.21       5
     O     355      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 1870
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 374
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 374
          Classifications: {'peptide': 49}
          Link IDs: {'PTRANS': 4, 'TRANS': 44}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 1.69, per 1000 atoms: 0.90
  Number of scatterers: 1870
  At special positions: 0
  Unit cell: (63.64, 61.06, 48.16, 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       5     16.00
     O     355      8.00
     N     300      7.00
     C    1210      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: 0.40
  Conformation dependent library (CDL) restraints added in 223.3 milliseconds
  

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  430

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 1 sheets defined
      0.0% alpha, 10.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 32 through 37
      removed outlier: 6.782A  pdb=" N   MET A  33 " --> pdb=" O   LEU C  34 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   GLN C  36 " --> pdb=" O   MET A  33 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   PHE A  35 " --> pdb=" O   GLN C  36 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   MET C  33 " --> pdb=" O   LEU E  34 " (cutoff:3.500A)
      removed outlier: 8.267A  pdb=" N   GLN E  36 " --> pdb=" O   MET C  33 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   PHE C  35 " --> pdb=" O   GLN E  36 " (cutoff:3.500A)

    10 hydrogen bonds defined for protein.
    30 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: 0.30

  Time building geometry restraints manager: 0.49 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 585
        1.34 -     1.46: 441
        1.46 -     1.57: 904
        1.57 -     1.69: 0
        1.69 -     1.80: 10
  Bond restraints: 1940
  Sorted by residual:
  bond pdb=" CB  VAL A  29 "
       pdb=" CG1 VAL A  29 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.30e+00
  bond pdb=" CB  VAL D  29 "
       pdb=" CG1 VAL D  29 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.26e+00
  bond pdb=" CB  VAL E  29 "
       pdb=" CG1 VAL E  29 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.26e+00
  bond pdb=" CB  VAL B  29 "
       pdb=" CG1 VAL B  29 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.25e+00
  bond pdb=" CB  VAL C  29 "
       pdb=" CG1 VAL C  29 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.24e+00
  ... (remaining 1935 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.10: 2416
        1.10 -     2.19: 169
        2.19 -     3.29: 54
        3.29 -     4.39: 6
        4.39 -     5.48: 10
  Bond angle restraints: 2655
  Sorted by residual:
  angle pdb=" C   PRO D  39 "
        pdb=" N   HIS D  40 "
        pdb=" CA  HIS D  40 "
      ideal   model   delta    sigma   weight residual
     122.08  118.87    3.21 1.59e+00 3.96e-01 4.06e+00
  angle pdb=" C   PRO B  39 "
        pdb=" N   HIS B  40 "
        pdb=" CA  HIS B  40 "
      ideal   model   delta    sigma   weight residual
     122.08  118.90    3.18 1.59e+00 3.96e-01 4.01e+00
  angle pdb=" C   PRO E  39 "
        pdb=" N   HIS E  40 "
        pdb=" CA  HIS E  40 "
      ideal   model   delta    sigma   weight residual
     122.08  118.90    3.18 1.59e+00 3.96e-01 4.00e+00
  angle pdb=" C   PRO A  39 "
        pdb=" N   HIS A  40 "
        pdb=" CA  HIS A  40 "
      ideal   model   delta    sigma   weight residual
     122.08  118.94    3.14 1.59e+00 3.96e-01 3.89e+00
  angle pdb=" C   PRO C  39 "
        pdb=" N   HIS C  40 "
        pdb=" CA  HIS C  40 "
      ideal   model   delta    sigma   weight residual
     122.08  118.97    3.11 1.59e+00 3.96e-01 3.83e+00
  ... (remaining 2650 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     6.72: 796
        6.72 -    13.44: 129
       13.44 -    20.17: 75
       20.17 -    26.89: 30
       26.89 -    33.61: 20
  Dihedral angle restraints: 1050
    sinusoidal: 380
      harmonic: 670
  Sorted by residual:
  dihedral pdb=" CA  HIS A  40 "
           pdb=" C   HIS A  40 "
           pdb=" N   HIS A  41 "
           pdb=" CA  HIS A  41 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.78   19.22     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  HIS B  40 "
           pdb=" C   HIS B  40 "
           pdb=" N   HIS B  41 "
           pdb=" CA  HIS B  41 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.82   19.18     0      5.00e+00 4.00e-02 1.47e+01
  dihedral pdb=" CA  HIS D  40 "
           pdb=" C   HIS D  40 "
           pdb=" N   HIS D  41 "
           pdb=" CA  HIS D  41 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.83   19.17     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 1047 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 151
       0.030 -    0.060: 94
       0.060 -    0.090: 23
       0.090 -    0.120: 7
       0.120 -    0.150: 10
  Chirality restraints: 285
  Sorted by residual:
  chirality pdb=" CA  HIS C  40 "
            pdb=" N   HIS C  40 "
            pdb=" C   HIS C  40 "
            pdb=" CB  HIS C  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.61e-01
  chirality pdb=" CA  HIS B  40 "
            pdb=" N   HIS B  40 "
            pdb=" C   HIS B  40 "
            pdb=" CB  HIS B  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.49e-01
  chirality pdb=" CA  HIS E  40 "
            pdb=" N   HIS E  40 "
            pdb=" C   HIS E  40 "
            pdb=" CB  HIS E  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.45e-01
  ... (remaining 282 not shown)

