Starting phenix.real_space_refine
on Tue Feb 11 03:13:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xor_33357/02_2025/7xor_33357.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xor_33357/02_2025/7xor_33357.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xor_33357/02_2025/7xor_33357.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xor_33357/02_2025/7xor_33357.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xor_33357/02_2025/7xor_33357.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xor_33357/02_2025/7xor_33357.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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      20      5.16       5
     C    2397      2.51       5
     N     665      2.21       5
     O     773      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3855
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "K"
      Number of atoms: 3855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 3855
          Classifications: {'peptide': 524}
          Link IDs: {'PTRANS': 14, 'TRANS': 509}
  Time building chain proxies: 3.28, per 1000 atoms: 0.85
  Number of scatterers: 3855
  At special positions: 0
  Unit cell: (73.08, 87, 70.47, 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      20     16.00
     O     773      8.00
     N     665      7.00
     C    2397      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: 0.85
  Conformation dependent library (CDL) restraints added in 480.5 milliseconds
  

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  948

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 7 sheets defined
      59.5% alpha, 11.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'K' and resid 9 through 29
      removed outlier: 4.129A  pdb=" N   VAL K  29 " --> pdb=" O   ASP K  25 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 52 through 60
      removed outlier: 3.709A  pdb=" N   VAL K  56 " --> pdb=" O   ASP K  52 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 64 through 86
    Processing helix  chain 'K' and resid 88 through 110
    Processing helix  chain 'K' and resid 112 through 135
    Processing helix  chain 'K' and resid 140 through 152
    Processing helix  chain 'K' and resid 155 through 170
    Processing helix  chain 'K' and resid 201 through 205
      removed outlier: 3.590A  pdb=" N   PHE K 204 " --> pdb=" O   SER K 201 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 233 through 244
      removed outlier: 3.529A  pdb=" N   LEU K 237 " --> pdb=" O   MET K 233 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 256 through 269
    Processing helix  chain 'K' and resid 282 through 297
      removed outlier: 3.541A  pdb=" N   LYS K 286 " --> pdb=" O   GLY K 282 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 338 through 355
    Processing helix  chain 'K' and resid 358 through 375
      removed outlier: 3.932A  pdb=" N   GLY K 375 " --> pdb=" O   LYS K 371 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 385 through 409
    Processing helix  chain 'K' and resid 416 through 426
    Processing helix  chain 'K' and resid 433 through 459
      Proline residue:  K 450  - end of helix
    Processing helix  chain 'K' and resid 461 through 472
      removed outlier: 4.075A  pdb=" N   VAL K 465 " --> pdb=" O   GLU K 461 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 488 through 492
    Processing helix  chain 'K' and resid 497 through 516
    Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 8
    Processing sheet with id=AA2, first strand: chain 'K' and resid 38 through 40
    Processing sheet with id=AA3, first strand: chain 'K' and resid 174 through 179
      removed outlier: 3.541A  pdb=" N   ALA K 377 " --> pdb=" O   VAL K 174 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'K' and resid 193 through 195
    Processing sheet with id=AA5, first strand: chain 'K' and resid 273 through 277
      removed outlier: 6.289A  pdb=" N   LEU K 247 " --> pdb=" O   ALA K 274 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   VAL K 276 " --> pdb=" O   LEU K 247 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   ILE K 249 " --> pdb=" O   VAL K 276 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'K' and resid 411 through 413
    Processing sheet with id=AA7, first strand: chain 'K' and resid 476 through 479

    268 hydrogen bonds defined for protein.
    771 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.30

