Starting phenix.real_space_refine
on Mon Mar 11 04:21:37 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7q_15899/03_2024/8b7q_15899.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7q_15899/03_2024/8b7q_15899.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7q_15899/03_2024/8b7q_15899.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7q_15899/03_2024/8b7q_15899.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7q_15899/03_2024/8b7q_15899.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7q_15899/03_2024/8b7q_15899.pdb"
  }
  resolution = 4.02
  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=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3495 atoms to isotropic.
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      18      5.16       5
     C    2236      2.51       5
     N     594      2.21       5
     O     663      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B PHE  568": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  587": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  334": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  391": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 3511
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1064
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1064
          Classifications: {'peptide': 138}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 131}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1637
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1637
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 190}
    Chain: "F"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 810
          Unusual residues: {'NAG': 1}
          Classifications: {'peptide': 97, 'undetermined': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 92, None: 1}
            Not linked:
              pdbres="ILE F 426 "
              pdbres="NAG F 901 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.33, per 1000 atoms: 0.66
  Number of scatterers: 3511
  At special positions: 0
  Unit cell: (79.584, 98.651, 88.703, 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      18     16.00
     O     663      8.00
     N     594      7.00
     C    2236      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 117 " - pdb=" SG  CYS A 167 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 434 " - pdb=" SG  CYS B 445 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 471 " - pdb=" SG  CYS B 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 486 " - pdb=" SG  CYS B 496 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 350 " - pdb=" SG  CYS F 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 411 " - pdb=" SG  CYS F 416 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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
  Links applied
    NAG-ASN
      " NAG F 901 " - " ASN F 345 "
  Time building additional restraints: 1.19
  Conformation dependent library (CDL) restraints added in 744.0 milliseconds
  

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  850

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 8 sheets defined
      25.9% alpha, 32.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 45
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 3.870A  pdb=" N   GLN A  49 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   SER A  50 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 45 through 50'
    Processing helix  chain 'A' and resid 71 through 89
      removed outlier: 3.647A  pdb=" N   SER A  88 " --> pdb=" O   GLN A  84 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU A  89 " --> pdb=" O   VAL A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 113
    Processing helix  chain 'A' and resid 130 through 138
    Processing helix  chain 'A' and resid 138 through 162
      removed outlier: 4.117A  pdb=" N   ASP A 162 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 528 through 533
      removed outlier: 3.963A  pdb=" N   VAL B 533 " --> pdb=" O   ASP B 530 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 375 through 377
      No H-bonds generated for 'chain 'F' and resid 375 through 377'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 432 through 436
      removed outlier: 3.536A  pdb=" N   TRP B 447 " --> pdb=" O   TYR B 494 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 482 through 484
      removed outlier: 4.491A  pdb=" N   LEU B 462 " --> pdb=" O   LYS B 484 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR B 459 " --> pdb=" O   ASN B 514 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 482 through 484
      removed outlier: 4.491A  pdb=" N   LEU B 462 " --> pdb=" O   LYS B 484 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR B 459 " --> pdb=" O   ASN B 514 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 539 through 546
      removed outlier: 5.035A  pdb=" N   ASN B 540 " --> pdb=" O   GLU B 557 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   GLU B 557 " --> pdb=" O   ASN B 540 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 582 through 586
    Processing sheet with id=AA6, first strand: chain 'F' and resid 331 through 334
    Processing sheet with id=AA7, first strand: chain 'F' and resid 331 through 334
      removed outlier: 3.552A  pdb=" N   ALA F 346 " --> pdb=" O   PHE F 391 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 337 through 340
      removed outlier: 7.582A  pdb=" N   HIS F 417 " --> pdb=" O   ASN F 412 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   ASN F 412 " --> pdb=" O   HIS F 417 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ARG F 419 " --> pdb=" O   CYS F 410 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   CYS F 410 " --> pdb=" O   ARG F 419 " (cutoff:3.500A)

    175 hydrogen bonds defined for protein.
    474 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.94

