Starting phenix.real_space_refine
on Wed Mar  5 22:23:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xor_33357/03_2025/7xor_33357.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xor_33357/03_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_33357/03_2025/7xor_33357.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xor_33357/03_2025/7xor_33357.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xor_33357/03_2025/7xor_33357.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xor_33357/03_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-5624/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: 3.35, per 1000 atoms: 0.87
  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: 0.96
  Conformation dependent library (CDL) restraints added in 652.2 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: 0.46
  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: 1.11

  Time building geometry restraints manager: 1.15 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:             2.620
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.480
  Find NCS groups from input model:        0.030
  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:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.220
-------------------------------------------------------------------------------
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  : 0.471 
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: 0.1818
  time to fit residues: 10.8664
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:    0.8980
   chunk 15 optimal weight:    7.9990
   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:    1.3186

-------------------------------------------------------------------------------
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 = 0.3494 r_free = 0.3494 target = 0.079215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.066970 restraints weight = 11793.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.84
r_work: 0.3100 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.0995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3883  Z= 0.164
  Angle     :  0.504   6.513   5243  Z= 0.273
  Chirality :  0.040   0.136    638
  Planarity :  0.003   0.040    687
  Dihedral  :  3.569  14.147    552
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  8.42 %
    Favored  : 91.09 %
  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:  2.21 (0.36), residues: 522
  helix:  2.34 (0.28), residues: 301
  sheet:  1.11 (0.60), residues: 72
  loop : -0.17 (0.49), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS K 401 
 PHE   0.019   0.002   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
  38 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
REVERT: K  105 LYS cc_start: 0.6179 (tmtt) cc_final: 0.5379 (tttm)
REVERT: K  267 MET cc_start: 0.8302 (mmt) cc_final: 0.7779 (mtm)
REVERT: K  352 GLN cc_start: 0.8822 (mt0) cc_final: 0.8338 (mt0)
REVERT: K  388 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7858 (tp30)
  outliers start: 2
  outliers final: 1
  residues processed: 37
  average time/residue: 0.1476
  time to fit residues: 7.2907
Evaluate side-chains
  33 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 32
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  236 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 14 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   chunk 25 optimal weight:   20.0000
   chunk 17 optimal weight:    9.9990
   chunk 2 optimal weight:    7.9990
   chunk 27 optimal weight:    7.9990
   chunk 22 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
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 = 0.3414 r_free = 0.3414 target = 0.075447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.062657 restraints weight = 11856.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 2.86
r_work: 0.3002 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8727
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3883  Z= 0.352
  Angle     :  0.544   6.419   5243  Z= 0.295
  Chirality :  0.043   0.133    638
  Planarity :  0.003   0.027    687
  Dihedral  :  3.774  16.142    552
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  9.16 %
    Favored  : 89.11 %
  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:  1.98 (0.35), residues: 522
  helix:  2.21 (0.28), residues: 302
  sheet:  1.07 (0.61), residues: 72
  loop : -0.44 (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   0.006   0.001   TYR K 476 
 ARG   0.003   0.000   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  : 0.492 
Fit side-chains
   revert: symmetry clash
REVERT: K  105 LYS cc_start: 0.6223 (tmtt) cc_final: 0.5459 (tttm)
REVERT: K  352 GLN cc_start: 0.8828 (mt0) cc_final: 0.8427 (mt0)
REVERT: K  366 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7922 (mp10)
REVERT: K  388 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7962 (tp30)
  outliers start: 7
  outliers final: 4
  residues processed: 38
  average time/residue: 0.1593
  time to fit residues: 7.9973
Evaluate side-chains
  38 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 37 optimal weight:    9.9990
   chunk 50 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   chunk 22 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    3.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.076232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.063375 restraints weight = 11991.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 2.95
r_work: 0.3010 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.1625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3883  Z= 0.273
  Angle     :  0.503   5.394   5243  Z= 0.272
  Chirality :  0.041   0.130    638
  Planarity :  0.003   0.025    687
  Dihedral  :  3.774  15.789    552
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 10.15 %
    Favored  : 87.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.36), residues: 522
  helix:  2.13 (0.28), residues: 302
  sheet:  0.94 (0.60), residues: 72
  loop : -0.35 (0.49), residues: 148