  Time building geometry restraints manager: 0.96 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: 1340
        1.34 -     1.46: 576
        1.46 -     1.58: 1930
        1.58 -     1.69: 0
        1.69 -     1.81: 37
  Bond restraints: 3883
  Sorted by residual:
  bond pdb=" CG  GLU K 354 "
       pdb=" CD  GLU K 354 "
    ideal  model  delta    sigma   weight residual
    1.516  1.488  0.028 2.50e-02 1.60e+03 1.25e+00
  bond pdb=" CD  GLU K 354 "
       pdb=" OE1 GLU K 354 "
    ideal  model  delta    sigma   weight residual
    1.249  1.230  0.019 1.90e-02 2.77e+03 9.55e-01
  bond pdb=" N   GLU K 354 "
       pdb=" CA  GLU K 354 "
    ideal  model  delta    sigma   weight residual
    1.459  1.470 -0.011 1.19e-02 7.06e+03 8.10e-01
  bond pdb=" CA  GLU K 355 "
       pdb=" CB  GLU K 355 "
    ideal  model  delta    sigma   weight residual
    1.530  1.542 -0.012 1.51e-02 4.39e+03 6.06e-01
  bond pdb=" CG1 ILE K 150 "
       pdb=" CD1 ILE K 150 "
    ideal  model  delta    sigma   weight residual
    1.513  1.483  0.030 3.90e-02 6.57e+02 6.06e-01
  ... (remaining 3878 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.10: 5038
        1.10 -     2.20: 158
        2.20 -     3.30: 28
        3.30 -     4.40: 15
        4.40 -     5.50: 4
  Bond angle restraints: 5243
  Sorted by residual:
  angle pdb=" N   GLU K 354 "
        pdb=" CA  GLU K 354 "
        pdb=" CB  GLU K 354 "
      ideal   model   delta    sigma   weight residual
     110.01  115.51   -5.50 1.45e+00 4.76e-01 1.44e+01
  angle pdb=" C   GLU K 354 "
        pdb=" N   GLU K 355 "
        pdb=" CA  GLU K 355 "
      ideal   model   delta    sigma   weight residual
     122.65  117.51    5.14 1.66e+00 3.63e-01 9.60e+00
  angle pdb=" C   ILE K 353 "
        pdb=" N   GLU K 354 "
        pdb=" CA  GLU K 354 "
      ideal   model   delta    sigma   weight residual
     120.44  116.71    3.73 1.30e+00 5.92e-01 8.21e+00
  angle pdb=" N   GLY K 486 "
        pdb=" CA  GLY K 486 "
        pdb=" C   GLY K 486 "
      ideal   model   delta    sigma   weight residual
     110.46  113.83   -3.37 1.43e+00 4.89e-01 5.57e+00
  angle pdb=" N   ALA K 449 "
        pdb=" CA  ALA K 449 "
        pdb=" C   ALA K 449 "
      ideal   model   delta    sigma   weight residual
     112.75  115.77   -3.02 1.36e+00 5.41e-01 4.94e+00
  ... (remaining 5238 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 2239
       17.98 -    35.97: 142
       35.97 -    53.95: 21
       53.95 -    71.93: 6
       71.93 -    89.92: 4
  Dihedral angle restraints: 2412
    sinusoidal: 934
      harmonic: 1478
  Sorted by residual:
  dihedral pdb=" CB  GLU K 102 "
           pdb=" CG  GLU K 102 "
           pdb=" CD  GLU K 102 "
           pdb=" OE1 GLU K 102 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.92  -89.92     1      3.00e+01 1.11e-03 1.07e+01
  dihedral pdb=" CB  MET K 114 "
           pdb=" CG  MET K 114 "
           pdb=" SD  MET K 114 "
           pdb=" CE  MET K 114 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.85  -59.85     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  GLU K 355 "
           pdb=" C   GLU K 355 "
           pdb=" N   ALA K 356 "
           pdb=" CA  ALA K 356 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.55   14.45     0      5.00e+00 4.00e-02 8.35e+00
  ... (remaining 2409 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 389
       0.030 -    0.059: 166
       0.059 -    0.089: 53
       0.089 -    0.118: 27
       0.118 -    0.148: 3
  Chirality restraints: 638
  Sorted by residual:
  chirality pdb=" CA  GLU K 355 "
            pdb=" N   GLU K 355 "
            pdb=" C   GLU K 355 "
            pdb=" CB  GLU K 355 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.44e-01
  chirality pdb=" CA  GLU K 354 "
            pdb=" N   GLU K 354 "
            pdb=" C   GLU K 354 "
            pdb=" CB  GLU K 354 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.33e-01
  chirality pdb=" CA  VAL K 136 "
            pdb=" N   VAL K 136 "
            pdb=" C   VAL K 136 "
            pdb=" CB  VAL K 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.75e-01
  ... (remaining 635 not shown)