  Planarity restraints: 350
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN E  43 "    0.022 5.00e-02 4.00e+02   3.39e-02 1.84e+00
        pdb=" N   PRO E  44 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO E  44 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO E  44 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A  43 "    0.022 5.00e-02 4.00e+02   3.39e-02 1.84e+00
        pdb=" N   PRO A  44 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A  44 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  44 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B  43 "    0.022 5.00e-02 4.00e+02   3.38e-02 1.83e+00
        pdb=" N   PRO B  44 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO B  44 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B  44 "    0.019 5.00e-02 4.00e+02
  ... (remaining 347 not shown)

  Histogram of nonbonded interaction distances:
        2.61 -     3.07: 1221
        3.07 -     3.53: 1837
        3.53 -     3.99: 2653
        3.99 -     4.44: 3041
        4.44 -     4.90: 5102
  Nonbonded interactions: 13854
  Sorted by model distance:
  nonbonded pdb=" O   HIS D  40 "
            pdb=" ND1 HIS D  41 "
     model   vdw
     2.614 3.120
  nonbonded pdb=" O   HIS B  40 "
            pdb=" ND1 HIS B  41 "
     model   vdw
     2.614 3.120
  nonbonded pdb=" O   HIS E  40 "
            pdb=" ND1 HIS E  41 "
     model   vdw
     2.614 3.120
  nonbonded pdb=" O   HIS A  40 "
            pdb=" ND1 HIS A  41 "
     model   vdw
     2.614 3.120
  nonbonded pdb=" O   HIS C  40 "
            pdb=" ND1 HIS C  41 "
     model   vdw
     2.614 3.120
  ... (remaining 13849 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'
}

