Starting phenix.real_space_refine
on Fri Aug 22 13:17:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xtk_33451/08_2025/7xtk_33451_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xtk_33451/08_2025/7xtk_33451.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xtk_33451/08_2025/7xtk_33451.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xtk_33451/08_2025/7xtk_33451.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xtk_33451/08_2025/7xtk_33451_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xtk_33451/08_2025/7xtk_33451_neut.cif"
  }
  resolution = 2.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.062
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      10      5.16       5
     C    2105      2.51       5
     N     516      2.21       5
     O     528      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3159
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3159
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 395, 3159
          Classifications: {'peptide': 395}
          Link IDs: {'PTRANS': 13, 'TRANS': 381}
          Chain breaks: 1
  Time building chain proxies: 0.71, per 1000 atoms: 0.22
  Number of scatterers: 3159
  At special positions: 0
  Unit cell: (72.165, 54.336, 73.014, 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      10     16.00
     O     528      8.00
     N     516      7.00
     C    2105      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: 0.16
  Conformation dependent library (CDL) restraints added in 69.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  746

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 0 sheets defined
      80.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 38
    Processing helix  chain 'A' and resid 47 through 53
    Processing helix  chain 'A' and resid 60 through 69
    Processing helix  chain 'A' and resid 69 through 91
      removed outlier: 4.200A  pdb=" N   SER A  73 " --> pdb=" O   THR A  69 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   TYR A  74 " --> pdb=" O   PRO A  70 " (cutoff:3.500A)
      Proline residue:  A  82  - end of helix
      removed outlier: 4.672A  pdb=" N   LEU A  85 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ASP A  88 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 112
      removed outlier: 4.155A  pdb=" N   VAL A  95 " --> pdb=" O   ARG A  91 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LEU A 111 " --> pdb=" O   TRP A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 133
      removed outlier: 3.899A  pdb=" N   MET A 119 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 144
    Processing helix  chain 'A' and resid 148 through 176
      removed outlier: 3.510A  pdb=" N   LEU A 161 " --> pdb=" O   ARG A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 200
      removed outlier: 3.748A  pdb=" N   LEU A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ASN A 186 " --> pdb=" O   PHE A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 263
    Processing helix  chain 'A' and resid 266 through 288
      removed outlier: 3.802A  pdb=" N   TRP A 270 " --> pdb=" O   GLN A 266 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   SER A 271 " --> pdb=" O   LEU A 267 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   LEU A 272 " --> pdb=" O   ARG A 268 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   TRP A 273 " --> pdb=" O   LEU A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 296
      removed outlier: 3.769A  pdb=" N   GLU A 294 " --> pdb=" O   ILE A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 324
    Processing helix  chain 'A' and resid 336 through 355
      removed outlier: 3.542A  pdb=" N   LEU A 352 " --> pdb=" O   GLY A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 388
      removed outlier: 3.835A  pdb=" N   CYS A 365 " --> pdb=" O   SER A 361 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE A 369 " --> pdb=" O   CYS A 365 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU A 371 " --> pdb=" O   ALA A 367 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE A 372 " --> pdb=" O   ALA A 368 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   LEU A 379 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   VAL A 380 " --> pdb=" O   TYR A 376 " (cutoff:3.500A)
      Proline residue:  A 381  - end of helix
    Processing helix  chain 'A' and resid 392 through 419
      removed outlier: 3.734A  pdb=" N   ALA A 397 " --> pdb=" O   LYS A 393 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LEU A 398 " --> pdb=" O   GLU A 394 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR A 404 " --> pdb=" O   PHE A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 453

    217 hydrogen bonds defined for protein.