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   0.007   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
  45 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 36
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
REVERT: K  105 LYS cc_start: 0.6275 (tmtt) cc_final: 0.5415 (tttm)
REVERT: K  352 GLN cc_start: 0.8810 (mt0) cc_final: 0.8390 (mt0)
REVERT: K  388 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7932 (tp30)
  outliers start: 9
  outliers final: 5
  residues processed: 40
  average time/residue: 0.1599
  time to fit residues: 8.3281
Evaluate side-chains
  38 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
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
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:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 49 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 6 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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 = 0.3428 r_free = 0.3428 target = 0.076183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.063221 restraints weight = 12241.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 2.99
r_work: 0.3003 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8721
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3883  Z= 0.255
  Angle     :  0.512   7.457   5243  Z= 0.277
  Chirality :  0.041   0.131    638
  Planarity :  0.003   0.026    687
  Dihedral  :  3.763  16.148    552
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 11.14 %
    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:  1.94 (0.36), residues: 522
  helix:  2.21 (0.28), residues: 301
  sheet:  0.84 (0.60), residues: 72
  loop : -0.41 (0.48), residues: 149

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 476 
 ARG   0.002   0.000   ARG K 322 

*********************** 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
  42 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 33
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: K  105 LYS cc_start: 0.6226 (tmtt) cc_final: 0.5452 (tttm)
REVERT: K  234 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9212 (tp)
REVERT: K  352 GLN cc_start: 0.8829 (mt0) cc_final: 0.8449 (mt0)
REVERT: K  366 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8026 (mp10)
REVERT: K  388 GLU cc_start: 0.8464 (mt-10) cc_final: 0.7931 (tp30)
REVERT: K  518 GLU cc_start: 0.5778 (OUTLIER) cc_final: 0.5237 (mp0)
  outliers start: 9
  outliers final: 4
  residues processed: 40
  average time/residue: 0.1329
  time to fit residues: 7.1848
Evaluate side-chains
  39 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  175 ILE
Chi-restraints excluded: chain K residue  234 LEU
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
Chi-restraints excluded: chain K residue  518 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 14 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 42 optimal weight:    6.9990
   chunk 4 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 29 optimal weight:    9.9990
   chunk 24 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    1.7986

-------------------------------------------------------------------------------
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 = 0.3451 r_free = 0.3451 target = 0.077245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.064755 restraints weight = 11934.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 2.86
r_work: 0.3059 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3883  Z= 0.168
  Angle     :  0.461   5.949   5243  Z= 0.252
  Chirality :  0.040   0.132    638
  Planarity :  0.003   0.027    687
  Dihedral  :  3.667  15.818    552
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 12.87 %
    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:  2.06 (0.35), residues: 522
  helix:  2.32 (0.28), residues: 298
  sheet:  0.85 (0.60), residues: 72
  loop : -0.32 (0.47), residues: 152

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 360 
 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
  42 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: K  105 LYS cc_start: 0.6201 (tmtt) cc_final: 0.5440 (tttm)
REVERT: K  146 GLN cc_start: 0.8628 (tp40) cc_final: 0.8387 (tp40)
REVERT: K  234 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9206 (tp)
REVERT: K  352 GLN cc_start: 0.8822 (mt0) cc_final: 0.8355 (mt0)
REVERT: K  388 GLU cc_start: 0.8449 (mt-10) cc_final: 0.7898 (tp30)
  outliers start: 6
  outliers final: 4
  residues processed: 40
  average time/residue: 0.1496
  time to fit residues: 7.9084
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  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  175 ILE
Chi-restraints excluded: chain K residue  234 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 19 optimal weight:    9.9990
   chunk 20 optimal weight:    7.9990
   chunk 33 optimal weight:   10.0000
   chunk 46 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 23 optimal weight:    0.1980
   chunk 37 optimal weight:    7.9990
   chunk 48 optimal weight:    7.9990
   chunk 51 optimal weight:    8.9990
   chunk 12 optimal weight:    6.9990
   overall best weight:    3.8388