  Planarity restraints: 687
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU K 461 "   -0.024 5.00e-02 4.00e+02   3.63e-02 2.11e+00
        pdb=" N   PRO K 462 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO K 462 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO K 462 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN K 351 "    0.006 2.00e-02 2.50e+03   1.27e-02 1.62e+00
        pdb=" C   GLN K 351 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   GLN K 351 "    0.008 2.00e-02 2.50e+03
        pdb=" N   GLN K 352 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU K 234 "   -0.017 5.00e-02 4.00e+02   2.51e-02 1.01e+00
        pdb=" N   PRO K 235 "    0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO K 235 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO K 235 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 684 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 937
        2.80 -     3.32: 4004
        3.32 -     3.85: 6367
        3.85 -     4.37: 7060
        4.37 -     4.90: 12442
  Nonbonded interactions: 30810
  Sorted by model distance:
  nonbonded pdb=" O   VAL K 147 "
            pdb=" OG  SER K 151 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OD2 ASP K 155 "
            pdb=" NH2 ARG K 395 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" OD1 ASP K 291 "
            pdb=" NH2 ARG K 345 "
     model   vdw
     2.306 3.120
  nonbonded pdb=" OD1 ASP K 359 "
            pdb=" NH2 ARG K 362 "
     model   vdw
     2.351 3.120
  nonbonded pdb=" OD1 ASN K 206 "
            pdb=" NZ  LYS K 272 "
     model   vdw
     2.359 3.120
  ... (remaining 30805 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:             1.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.200
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3883  Z= 0.188
  Angle     :  0.519   5.499   5243  Z= 0.296
  Chirality :  0.040   0.148    638
  Planarity :  0.003   0.036    687
  Dihedral  : 12.604  89.918   1464
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  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:  2.15 (0.36), residues: 522
  helix:  2.32 (0.29), residues: 294
  sheet:  1.40 (0.61), residues: 72
  loop : -0.32 (0.48), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS K 401 
 PHE   0.008   0.001   PHE K 195 
 TYR   0.006   0.001   TYR K 476 
 ARG   0.002   0.000   ARG K 268 

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: K  105 LYS cc_start: 0.5421 (tmtt) cc_final: 0.5115 (tmtt)
REVERT: K  393 LYS cc_start: 0.8749 (tmmt) cc_final: 0.8547 (ttpp)
REVERT: K  491 MET cc_start: 0.8914 (mtm) cc_final: 0.8659 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.1974
  time to fit residues: 11.7409
Evaluate side-chains
  31 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 43 optimal weight:    8.9990
   chunk 39 optimal weight:    8.9990
   chunk 21 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 40 optimal weight:    0.4980
   chunk 15 optimal weight:   10.0000
   chunk 24 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   overall best weight:    1.2386

-------------------------------------------------------------------------------
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 = 0.3493 r_free = 0.3493 target = 0.079187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.066942 restraints weight = 11770.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 2.84
r_work: 0.3096 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.0930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3883  Z= 0.164
  Angle     :  0.507   6.099   5243  Z= 0.276
  Chirality :  0.040   0.136    638
  Planarity :  0.003   0.041    687
  Dihedral  :  3.545  13.920    552
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  7.67 %
    Favored  : 92.08 %
  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:  2.24 (0.36), residues: 522
  helix:  2.36 (0.28), residues: 301
  sheet:  1.16 (0.60), residues: 72
  loop : -0.16 (0.50), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS K 401 
 PHE   0.017   0.001   PHE K 195 
 TYR   0.007   0.001   TYR K 360 
 ARG   0.003   0.000   ARG K 421 