    651 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: 0.29

  Time building geometry restraints manager: 0.21 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: 935
        1.34 -     1.46: 745
        1.46 -     1.58: 1549
        1.58 -     1.69: 0
        1.69 -     1.81: 16
  Bond restraints: 3245
  Sorted by residual:
  bond pdb=" C   MET A 254 "
       pdb=" N   LEU A 255 "
    ideal  model  delta    sigma   weight residual
    1.332  1.294  0.038 1.40e-02 5.10e+03 7.37e+00
  bond pdb=" CB  ARG A 205 "
       pdb=" CG  ARG A 205 "
    ideal  model  delta    sigma   weight residual
    1.520  1.460  0.060 3.00e-02 1.11e+03 3.99e+00
  bond pdb=" C   VAL A  81 "
       pdb=" N   PRO A  82 "
    ideal  model  delta    sigma   weight residual
    1.334  1.363 -0.029 2.34e-02 1.83e+03 1.54e+00
  bond pdb=" CG  LEU A 258 "
       pdb=" CD2 LEU A 258 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.48e+00
  bond pdb=" C   LEU A 251 "
       pdb=" O   LEU A 251 "
    ideal  model  delta    sigma   weight residual
    1.233  1.250 -0.018 1.47e-02 4.63e+03 1.45e+00
  ... (remaining 3240 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 4320
        2.31 -     4.62: 87
        4.62 -     6.92: 12
        6.92 -     9.23: 2
        9.23 -    11.54: 2
  Bond angle restraints: 4423
  Sorted by residual:
  angle pdb=" N   ARG A 333 "
        pdb=" CA  ARG A 333 "
        pdb=" C   ARG A 333 "
      ideal   model   delta    sigma   weight residual
     114.64  103.10   11.54 1.52e+00 4.33e-01 5.76e+01
  angle pdb=" N   ARG A 205 "
        pdb=" CA  ARG A 205 "
        pdb=" C   ARG A 205 "
      ideal   model   delta    sigma   weight residual
     110.13  115.16   -5.03 1.15e+00 7.56e-01 1.91e+01
  angle pdb=" N   VAL A 327 "
        pdb=" CA  VAL A 327 "
        pdb=" C   VAL A 327 "
      ideal   model   delta    sigma   weight residual
     106.21  110.71   -4.50 1.07e+00 8.73e-01 1.77e+01
  angle pdb=" N   ARG A 148 "
        pdb=" CA  ARG A 148 "
        pdb=" C   ARG A 148 "
      ideal   model   delta    sigma   weight residual
     114.64  108.47    6.17 1.52e+00 4.33e-01 1.65e+01
  angle pdb=" CA  ARG A 333 "
        pdb=" C   ARG A 333 "
        pdb=" N   TRP A 334 "
      ideal   model   delta    sigma   weight residual
     119.58  114.22    5.36 1.39e+00 5.18e-01 1.48e+01
  ... (remaining 4418 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.46: 1668
       16.46 -    32.91: 160
       32.91 -    49.37: 29
       49.37 -    65.83: 6
       65.83 -    82.28: 2
  Dihedral angle restraints: 1865
    sinusoidal: 703
      harmonic: 1162
  Sorted by residual:
  dihedral pdb=" CA  ALA A 252 "
           pdb=" C   ALA A 252 "
           pdb=" N   ARG A 253 "
           pdb=" CA  ARG A 253 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -145.79  -34.21     0      5.00e+00 4.00e-02 4.68e+01
  dihedral pdb=" CA  LEU A 255 "
           pdb=" C   LEU A 255 "
           pdb=" N   ARG A 256 "
           pdb=" CA  ARG A 256 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.93   27.07     0      5.00e+00 4.00e-02 2.93e+01
  dihedral pdb=" CA  ARG A  91 "
           pdb=" C   ARG A  91 "
           pdb=" N   TYR A  92 "
           pdb=" CA  TYR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.56  -23.44     0      5.00e+00 4.00e-02 2.20e+01
  ... (remaining 1862 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 397
       0.046 -    0.092: 105
       0.092 -    0.137: 16
       0.137 -    0.183: 0
       0.183 -    0.229: 1
  Chirality restraints: 519
  Sorted by residual:
  chirality pdb=" CA  PHE A 202 "
            pdb=" N   PHE A 202 "
            pdb=" C   PHE A 202 "
            pdb=" CB  PHE A 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CA  THR A  49 "
            pdb=" N   THR A  49 "
            pdb=" C   THR A  49 "
            pdb=" CB  THR A  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.41    0.12 2.00e-01 2.50e+01 3.62e-01
  chirality pdb=" CA  TRP A 107 "
            pdb=" N   TRP A 107 "
            pdb=" C   TRP A 107 "
            pdb=" CB  TRP A 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.50e-01
  ... (remaining 516 not shown)

  Planarity restraints: 534
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 254 "    0.026 2.00e-02 2.50e+03   5.25e-02 2.76e+01
        pdb=" C   MET A 254 "   -0.091 2.00e-02 2.50e+03
        pdb=" O   MET A 254 "    0.035 2.00e-02 2.50e+03
        pdb=" N   LEU A 255 "    0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  81 "   -0.056 5.00e-02 4.00e+02   8.65e-02 1.20e+01
        pdb=" N   PRO A  82 "    0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO A  82 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A  82 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  69 "    0.045 5.00e-02 4.00e+02   6.75e-02 7.30e+00