  Time building geometry restraints manager: 1.33 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: 1124
        1.34 -     1.46: 812
        1.46 -     1.58: 1630
        1.58 -     1.70: 0
        1.70 -     1.82: 22
  Bond restraints: 3588
  Sorted by residual:
  bond pdb=" C1  NAG F 901 "
       pdb=" O5  NAG F 901 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.75e+00
  bond pdb=" C5  NAG F 901 "
       pdb=" O5  NAG F 901 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.24e+00
  bond pdb=" C3  NAG F 901 "
       pdb=" O3  NAG F 901 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 9.76e-01
  bond pdb=" C   TRP B 447 "
       pdb=" N   SER B 448 "
    ideal  model  delta    sigma   weight residual
    1.332  1.347 -0.015 1.92e-02 2.71e+03 6.28e-01
  bond pdb=" N   SER A 114 "
       pdb=" CA  SER A 114 "
    ideal  model  delta    sigma   weight residual
    1.463  1.455  0.008 1.08e-02 8.57e+03 5.33e-01
  ... (remaining 3583 not shown)

  Histogram of bond angle deviations from ideal:
      100.40 -   107.12: 133
      107.12 -   113.83: 2086
      113.83 -   120.54: 1280
      120.54 -   127.26: 1342
      127.26 -   133.97: 44
  Bond angle restraints: 4885
  Sorted by residual:
  angle pdb=" C   ILE A  63 "
        pdb=" N   PRO A  64 "
        pdb=" CA  PRO A  64 "
      ideal   model   delta    sigma   weight residual
     119.84  122.92   -3.08 1.25e+00 6.40e-01 6.05e+00
  angle pdb=" C   PHE A 113 "
        pdb=" N   SER A 114 "
        pdb=" CA  SER A 114 "
      ideal   model   delta    sigma   weight residual
     120.89  124.35   -3.46 1.50e+00 4.44e-01 5.32e+00
  angle pdb=" N   SER A  46 "
        pdb=" CA  SER A  46 "
        pdb=" C   SER A  46 "
      ideal   model   delta    sigma   weight residual
     111.37  115.17   -3.80 1.65e+00 3.67e-01 5.30e+00
  angle pdb=" C   ILE A  45 "
        pdb=" N   SER A  46 "
        pdb=" CA  SER A  46 "
      ideal   model   delta    sigma   weight residual
     120.82  124.00   -3.18 1.50e+00 4.44e-01 4.50e+00
  angle pdb=" N   LEU B 503 "
        pdb=" CA  LEU B 503 "
        pdb=" C   LEU B 503 "
      ideal   model   delta    sigma   weight residual
     111.33  113.75   -2.42 1.21e+00 6.83e-01 4.01e+00
  ... (remaining 4880 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.92: 2086
       15.92 -    31.83: 94
       31.83 -    47.75: 22
       47.75 -    63.66: 4
       63.66 -    79.58: 2
  Dihedral angle restraints: 2208
    sinusoidal: 903
      harmonic: 1305
  Sorted by residual:
  dihedral pdb=" CB  CYS F 350 "
           pdb=" SG  CYS F 350 "
           pdb=" SG  CYS F 410 "
           pdb=" CB  CYS F 410 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   63.39   29.61     1      1.00e+01 1.00e-02 1.25e+01
  dihedral pdb=" N   LEU A 161 "
           pdb=" CA  LEU A 161 "
           pdb=" CB  LEU A 161 "
           pdb=" CG  LEU A 161 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.82  -58.18     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" N   PHE F 334 "
           pdb=" CA  PHE F 334 "
           pdb=" CB  PHE F 334 "
           pdb=" CG  PHE F 334 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -111.09   51.09     3      1.50e+01 4.44e-03 8.98e+00
  ... (remaining 2205 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 349
       0.031 -    0.062: 154
       0.062 -    0.092: 33
       0.092 -    0.123: 31
       0.123 -    0.154: 5
  Chirality restraints: 572
  Sorted by residual:
  chirality pdb=" CA  ILE F 351 "
            pdb=" N   ILE F 351 "
            pdb=" C   ILE F 351 "
            pdb=" CB  ILE F 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.91e-01
  chirality pdb=" CA  PRO A  64 "
            pdb=" N   PRO A  64 "
            pdb=" C   PRO A  64 "
            pdb=" CB  PRO A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.73e-01
  chirality pdb=" CA  ILE F 374 "
            pdb=" N   ILE F 374 "
            pdb=" C   ILE F 374 "
            pdb=" CB  ILE F 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.90e-01
  ... (remaining 569 not shown)