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
REVERT: K  105 LYS cc_start: 0.6179 (tmtt) cc_final: 0.5509 (tttm)
REVERT: K  267 MET cc_start: 0.8315 (mmt) cc_final: 0.7779 (mtm)
REVERT: K  352 GLN cc_start: 0.8819 (mt0) cc_final: 0.8336 (mt0)
REVERT: K  388 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7868 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1522
  time to fit residues: 7.5065
Evaluate side-chains
  31 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   chunk 25 optimal weight:   20.0000
   chunk 17 optimal weight:    7.9990
   chunk 2 optimal weight:    6.9990
   chunk 27 optimal weight:    7.9990
   chunk 22 optimal weight:    8.9990
   chunk 36 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    5.3988

-------------------------------------------------------------------------------
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 = 0.3412 r_free = 0.3412 target = 0.075496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.062540 restraints weight = 12021.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 2.93
r_work: 0.2987 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8742
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   3883  Z= 0.375
  Angle     :  0.565   6.423   5243  Z= 0.305
  Chirality :  0.043   0.127    638
  Planarity :  0.003   0.028    687
  Dihedral  :  3.828  16.207    552
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  9.65 %
    Favored  : 88.61 %
  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:  1.91 (0.35), residues: 522
  helix:  2.13 (0.28), residues: 302
  sheet:  1.06 (0.60), residues: 72
  loop : -0.43 (0.47), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS K 401 
 PHE   0.015   0.002   PHE K 195 
 TYR   0.007   0.001   TYR K 476 
 ARG   0.003   0.001   ARG K 322 

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
REVERT: K  105 LYS cc_start: 0.6293 (tmtt) cc_final: 0.5574 (tttm)
REVERT: K  352 GLN cc_start: 0.8826 (mt0) cc_final: 0.8357 (mt0)
REVERT: K  366 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7935 (mp10)
REVERT: K  388 GLU cc_start: 0.8518 (mt-10) cc_final: 0.7968 (tp30)
  outliers start: 7
  outliers final: 4
  residues processed: 38
  average time/residue: 0.1566
  time to fit residues: 7.8344
Evaluate side-chains
  37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  175 ILE
Chi-restraints excluded: chain K residue  236 VAL
Chi-restraints excluded: chain K residue  354 GLU
Chi-restraints excluded: chain K residue  366 GLN
Chi-restraints excluded: chain K residue  385 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 41 optimal weight:    4.9990
   chunk 37 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 22 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3462 r_free = 0.3462 target = 0.077871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.065067 restraints weight = 11864.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 2.95
r_work: 0.3058 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.1514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3883  Z= 0.141
  Angle     :  0.461   5.036   5243  Z= 0.250
  Chirality :  0.040   0.135    638
  Planarity :  0.003   0.029    687
  Dihedral  :  3.679  15.331    552
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  9.90 %
    Favored  : 88.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.13 (0.36), residues: 522
  helix:  2.32 (0.28), residues: 299
  sheet:  0.98 (0.60), residues: 72
  loop : -0.20 (0.49), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS K 401 
 PHE   0.016   0.001   PHE K 195 
 TYR   0.007   0.001   TYR K 360 
 ARG   0.002   0.000   ARG K 322 

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  105 LYS cc_start: 0.6205 (tmtt) cc_final: 0.5314 (tttm)
REVERT: K  352 GLN cc_start: 0.8801 (mt0) cc_final: 0.8358 (mt0)
REVERT: K  388 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7910 (tp30)
REVERT: K  488 MET cc_start: 0.8772 (mmp) cc_final: 0.8311 (mmt)
  outliers start: 7
  outliers final: 4
  residues processed: 44
  average time/residue: 0.1535
  time to fit residues: 8.7805
Evaluate side-chains
  37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  175 ILE
Chi-restraints excluded: chain K residue  354 GLU
Chi-restraints excluded: chain K residue  360 TYR
Chi-restraints excluded: chain K residue  385 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 32 optimal weight:    7.9990
   chunk 1 optimal weight:    9.9990
   chunk 49 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 15 optimal weight:    8.9990
   chunk 18 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    3.7988