-------------------------------------------------------------------------------
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 = 0.3422 r_free = 0.3422 target = 0.075894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.063018 restraints weight = 12106.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.99
r_work: 0.2998 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8728
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3883  Z= 0.280
  Angle     :  0.526   6.401   5243  Z= 0.281
  Chirality :  0.041   0.133    638
  Planarity :  0.003   0.025    687
  Dihedral  :  3.729  16.390    552
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 13.61 %
    Favored  : 84.65 %
  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:  1.94 (0.35), residues: 522
  helix:  2.20 (0.28), residues: 301
  sheet:  0.94 (0.61), residues: 72
  loop : -0.42 (0.47), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS K 401 
 PHE   0.012   0.001   PHE K 195 
 TYR   0.007   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
  40 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
REVERT: K  105 LYS cc_start: 0.6257 (tmtt) cc_final: 0.5490 (tttm)
REVERT: K  146 GLN cc_start: 0.8657 (tp40) cc_final: 0.8364 (tp40)
REVERT: K  234 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9215 (tp)
REVERT: K  352 GLN cc_start: 0.8828 (mt0) cc_final: 0.8522 (mt0)
REVERT: K  388 GLU cc_start: 0.8534 (mt-10) cc_final: 0.7985 (tp30)
REVERT: K  518 GLU cc_start: 0.5710 (OUTLIER) cc_final: 0.5172 (mt-10)
  outliers start: 7
  outliers final: 4
  residues processed: 38
  average time/residue: 0.1525
  time to fit residues: 7.7085
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  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  175 ILE
Chi-restraints excluded: chain K residue  234 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 25 optimal weight:   20.0000
   chunk 38 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 30 optimal weight:    7.9990
   chunk 49 optimal weight:    9.9990
   chunk 44 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 48 optimal weight:    9.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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 = 0.3443 r_free = 0.3443 target = 0.076920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.064082 restraints weight = 12093.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.97
r_work: 0.3027 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3883  Z= 0.194
  Angle     :  0.473   6.672   5243  Z= 0.256
  Chirality :  0.040   0.135    638
  Planarity :  0.003   0.027    687
  Dihedral  :  3.672  15.841    552
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 14.11 %
    Favored  : 84.41 %
  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:  1.98 (0.35), residues: 522
  helix:  2.23 (0.28), residues: 301
  sheet:  0.95 (0.60), residues: 72
  loop : -0.41 (0.47), residues: 149

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
  39 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
REVERT: K  105 LYS cc_start: 0.6211 (tmtt) cc_final: 0.5440 (tttm)
REVERT: K  146 GLN cc_start: 0.8599 (tp40) cc_final: 0.8333 (tp40)
REVERT: K  234 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9210 (tp)
REVERT: K  352 GLN cc_start: 0.8855 (mt0) cc_final: 0.8474 (mt0)
REVERT: K  388 GLU cc_start: 0.8509 (mt-10) cc_final: 0.7943 (tp30)
  outliers start: 6
  outliers final: 4
  residues processed: 37
  average time/residue: 0.1399
  time to fit residues: 7.0009
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  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  175 ILE
Chi-restraints excluded: chain K residue  234 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 3 optimal weight:    8.9990
   chunk 41 optimal weight:    6.9990
   chunk 20 optimal weight:    8.9990
   chunk 19 optimal weight:    8.9990
   chunk 15 optimal weight:    5.9990
   chunk 31 optimal weight:   20.0000
   chunk 39 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 21 optimal weight:    8.9990
   chunk 47 optimal weight:    4.9990
   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 = 0.3423 r_free = 0.3423 target = 0.075938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.063005 restraints weight = 12199.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 2.99
r_work: 0.2999 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8728
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3883  Z= 0.286
  Angle     :  0.506   6.587   5243  Z= 0.274
  Chirality :  0.042   0.139    638
  Planarity :  0.003   0.025    687
  Dihedral  :  3.734  16.274    552
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.86 %
    Favored  : 84.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.35), residues: 522
  helix:  2.16 (0.28), residues: 301
  sheet:  0.96 (0.61), residues: 72
  loop : -0.44 (0.47), residues: 149