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:             2.360
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     9.310
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
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      :  0.006   0.038   1940  Z= 0.239
  Angle     :  0.753   5.482   2655  Z= 0.403
  Chirality :  0.045   0.150    285
  Planarity :  0.005   0.034    350
  Dihedral  : 10.816  33.609    620
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  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: -3.14 (0.42), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.38 (0.32), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.001   TRP D  10 
 HIS   0.005   0.002   HIS D  40 
 PHE   0.012   0.002   PHE A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21596 (   10)
  hydrogen bonds       : angle       7.11050 (   30)
  covalent geometry    : bond        0.00577 ( 1940)
  covalent geometry    : angle       0.75278 ( 2655)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.207 
Fit side-chains
REVERT: C   10 TRP cc_start: 0.7650 (t-100) cc_final: 0.6809 (t-100)
REVERT: D   19 GLU cc_start: 0.7977 (tt0) cc_final: 0.7568 (tm-30)
REVERT: E   33 MET cc_start: 0.8984 (mtp) cc_final: 0.8663 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.7518
  time to fit residues: 34.0301
Evaluate side-chains
  18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 = 0.3998 r_free = 0.3998 target = 0.097388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.082767 restraints weight = 4571.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3816 rms_B_bonded: 3.62
r_work: 0.3718 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   1940  Z= 0.142
  Angle     :  0.684   5.093   2655  Z= 0.344
  Chirality :  0.042   0.145    285
  Planarity :  0.003   0.018    350
  Dihedral  :  6.227  20.563    240
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 15.24 %
    Favored  : 82.38 %
  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: -2.77 (0.44), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.34), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  10 
 HIS   0.006   0.001   HIS C  40 
 PHE   0.011   0.001   PHE A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03721 (   10)
  hydrogen bonds       : angle       5.80590 (   30)
  covalent geometry    : bond        0.00357 ( 1940)
  covalent geometry    : angle       0.68421 ( 2655)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
REVERT: C   10 TRP cc_start: 0.7834 (t-100) cc_final: 0.7041 (t-100)
REVERT: D   19 GLU cc_start: 0.7858 (tt0) cc_final: 0.7414 (tm-30)
REVERT: E   33 MET cc_start: 0.9099 (mtp) cc_final: 0.8845 (mtt)
  outliers start: 5
  outliers final: 4
  residues processed: 32
  average time/residue: 0.7373
  time to fit residues: 24.3870
Evaluate side-chains
  25 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain D residue   21 SER
Chi-restraints excluded: chain D residue   49 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 10 optimal weight:    0.3980
   chunk 4 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 0 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.095044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.079624 restraints weight = 4406.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3911 rms_B_bonded: 3.76
r_work: 0.3803 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   1940  Z= 0.101
  Angle     :  0.630   6.059   2655  Z= 0.306
  Chirality :  0.040   0.137    285
  Planarity :  0.003   0.018    350
  Dihedral  :  5.693  20.409    240
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 17.62 %
    Favored  : 80.00 %
  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: -2.72 (0.44), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.34), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  10 
 HIS   0.005   0.001   HIS A  40 
 PHE   0.009   0.001   PHE C  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02268 (   10)
  hydrogen bonds       : angle       5.15890 (   30)
  covalent geometry    : bond        0.00257 ( 1940)
  covalent geometry    : angle       0.63035 ( 2655)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: C   10 TRP cc_start: 0.7832 (t-100) cc_final: 0.6592 (t-100)
REVERT: E   10 TRP cc_start: 0.7256 (t-100) cc_final: 0.5592 (p-90)
REVERT: E   33 MET cc_start: 0.8960 (mtp) cc_final: 0.7980 (pmt)
  outliers start: 5
  outliers final: 2
  residues processed: 29
  average time/residue: 0.5221
  time to fit residues: 15.8746
Evaluate side-chains
  24 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain D residue   49 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.092921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.077635 restraints weight = 4554.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 3.76
r_work: 0.3668 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   1940  Z= 0.136
  Angle     :  0.638   7.237   2655  Z= 0.313
  Chirality :  0.041   0.142    285
  Planarity :  0.003   0.024    350
  Dihedral  :  5.802  20.194    240
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 19.52 %
    Favored  : 78.57 %
  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: -2.62 (0.44), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.99 (0.34), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E  10 
 HIS   0.005   0.002   HIS C  40 
 PHE   0.011   0.001   PHE A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02453 (   10)
  hydrogen bonds       : angle       4.83946 (   30)
  covalent geometry    : bond        0.00344 ( 1940)
  covalent geometry    : angle       0.63806 ( 2655)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 27
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
REVERT: C   10 TRP cc_start: 0.7975 (t-100) cc_final: 0.6635 (t-100)
REVERT: E   10 TRP cc_start: 0.7305 (t-100) cc_final: 0.5493 (p-90)
REVERT: E   33 MET cc_start: 0.9158 (mtp) cc_final: 0.8014 (pmt)
  outliers start: 4
  outliers final: 1
  residues processed: 29
  average time/residue: 0.5169
  time to fit residues: 15.7150
Evaluate side-chains
  23 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   49 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 17 optimal weight:    0.0270
   chunk 4 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    1.1644