        pdb=" N   PRO A  70 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A  70 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A  70 "    0.038 5.00e-02 4.00e+02
  ... (remaining 531 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.48: 13
        2.48 -     3.08: 2206
        3.08 -     3.69: 4527
        3.69 -     4.29: 7039
        4.29 -     4.90: 11724
  Nonbonded interactions: 25509
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 253 "
            pdb=" N   LEU A 255 "
     model   vdw
     1.873 3.120
  nonbonded pdb=" O   TYR A 139 "
            pdb=" NH2 ARG A 205 "
     model   vdw
     2.099 3.120
  nonbonded pdb=" O   PRO A  43 "
            pdb=" OG  SER A 189 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O   ILE A  41 "
            pdb=" OG  SER A 167 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   LEU A 251 "
            pdb=" O   ARG A 253 "
     model   vdw
     2.263 3.040
  ... (remaining 25504 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.890
  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:          0.030
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.490
  Find NCS groups from input model:        0.010
  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:5.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
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      :  0.004   0.060   3245  Z= 0.207
  Angle     :  0.872  11.540   4423  Z= 0.539
  Chirality :  0.041   0.229    519
  Planarity :  0.008   0.087    534
  Dihedral  : 13.372  82.282   1119
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  1.28 %
    Allowed  :  6.39 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.05 (0.43), residues: 391
  helix:  0.43 (0.31), residues: 298
  sheet:  None (None), residues: 0
  loop : -4.46 (0.50), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 133 
 TYR   0.025   0.002   TYR A 139 
 PHE   0.015   0.001   PHE A  84 
 TRP   0.013   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 289 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 3245)
  covalent geometry    : angle       0.87198 ( 4423)
  hydrogen bonds       : bond        0.17000 (  217)
  hydrogen bonds       : angle       6.01405 (  651)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.095 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.2356
  time to fit residues: 8.6702
Evaluate side-chains
  28 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.4980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0770
   chunk 30 optimal weight:    0.0870
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.3916

-------------------------------------------------------------------------------
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 = 0.3699 r_free = 0.3699 target = 0.148358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.124063 restraints weight = 3442.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 1.89
r_work: 0.3380 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3256 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.0846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   3245  Z= 0.163
  Angle     :  0.691   8.416   4423  Z= 0.358
  Chirality :  0.040   0.197    519
  Planarity :  0.007   0.065    534
  Dihedral  :  5.356  27.035    440
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  1.02 %
    Allowed  :  6.65 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  6.19 %
    Favored  : 92.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.44), residues: 391
  helix:  1.09 (0.31), residues: 302
  sheet:  None (None), residues: 0
  loop : -4.40 (0.52), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 133 
 TYR   0.016   0.001   TYR A 139 
 PHE   0.009   0.001   PHE A 372 
 TRP   0.010   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 289 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 3245)
  covalent geometry    : angle       0.69095 ( 4423)
  hydrogen bonds       : bond        0.06084 (  217)
  hydrogen bonds       : angle       4.84675 (  651)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.117 
Fit side-chains
  outliers start: 3
  outliers final: 0
  residues processed: 36
  average time/residue: 0.2698
  time to fit residues: 10.2421
Evaluate side-chains
  30 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A  66 ASN
A 277 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.143004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.119315 restraints weight = 3476.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 1.83
r_work: 0.3342 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.1260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.073   3245  Z= 0.228
  Angle     :  0.736   7.744   4423  Z= 0.377
  Chirality :  0.042   0.208    519
  Planarity :  0.007   0.063    534
  Dihedral  :  5.519  31.433    440
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  1.02 %