-------------------------------------------------------------------------------
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 = 0.3438 r_free = 0.3438 target = 0.076603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.063608 restraints weight = 12226.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 2.99
r_work: 0.3014 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8715
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3883  Z= 0.275
  Angle     :  0.515   7.043   5243  Z= 0.278
  Chirality :  0.041   0.129    638
  Planarity :  0.003   0.026    687
  Dihedral  :  3.705  16.287    552
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 11.88 %
    Favored  : 86.63 %
  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:  2.09 (0.36), residues: 522
  helix:  2.29 (0.28), residues: 299
  sheet:  0.95 (0.60), residues: 72
  loop : -0.23 (0.48), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS K 401 
 PHE   0.012   0.001   PHE K 195 
 TYR   0.007   0.001   TYR K 476 
 ARG   0.003   0.000   ARG K 362 

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  105 LYS cc_start: 0.6241 (tmtt) cc_final: 0.5482 (tttm)
REVERT: K  352 GLN cc_start: 0.8838 (mt0) cc_final: 0.8457 (mt0)
REVERT: K  366 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7955 (mp10)
REVERT: K  388 GLU cc_start: 0.8510 (mt-10) cc_final: 0.7962 (tp30)
REVERT: K  488 MET cc_start: 0.8831 (mmp) cc_final: 0.8296 (mmt)
  outliers start: 6
  outliers final: 3
  residues processed: 38
  average time/residue: 0.1458
  time to fit residues: 7.4815
Evaluate side-chains
  37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  175 ILE
Chi-restraints excluded: chain K residue  354 GLU
Chi-restraints excluded: chain K residue  366 GLN
Chi-restraints excluded: chain K residue  385 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 45 optimal weight:    7.9990
   chunk 14 optimal weight:   10.0000
   chunk 39 optimal weight:    7.9990
   chunk 46 optimal weight:    8.9990
   chunk 42 optimal weight:    2.9990
   chunk 4 optimal weight:    8.9990
   chunk 49 optimal weight:    7.9990
   chunk 29 optimal weight:    8.9990
   chunk 24 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    4.5988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.075222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.062574 restraints weight = 11849.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 2.84
r_work: 0.2997 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8734
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3883  Z= 0.325
  Angle     :  0.533   6.550   5243  Z= 0.288
  Chirality :  0.042   0.131    638
  Planarity :  0.003   0.026    687
  Dihedral  :  3.803  16.161    552
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.88 %
    Favored  : 86.39 %
  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:  1.88 (0.35), residues: 522
  helix:  2.13 (0.28), residues: 301
  sheet:  0.87 (0.60), residues: 72
  loop : -0.39 (0.48), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS K 401 
 PHE   0.012   0.001   PHE K 195 
 TYR   0.008   0.001   TYR K 476 
 ARG   0.002   0.000   ARG K 322 

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
REVERT: K  105 LYS cc_start: 0.6246 (tmtt) cc_final: 0.5499 (tttm)
REVERT: K  267 MET cc_start: 0.8404 (mmt) cc_final: 0.7931 (mtp)
REVERT: K  352 GLN cc_start: 0.8833 (mt0) cc_final: 0.8343 (mt0)
REVERT: K  388 GLU cc_start: 0.8501 (mt-10) cc_final: 0.7971 (tp30)
REVERT: K  518 GLU cc_start: 0.5703 (OUTLIER) cc_final: 0.5168 (mt-10)
  outliers start: 7
  outliers final: 5
  residues processed: 38
  average time/residue: 0.1381
  time to fit residues: 7.0116
Evaluate side-chains
  38 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  175 ILE
Chi-restraints excluded: chain K residue  236 VAL
Chi-restraints excluded: chain K residue  354 GLU
Chi-restraints excluded: chain K residue  360 TYR
Chi-restraints excluded: chain K residue  385 THR
Chi-restraints excluded: chain K residue  518 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 19 optimal weight:    9.9990
   chunk 20 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 37 optimal weight:    6.9990
   chunk 48 optimal weight:    7.9990
   chunk 51 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
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 = 0.3444 r_free = 0.3444 target = 0.076901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.064080 restraints weight = 12000.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.98
r_work: 0.3028 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8699
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3883  Z= 0.194
  Angle     :  0.483   7.873   5243  Z= 0.259
  Chirality :  0.041   0.133    638
  Planarity :  0.003   0.029    687
  Dihedral  :  3.696  16.067    552
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 12.87 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.02 (0.36), residues: 522
  helix:  2.26 (0.28), residues: 301
  sheet:  0.89 (0.60), residues: 72
  loop : -0.33 (0.48), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS K 401 
 PHE   0.014   0.001   PHE K 195 
 TYR   0.006   0.001   TYR K 476 
 ARG   0.002   0.000   ARG K 322 