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

Flipped N/Q/H residues before XYZ refinement:
B  36 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.092553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.076998 restraints weight = 4596.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3869 rms_B_bonded: 3.75
r_work: 0.3746 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   1940  Z= 0.124
  Angle     :  0.629   8.602   2655  Z= 0.305
  Chirality :  0.040   0.138    285
  Planarity :  0.003   0.023    350
  Dihedral  :  5.786  20.199    240
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 20.48 %
    Favored  : 77.14 %
  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: -2.63 (0.44), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.99 (0.34), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  10 
 HIS   0.005   0.001   HIS C  40 
 PHE   0.009   0.001   PHE C  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02015 (   10)
  hydrogen bonds       : angle       4.51742 (   30)
  covalent geometry    : bond        0.00322 ( 1940)
  covalent geometry    : angle       0.62906 ( 2655)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8392 (p0)
REVERT: C   10 TRP cc_start: 0.7964 (t-100) cc_final: 0.6779 (t-100)
REVERT: E   10 TRP cc_start: 0.7311 (t-100) cc_final: 0.5472 (p-90)
REVERT: E   33 MET cc_start: 0.8983 (mtp) cc_final: 0.8054 (pmt)
  outliers start: 5
  outliers final: 2
  residues processed: 31
  average time/residue: 0.6230
  time to fit residues: 20.1376
Evaluate side-chains
  25 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain D residue   14 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
** B  36 GLN ** 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 = 0.3905 r_free = 0.3905 target = 0.087461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.072769 restraints weight = 4738.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 3.66
r_work: 0.3634 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   1940  Z= 0.197
  Angle     :  0.678   8.688   2655  Z= 0.342
  Chirality :  0.043   0.151    285
  Planarity :  0.003   0.023    350
  Dihedral  :  6.170  19.836    240
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 19.52 %
    Favored  : 74.76 %
  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: -2.70 (0.43), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.05 (0.33), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP E  10 
 HIS   0.005   0.002   HIS C  40 
 PHE   0.012   0.002   PHE C  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02777 (   10)
  hydrogen bonds       : angle       4.46324 (   30)
  covalent geometry    : bond        0.00485 ( 1940)
  covalent geometry    : angle       0.67835 ( 2655)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 19
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
REVERT: C   10 TRP cc_start: 0.8118 (t-100) cc_final: 0.7370 (t-100)
REVERT: E   33 MET cc_start: 0.9353 (mtp) cc_final: 0.8192 (pmt)
  outliers start: 12
  outliers final: 8
  residues processed: 28
  average time/residue: 0.4101
  time to fit residues: 12.1700
Evaluate side-chains
  26 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 18
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain D residue   14 THR
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   42 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0670
   chunk 9 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    1.4124