    Allowed  :  7.16 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  7.96 %
    Favored  : 91.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.44), residues: 391
  helix:  1.14 (0.31), residues: 301
  sheet:  None (None), residues: 0
  loop : -4.34 (0.50), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 205 
 TYR   0.024   0.002   TYR A 139 
 PHE   0.024   0.002   PHE A 202 
 TRP   0.009   0.002   TRP A 107 
 HIS   0.003   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 ( 3245)
  covalent geometry    : angle       0.73594 ( 4423)
  hydrogen bonds       : bond        0.07001 (  217)
  hydrogen bonds       : angle       4.87809 (  651)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.069 
Fit side-chains
REVERT: A  303 ARG cc_start: 0.7941 (mtp85) cc_final: 0.7606 (mtp-110)
  outliers start: 3
  outliers final: 2
  residues processed: 39
  average time/residue: 0.4016
  time to fit residues: 16.1703
Evaluate side-chains
  32 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 30
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  258 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3684 r_free = 0.3684 target = 0.146116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.123204 restraints weight = 3453.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.70
r_work: 0.3343 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   3245  Z= 0.172
  Angle     :  0.644   7.896   4423  Z= 0.333
  Chirality :  0.040   0.197    519
  Planarity :  0.006   0.063    534
  Dihedral  :  5.416  30.683    440
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  1.02 %
    Allowed  :  7.16 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  9.73 %
    Favored  : 88.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.44), residues: 391
  helix:  1.40 (0.31), residues: 299
  sheet:  None (None), residues: 0
  loop : -4.10 (0.53), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 208 
 TYR   0.023   0.002   TYR A 139 
 PHE   0.012   0.001   PHE A 202 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 3245)
  covalent geometry    : angle       0.64363 ( 4423)
  hydrogen bonds       : bond        0.05939 (  217)
  hydrogen bonds       : angle       4.71217 (  651)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 0.069 
Fit side-chains
REVERT: A   58 ASN cc_start: 0.8685 (m-40) cc_final: 0.8358 (m-40)
  outliers start: 7
  outliers final: 3
  residues processed: 39
  average time/residue: 0.2330
  time to fit residues: 9.6529
Evaluate side-chains
  33 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 30
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  258 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3669 r_free = 0.3669 target = 0.144472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.121484 restraints weight = 3444.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 1.71
r_work: 0.3321 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   3245  Z= 0.188
  Angle     :  0.660   7.708   4423  Z= 0.340
  Chirality :  0.040   0.196    519
  Planarity :  0.006   0.060    534
  Dihedral  :  5.380  29.969    440
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  :  7.16 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 11.50 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.44), residues: 391
  helix:  1.32 (0.31), residues: 303
  sheet:  None (None), residues: 0
  loop : -3.92 (0.56), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 208 
 TYR   0.024   0.002   TYR A 139 
 PHE   0.014   0.001   PHE A 372 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 3245)
  covalent geometry    : angle       0.65988 ( 4423)
  hydrogen bonds       : bond        0.06178 (  217)
  hydrogen bonds       : angle       4.72965 (  651)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.100 
Fit side-chains
REVERT: A  303 ARG cc_start: 0.7850 (mtp85) cc_final: 0.7518 (mtp-110)
  outliers start: 7
  outliers final: 3
  residues processed: 37
  average time/residue: 0.2790
  time to fit residues: 10.8513
Evaluate side-chains
  33 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 30
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  138 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 4 optimal weight:    0.3980
   chunk 32 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3683 r_free = 0.3683 target = 0.145620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.122805 restraints weight = 3400.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.69
r_work: 0.3343 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   3245  Z= 0.170
  Angle     :  0.628   7.645   4423  Z= 0.325
  Chirality :  0.040   0.191    519
  Planarity :  0.006   0.054    534
  Dihedral  :  5.309  29.361    440
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  :  7.42 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 11.80 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.45), residues: 391