  Planarity restraints: 616
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 155 "    0.008 2.00e-02 2.50e+03   1.60e-02 2.57e+00
        pdb=" C   GLN A 155 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   GLN A 155 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASP A 156 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 448 "    0.023 5.00e-02 4.00e+02   3.52e-02 1.98e+00
        pdb=" N   PRO B 449 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B 449 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 449 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 148 "    0.006 2.00e-02 2.50e+03   1.28e-02 1.63e+00
        pdb=" C   SER A 148 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   SER A 148 "    0.008 2.00e-02 2.50e+03
        pdb=" N   ARG A 149 "    0.007 2.00e-02 2.50e+03
  ... (remaining 613 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 532
        2.77 -     3.30: 3250
        3.30 -     3.83: 5553
        3.83 -     4.37: 6419
        4.37 -     4.90: 11088
  Nonbonded interactions: 26842
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 141 "
            pdb=" OH  TYR F 409 "
     model   vdw
     2.234 2.440
  nonbonded pdb=" O   PRO A  64 "
            pdb=" OH  TYR A  82 "
     model   vdw
     2.242 2.440
  nonbonded pdb=" OD2 ASP A  30 "
            pdb=" OH  TYR B 470 "
     model   vdw
     2.256 2.440
  nonbonded pdb=" NH2 ARG B 571 "
            pdb=" OE1 GLN B 608 "
     model   vdw
     2.362 2.520
  nonbonded pdb=" NH2 ARG F 400 "
            pdb=" O   TYR F 405 "
     model   vdw
     2.378 2.520
  ... (remaining 26837 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 group one per residue
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:             6.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          18.600
  Check model and map are aligned:         0.060
  Set scattering table:                    0.040
  Process input model:                     13.910
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
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   0.026   3588  Z= 0.173
  Angle     :  0.599   7.021   4885  Z= 0.335
  Chirality :  0.043   0.154    572
  Planarity :  0.004   0.035    615
  Dihedral  :  9.873  79.577   1340
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  3.93 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  :  6.13 %
    Favored  : 90.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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:  0.29 (0.38), residues: 433
  helix:  0.92 (0.47), residues: 97
  sheet:  0.83 (0.39), residues: 134
  loop : -0.57 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F 367 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.010   0.001   PHE B 493 
 TYR   0.009   0.001   TYR F 424 
 ARG   0.002   0.000   ARG B 467 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ILE cc_start: 0.7042 (mt) cc_final: 0.6621 (mm)
REVERT: A   63 ILE cc_start: 0.8987 (mt) cc_final: 0.8664 (tt)
REVERT: A   93 ASN cc_start: 0.7569 (m-40) cc_final: 0.7287 (m-40)
REVERT: B  436 THR cc_start: 0.9047 (m) cc_final: 0.8331 (m)
REVERT: B  540 ASN cc_start: 0.8477 (t0) cc_final: 0.8226 (t0)
REVERT: B  565 ASN cc_start: 0.8276 (m-40) cc_final: 0.7795 (p0)
REVERT: B  572 TYR cc_start: 0.8019 (p90) cc_final: 0.7631 (p90)
REVERT: B  585 GLU cc_start: 0.8506 (mp0) cc_final: 0.8236 (pm20)
REVERT: B  609 VAL cc_start: 0.9427 (t) cc_final: 0.9200 (m)
REVERT: B  612 ARG cc_start: 0.8665 (ttt180) cc_final: 0.7832 (ttt-90)
REVERT: F  365 VAL cc_start: 0.8987 (m) cc_final: 0.8090 (p)
REVERT: F  388 LYS cc_start: 0.8796 (tttt) cc_final: 0.8555 (tttp)
REVERT: F  393 ASN cc_start: 0.7524 (t0) cc_final: 0.7077 (t0)
  outliers start: 12
  outliers final: 2
  residues processed: 155
  average time/residue: 0.1646
  time to fit residues: 30.5737
Evaluate side-chains
  97 residues out of total 408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.3462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3588  Z= 0.236
  Angle     :  0.628  10.806   4885  Z= 0.323