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.446 
Fit side-chains
REVERT: K  105 LYS cc_start: 0.6223 (tmtt) cc_final: 0.5473 (tttm)
REVERT: K  352 GLN cc_start: 0.8799 (mt0) cc_final: 0.8412 (mt0)
REVERT: K  388 GLU cc_start: 0.8509 (mt-10) cc_final: 0.7959 (tp30)
  outliers start: 5
  outliers final: 3
  residues processed: 37
  average time/residue: 0.1637
  time to fit residues: 7.9692
Evaluate side-chains
  34 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  175 ILE
Chi-restraints excluded: chain K residue  360 TYR
Chi-restraints excluded: chain K residue  385 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 25 optimal weight:    7.9990
   chunk 38 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   chunk 30 optimal weight:    0.4980
   chunk 49 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 48 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
K 146 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.077457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.065103 restraints weight = 11791.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 2.84
r_work: 0.3055 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8675
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   0.034   3883  Z= 0.170
  Angle     :  0.516   8.151   5243  Z= 0.276
  Chirality :  0.041   0.176    638
  Planarity :  0.003   0.029    687
  Dihedral  :  3.635  16.315    552
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 13.12 %
    Favored  : 85.64 %
  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:  2.11 (0.36), residues: 522
  helix:  2.32 (0.28), residues: 299
  sheet:  0.96 (0.60), residues: 72
  loop : -0.23 (0.48), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS K 401 
 PHE   0.013   0.001   PHE K 195 
 TYR   0.006   0.001   TYR K 360 
 ARG   0.002   0.000   ARG K 322 

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.433 
Fit side-chains
REVERT: K  105 LYS cc_start: 0.6187 (tmtt) cc_final: 0.5409 (tttm)
REVERT: K  146 GLN cc_start: 0.8448 (tp-100) cc_final: 0.8238 (tp40)
REVERT: K  267 MET cc_start: 0.8363 (mmt) cc_final: 0.7892 (mtp)
REVERT: K  352 GLN cc_start: 0.8850 (mt0) cc_final: 0.8505 (mt0)
REVERT: K  388 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7942 (tp30)
REVERT: K  488 MET cc_start: 0.8806 (mmp) cc_final: 0.8307 (mmt)
REVERT: K  518 GLU cc_start: 0.5717 (OUTLIER) cc_final: 0.5250 (mt-10)
  outliers start: 5
  outliers final: 3
  residues processed: 38
  average time/residue: 0.1551
  time to fit residues: 7.8250
Evaluate side-chains
  37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  175 ILE
Chi-restraints excluded: chain K residue  360 TYR
Chi-restraints excluded: chain K residue  385 THR
Chi-restraints excluded: chain K residue  518 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 41 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   chunk 15 optimal weight:    4.9990
   chunk 31 optimal weight:    0.2980
   chunk 39 optimal weight:    5.9990
   chunk 36 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.3457 r_free = 0.3457 target = 0.077443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.064619 restraints weight = 12070.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 3.00
r_work: 0.3041 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.1898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3883  Z= 0.183
  Angle     :  0.504   7.537   5243  Z= 0.272
  Chirality :  0.041   0.155    638
  Planarity :  0.003   0.029    687
  Dihedral  :  3.605  16.327    552
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 13.61 %
    Favored  : 85.40 %
  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:  2.11 (0.35), residues: 522
  helix:  2.33 (0.28), residues: 300
  sheet:  1.18 (0.64), residues: 60
  loop : -0.30 (0.46), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS K 401 
 PHE   0.012   0.001   PHE K 195 
 TYR   0.006   0.001   TYR K 360 
 ARG   0.002   0.000   ARG K 322 