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

Flipped N/Q/H residues before XYZ refinement:
** B  36 GLN ** 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 = 0.4071 r_free = 0.4071 target = 0.105537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 20)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.089357 restraints weight = 4721.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3890 rms_B_bonded: 3.37
r_work: 0.3784 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   1940  Z= 0.142
  Angle     :  0.649   9.452   2655  Z= 0.315
  Chirality :  0.040   0.141    285
  Planarity :  0.003   0.023    350
  Dihedral  :  5.959  20.197    240
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 20.95 %
    Favored  : 74.29 %
  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: -2.73 (0.44), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.33), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  10 
 HIS   0.005   0.001   HIS C  40 
 PHE   0.010   0.001   PHE A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01999 (   10)
  hydrogen bonds       : angle       4.18582 (   30)
  covalent geometry    : bond        0.00364 ( 1940)
  covalent geometry    : angle       0.64895 ( 2655)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 19
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: C   10 TRP cc_start: 0.7997 (t-100) cc_final: 0.7342 (t-100)
REVERT: E   33 MET cc_start: 0.9265 (mtp) cc_final: 0.8242 (pmt)
REVERT: E   49 THR cc_start: 0.8726 (p) cc_final: 0.8421 (t)
  outliers start: 10
  outliers final: 9
  residues processed: 26
  average time/residue: 0.4808
  time to fit residues: 13.1965
Evaluate side-chains
  27 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 18
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain D residue   14 THR
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   42 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** B  36 GLN ** 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 = 0.3982 r_free = 0.3982 target = 0.092946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.077111 restraints weight = 4862.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 3.71
r_work: 0.3752 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.2885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   1940  Z= 0.164
  Angle     :  0.656   9.572   2655  Z= 0.323
  Chirality :  0.041   0.145    285
  Planarity :  0.003   0.022    350
  Dihedral  :  6.002  19.716    240
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 20.95 %
    Favored  : 74.29 %
  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: -2.74 (0.44), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.08 (0.33), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  10 
 HIS   0.005   0.001   HIS C  40 
 PHE   0.011   0.001   PHE C  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02228 (   10)
  hydrogen bonds       : angle       4.25522 (   30)
  covalent geometry    : bond        0.00413 ( 1940)
  covalent geometry    : angle       0.65638 ( 2655)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 19
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
REVERT: C   10 TRP cc_start: 0.8104 (t-100) cc_final: 0.7359 (t-100)
REVERT: E   33 MET cc_start: 0.9329 (mtp) cc_final: 0.8239 (pmt)
REVERT: E   49 THR cc_start: 0.8668 (p) cc_final: 0.8369 (t)
  outliers start: 10
  outliers final: 10
  residues processed: 26
  average time/residue: 0.3832
  time to fit residues: 10.6676
Evaluate side-chains
  29 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 19
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain D residue   14 THR
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   42 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 4 optimal weight:    0.1980
   chunk 0 optimal weight:    2.9990
   chunk 12 optimal weight:    0.1980
   chunk 14 optimal weight:    0.2980
   chunk 15 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
B  36 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.177653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4622 r_free = 0.4622 target = 0.146864 restraints weight = 4902.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 2.26
r_work: 0.3849 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3779 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   1940  Z= 0.101
  Angle     :  0.615   9.554   2655  Z= 0.291
  Chirality :  0.039   0.130    285
  Planarity :  0.003   0.023    350
  Dihedral  :  5.571  20.459    240
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 20.95 %
    Favored  : 74.29 %
  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: -2.73 (0.44), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.34), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  10 
 HIS   0.005   0.001   HIS C  40 
 PHE   0.009   0.001   PHE B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01319 (   10)
  hydrogen bonds       : angle       3.94950 (   30)
  covalent geometry    : bond        0.00274 ( 1940)
  covalent geometry    : angle       0.61466 ( 2655)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 28
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: C   10 TRP cc_start: 0.7921 (t-100) cc_final: 0.6619 (t-100)
REVERT: E   10 TRP cc_start: 0.7342 (t-100) cc_final: 0.5593 (p-90)
REVERT: E   22 PHE cc_start: 0.8482 (m-10) cc_final: 0.8274 (m-10)
REVERT: E   33 MET cc_start: 0.8999 (mtp) cc_final: 0.8074 (pmt)
REVERT: E   49 THR cc_start: 0.8426 (p) cc_final: 0.8135 (t)
  outliers start: 10
  outliers final: 8
  residues processed: 35
  average time/residue: 0.4552
  time to fit residues: 16.7586
Evaluate side-chains
  31 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 23
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain D residue   14 THR
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   49 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 4 optimal weight:    0.0980
   chunk 1 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** B  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  40 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.105603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.089292 restraints weight = 4879.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3892 rms_B_bonded: 3.44
r_work: 0.3793 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   1940  Z= 0.155
  Angle     :  0.696   9.884   2655  Z= 0.327
  Chirality :  0.042   0.142    285
  Planarity :  0.003   0.020    350
  Dihedral  :  5.730  18.799    240
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 23.33 %
    Favored  : 72.38 %
  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: -2.74 (0.44), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.08 (0.33), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  10 
 HIS   0.005   0.002   HIS C  40 
 PHE   0.012   0.001   PHE C  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02479 (   10)
  hydrogen bonds       : angle       4.06399 (   30)
  covalent geometry    : bond        0.00394 ( 1940)
  covalent geometry    : angle       0.69605 ( 2655)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 18
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: C   10 TRP cc_start: 0.7940 (t-100) cc_final: 0.7288 (t-100)
REVERT: E   33 MET cc_start: 0.9265 (mtp) cc_final: 0.8263 (pmt)
REVERT: E   49 THR cc_start: 0.8484 (p) cc_final: 0.8173 (t)
  outliers start: 9
  outliers final: 9
  residues processed: 25
  average time/residue: 0.4000
  time to fit residues: 10.6519
Evaluate side-chains
  27 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 18
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain D residue   14 THR
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   40 HIS
Chi-restraints excluded: chain D residue   49 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 14 optimal weight:    0.0980
   chunk 6 optimal weight:    0.8980
   chunk 5 optimal weight:    8.9990
   chunk 11 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  36 GLN
D  40 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.108484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.092357 restraints weight = 4854.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 3.45
r_work: 0.3846 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.3147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   1940  Z= 0.101
  Angle     :  0.668   9.845   2655  Z= 0.304
  Chirality :  0.040   0.133    285
  Planarity :  0.003   0.019    350
  Dihedral  :  5.574  19.402    240
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 23.81 %
    Favored  : 72.38 %
  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: -2.72 (0.44), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.34), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  10 
 HIS   0.005   0.001   HIS C  40 
 PHE   0.009   0.001   PHE B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01314 (   10)
  hydrogen bonds       : angle       3.93052 (   30)
  covalent geometry    : bond        0.00276 ( 1940)
  covalent geometry    : angle       0.66783 ( 2655)

===============================================================================
Job complete
usr+sys time: 1625.25 seconds
wall clock time: 28 minutes 51.37 seconds (1731.37 seconds total)