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 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
  40 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
REVERT: K  105 LYS cc_start: 0.6321 (tmtt) cc_final: 0.5559 (tttm)
REVERT: K  146 GLN cc_start: 0.8638 (tp40) cc_final: 0.8368 (tp40)
REVERT: K  234 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9224 (tp)
REVERT: K  267 MET cc_start: 0.8393 (mmt) cc_final: 0.7948 (mtp)
REVERT: K  352 GLN cc_start: 0.8870 (mt0) cc_final: 0.8479 (mt0)
REVERT: K  388 GLU cc_start: 0.8560 (mt-10) cc_final: 0.7969 (tp30)
REVERT: K  518 GLU cc_start: 0.5614 (OUTLIER) cc_final: 0.5062 (mt-10)
  outliers start: 8
  outliers final: 5
  residues processed: 37
  average time/residue: 0.1436
  time to fit residues: 7.2797
Evaluate side-chains
  39 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  175 ILE
Chi-restraints excluded: chain K residue  234 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 36 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0270
   chunk 49 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    2.0044

-------------------------------------------------------------------------------
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 = 0.3439 r_free = 0.3439 target = 0.076622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.064088 restraints weight = 11942.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 2.89
r_work: 0.3048 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.1919

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= 0.177
  Angle     :  0.478   6.873   5243  Z= 0.256
  Chirality :  0.041   0.141    638
  Planarity :  0.003   0.027    687
  Dihedral  :  3.672  15.397    552
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 14.36 %
    Favored  : 84.41 %
  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:  2.24 (0.28), residues: 302
  sheet:  1.02 (0.60), residues: 72
  loop : -0.39 (0.46), residues: 148

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 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
  38 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
REVERT: K  105 LYS cc_start: 0.6313 (tmtt) cc_final: 0.5540 (tttm)
REVERT: K  146 GLN cc_start: 0.8606 (tp40) cc_final: 0.8325 (tp40)
REVERT: K  234 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9207 (tp)
REVERT: K  267 MET cc_start: 0.8376 (mmt) cc_final: 0.7911 (mtp)
REVERT: K  352 GLN cc_start: 0.8866 (mt0) cc_final: 0.8426 (mt0)
REVERT: K  388 GLU cc_start: 0.8498 (mt-10) cc_final: 0.7914 (tp30)
  outliers start: 5
  outliers final: 4
  residues processed: 36
  average time/residue: 0.1421
  time to fit residues: 6.9830
Evaluate side-chains
  36 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    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  234 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 45 optimal weight:    0.9990
   chunk 8 optimal weight:   20.0000
   chunk 49 optimal weight:    6.9990
   chunk 19 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    1.7586

-------------------------------------------------------------------------------
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 = 0.3454 r_free = 0.3454 target = 0.077422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.064697 restraints weight = 11968.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 2.99
r_work: 0.3052 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          0.1933

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= 0.171
  Angle     :  0.484   6.983   5243  Z= 0.260
  Chirality :  0.040   0.134    638
  Planarity :  0.003   0.027    687
  Dihedral  :  3.609  14.694    552
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 14.11 %
    Favored  : 84.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.35), residues: 522
  helix:  2.29 (0.28), residues: 302
  sheet:  0.96 (0.60), residues: 72
  loop : -0.42 (0.47), residues: 148

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 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1687.39 seconds
wall clock time: 30 minutes 0.98 seconds (1800.98 seconds total)