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.437 
Fit side-chains
REVERT: K  105 LYS cc_start: 0.6226 (tmtt) cc_final: 0.5442 (tttm)
REVERT: K  146 GLN cc_start: 0.8481 (tp-100) cc_final: 0.8273 (tp40)
REVERT: K  183 LEU cc_start: 0.9065 (tt) cc_final: 0.8720 (mt)
REVERT: K  266 THR cc_start: 0.7902 (m) cc_final: 0.7654 (p)
REVERT: K  267 MET cc_start: 0.8346 (mmt) cc_final: 0.7924 (mtp)
REVERT: K  352 GLN cc_start: 0.8829 (mt0) cc_final: 0.8467 (mt0)
REVERT: K  388 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7979 (tp30)
REVERT: K  518 GLU cc_start: 0.5686 (OUTLIER) cc_final: 0.5176 (mt-10)
  outliers start: 4
  outliers final: 3
  residues processed: 36
  average time/residue: 0.1544
  time to fit residues: 7.5216
Evaluate side-chains
  38 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  175 ILE
Chi-restraints excluded: chain K residue  360 TYR
Chi-restraints excluded: chain K residue  385 THR
Chi-restraints excluded: chain K residue  518 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:   20.0000
   chunk 49 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.3418 r_free = 0.3418 target = 0.075613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.062807 restraints weight = 11959.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 2.89
r_work: 0.3005 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3883  Z= 0.296
  Angle     :  0.542   7.201   5243  Z= 0.294
  Chirality :  0.042   0.147    638
  Planarity :  0.003   0.027    687
  Dihedral  :  3.708  16.319    552
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 13.61 %
    Favored  : 85.40 %
  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:  2.02 (0.35), residues: 522
  helix:  2.23 (0.28), residues: 302
  sheet:  1.01 (0.60), residues: 72
  loop : -0.35 (0.48), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS K 401 
 PHE   0.011   0.001   PHE K 195 
 TYR   0.006   0.001   TYR K 360 
 ARG   0.002   0.000   ARG K 322 

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.418 
Fit side-chains
REVERT: K  105 LYS cc_start: 0.6268 (tmtt) cc_final: 0.5497 (tttm)
REVERT: K  146 GLN cc_start: 0.8506 (tp-100) cc_final: 0.8297 (tp40)
REVERT: K  267 MET cc_start: 0.8366 (mmt) cc_final: 0.7917 (mtp)
REVERT: K  352 GLN cc_start: 0.8836 (mt0) cc_final: 0.8455 (mt0)
REVERT: K  388 GLU cc_start: 0.8539 (mt-10) cc_final: 0.7968 (tp30)
REVERT: K  518 GLU cc_start: 0.5578 (OUTLIER) cc_final: 0.5028 (mt-10)
  outliers start: 4
  outliers final: 3
  residues processed: 35
  average time/residue: 0.1453
  time to fit residues: 6.8993
Evaluate side-chains
  37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  175 ILE
Chi-restraints excluded: chain K residue  360 TYR
Chi-restraints excluded: chain K residue  385 THR
Chi-restraints excluded: chain K residue  518 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 45 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9980
   chunk 49 optimal weight:    8.9990
   chunk 19 optimal weight:   10.0000
   chunk 10 optimal weight:    0.8980
   chunk 18 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.3466 r_free = 0.3466 target = 0.077855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.065423 restraints weight = 11655.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 2.85
r_work: 0.3076 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.1972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   3883  Z= 0.141
  Angle     :  0.496   7.893   5243  Z= 0.268
  Chirality :  0.040   0.154    638
  Planarity :  0.003   0.030    687
  Dihedral  :  3.568  15.945    552
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 14.36 %
    Favored  : 84.90 %
  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:  2.15 (0.35), residues: 522
  helix:  2.35 (0.28), residues: 301
  sheet:  1.31 (0.64), residues: 60
  loop : -0.33 (0.46), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.000   0.000   HIS K 401 
 PHE   0.013   0.001   PHE K 195 
 TYR   0.007   0.001   TYR K 506 
 ARG   0.003   0.000   ARG K 322 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1665.15 seconds
wall clock time: 30 minutes 43.37 seconds (1843.37 seconds total)