  helix:  1.43 (0.31), residues: 303
  sheet:  None (None), residues: 0
  loop : -3.87 (0.56), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 208 
 TYR   0.021   0.001   TYR A 139 
 PHE   0.012   0.001   PHE A 202 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 3245)
  covalent geometry    : angle       0.62839 ( 4423)
  hydrogen bonds       : bond        0.05777 (  217)
  hydrogen bonds       : angle       4.68516 (  651)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.069 
Fit side-chains
  outliers start: 7
  outliers final: 5
  residues processed: 37
  average time/residue: 0.2230
  time to fit residues: 8.6936
Evaluate side-chains
  35 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  175 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 6 optimal weight:    0.4980
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3678 r_free = 0.3678 target = 0.145062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.122099 restraints weight = 3562.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 1.75
r_work: 0.3265 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   3245  Z= 0.178
  Angle     :  0.645   9.283   4423  Z= 0.327
  Chirality :  0.040   0.191    519
  Planarity :  0.006   0.053    534
  Dihedral  :  5.227  28.712    440
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  :  7.16 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 12.98 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.44), residues: 391
  helix:  1.43 (0.31), residues: 303
  sheet:  None (None), residues: 0
  loop : -3.83 (0.56), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 208 
 TYR   0.021   0.002   TYR A 139 
 PHE   0.013   0.001   PHE A 372 
 TRP   0.009   0.001   TRP A 331 
 HIS   0.002   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 3245)
  covalent geometry    : angle       0.64477 ( 4423)
  hydrogen bonds       : bond        0.05946 (  217)
  hydrogen bonds       : angle       4.67054 (  651)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 0.068 
Fit side-chains
REVERT: A  148 ARG cc_start: 0.6046 (ttt180) cc_final: 0.5500 (mtm180)
REVERT: A  303 ARG cc_start: 0.7877 (mtp85) cc_final: 0.7662 (mtp-110)
  outliers start: 8
  outliers final: 4
  residues processed: 40
  average time/residue: 0.3146
  time to fit residues: 13.1134
Evaluate side-chains
  37 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  175 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:    0.0870
   chunk 8 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.5158

-------------------------------------------------------------------------------
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 = 0.3642 r_free = 0.3642 target = 0.142809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.118851 restraints weight = 3594.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 1.89
r_work: 0.3372 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   3245  Z= 0.157
  Angle     :  0.619   9.390   4423  Z= 0.312
  Chirality :  0.039   0.184    519
  Planarity :  0.005   0.052    534
  Dihedral  :  5.116  28.169    440
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  :  6.91 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 13.57 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.45), residues: 391
  helix:  1.49 (0.31), residues: 303
  sheet:  None (None), residues: 0
  loop : -3.76 (0.57), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 208 
 TYR   0.016   0.001   TYR A 139 
 PHE   0.011   0.001   PHE A 372 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.001   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 3245)
  covalent geometry    : angle       0.61913 ( 4423)
  hydrogen bonds       : bond        0.05497 (  217)
  hydrogen bonds       : angle       4.61371 (  651)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A   40 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7620 (mm-40)
  outliers start: 6
  outliers final: 4
  residues processed: 37
  average time/residue: 0.2653
  time to fit residues: 10.3793
Evaluate side-chains
  36 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLN
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  175 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 18 optimal weight:    0.1980
   chunk 35 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0020
   chunk 30 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 27 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.4188

-------------------------------------------------------------------------------
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 = 0.3631 r_free = 0.3631 target = 0.142553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.118541 restraints weight = 3532.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 1.86
r_work: 0.3352 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   3245  Z= 0.144
  Angle     :  0.595   9.544   4423  Z= 0.301
  Chirality :  0.038   0.174    519
  Planarity :  0.005   0.051    534
  Dihedral  :  4.971  27.942    440
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  :  6.91 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 14.75 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.45), residues: 391
  helix:  1.60 (0.30), residues: 303
  sheet:  None (None), residues: 0
  loop : -3.62 (0.58), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 208 
 TYR   0.012   0.001   TYR A 139 
 PHE   0.010   0.001   PHE A 372 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 3245)
  covalent geometry    : angle       0.59525 ( 4423)
  hydrogen bonds       : bond        0.05088 (  217)
  hydrogen bonds       : angle       4.55108 (  651)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A   40 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7747 (mm-40)
REVERT: A   58 ASN cc_start: 0.8678 (m-40) cc_final: 0.8387 (m-40)
  outliers start: 5
  outliers final: 3
  residues processed: 36
  average time/residue: 0.2857
  time to fit residues: 10.8348
Evaluate side-chains
  36 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLN
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  175 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0010
   chunk 32 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 3 optimal weight:    0.4980
   chunk 37 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.5186

-------------------------------------------------------------------------------
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 = 0.3706 r_free = 0.3706 target = 0.147325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.124556 restraints weight = 3524.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 1.73
r_work: 0.3346 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   3245  Z= 0.154
  Angle     :  0.601   8.452   4423  Z= 0.304
  Chirality :  0.039   0.175    519
  Planarity :  0.005   0.051    534
  Dihedral  :  4.995  27.849    440
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  :  7.42 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 14.45 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.44), residues: 391
  helix:  1.60 (0.30), residues: 303
  sheet:  None (None), residues: 0
  loop : -3.65 (0.58), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 208 
 TYR   0.017   0.001   TYR A 139 
 PHE   0.011   0.001   PHE A 372 
 TRP   0.008   0.001   TRP A 107 
 HIS   0.001   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 3245)
  covalent geometry    : angle       0.60104 ( 4423)
  hydrogen bonds       : bond        0.05318 (  217)
  hydrogen bonds       : angle       4.56454 (  651)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.068 
Fit side-chains
REVERT: A   40 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7673 (mm-40)
REVERT: A   58 ASN cc_start: 0.8688 (m-40) cc_final: 0.8396 (m-40)
REVERT: A  148 ARG cc_start: 0.5943 (ttt180) cc_final: 0.5564 (mtm180)
REVERT: A  303 ARG cc_start: 0.7895 (mtp85) cc_final: 0.7690 (mtp-110)
  outliers start: 5
  outliers final: 3
  residues processed: 39
  average time/residue: 0.3167
  time to fit residues: 12.8562
Evaluate side-chains
  37 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLN
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  175 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0870
   chunk 23 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.5358

-------------------------------------------------------------------------------
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 = 0.3611 r_free = 0.3611 target = 0.140983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.117076 restraints weight = 3564.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.87
r_work: 0.3315 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   3245  Z= 0.156
  Angle     :  0.610   9.798   4423  Z= 0.307
  Chirality :  0.039   0.173    519
  Planarity :  0.005   0.051    534
  Dihedral  :  5.002  27.985    440
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.77 %
    Allowed  :  7.93 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 14.16 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.44), residues: 391
  helix:  1.61 (0.30), residues: 303
  sheet:  None (None), residues: 0
  loop : -3.66 (0.57), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 208 
 TYR   0.017   0.001   TYR A 139 
 PHE   0.012   0.001   PHE A 372 
 TRP   0.009   0.001   TRP A 331 
 HIS   0.001   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 3245)
  covalent geometry    : angle       0.61038 ( 4423)
  hydrogen bonds       : bond        0.05401 (  217)
  hydrogen bonds       : angle       4.56693 (  651)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 875.87 seconds
wall clock time: 15 minutes 43.52 seconds (943.52 seconds total)