  Chirality :  0.045   0.248    572
  Planarity :  0.004   0.040    615
  Dihedral  :  4.504  18.682    496
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  1.96 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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:  1.02 (0.40), residues: 433
  helix:  2.31 (0.50), residues: 103
  sheet:  0.50 (0.39), residues: 126
  loop :  0.03 (0.46), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 620 
 HIS   0.003   0.001   HIS A  47 
 PHE   0.012   0.002   PHE F 348 
 TYR   0.018   0.002   TYR A  82 
 ARG   0.004   0.000   ARG F 419 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 114
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.8649 (ptm-80) cc_final: 0.8408 (ttp80)
REVERT: A   74 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8305 (ttpt)
REVERT: A   93 ASN cc_start: 0.7484 (m-40) cc_final: 0.7280 (m-40)
REVERT: B  429 ASN cc_start: 0.8754 (t0) cc_final: 0.8441 (t0)
REVERT: B  542 LYS cc_start: 0.8478 (mmtm) cc_final: 0.8270 (mmtm)
REVERT: B  553 LYS cc_start: 0.8035 (ptmm) cc_final: 0.7778 (pttm)
REVERT: B  609 VAL cc_start: 0.9537 (t) cc_final: 0.9296 (m)
REVERT: B  612 ARG cc_start: 0.8751 (ttt180) cc_final: 0.8212 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7650 (t0) cc_final: 0.7112 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1555
  time to fit residues: 21.7317
Evaluate side-chains
  92 residues out of total 408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN
A 103 ASN
B 461 GLN
B 499 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.4191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   3588  Z= 0.329
  Angle     :  0.677  13.947   4885  Z= 0.349
  Chirality :  0.048   0.226    572
  Planarity :  0.004   0.034    615
  Dihedral  :  4.815  26.701    496
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  2.70 %
    Favored  : 97.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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:  1.23 (0.40), residues: 433
  helix:  2.83 (0.50), residues: 97
  sheet:  0.61 (0.42), residues: 123
  loop :  0.05 (0.45), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 447 
 HIS   0.005   0.001   HIS B 465 
 PHE   0.013   0.002   PHE F 348 
 TYR   0.021   0.002   TYR F 352 
 ARG   0.002   0.000   ARG F 368 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.8599 (ptm-80) cc_final: 0.8299 (ttp-110)
REVERT: A   74 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8368 (ttpt)
REVERT: B  429 ASN cc_start: 0.8757 (t0) cc_final: 0.8474 (t0)
REVERT: B  612 ARG cc_start: 0.8758 (ttt180) cc_final: 0.8260 (ttt-90)
REVERT: B  629 THR cc_start: 0.7978 (p) cc_final: 0.7774 (p)
REVERT: F  381 ILE cc_start: 0.8810 (pt) cc_final: 0.8423 (mm)
REVERT: F  393 ASN cc_start: 0.7834 (t0) cc_final: 0.7006 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1505
  time to fit residues: 19.3290
Evaluate side-chains
  83 residues out of total 408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 4 optimal weight:    0.0070
   chunk 18 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 40 optimal weight:    0.1980
   chunk 20 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.4998

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 461 GLN
B 499 GLN
F 369 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.4478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3588  Z= 0.176
  Angle     :  0.584  11.594   4885  Z= 0.295
  Chirality :  0.044   0.199    572
  Planarity :  0.003   0.030    615
  Dihedral  :  4.433  24.568    496
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  2.21 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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:  1.48 (0.41), residues: 433
  helix:  2.99 (0.50), residues: 102
  sheet:  0.85 (0.42), residues: 127
  loop :  0.09 (0.46), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 623 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.008   0.001   PHE F 334 
 TYR   0.011   0.001   TYR B 494 
 ARG   0.001   0.000   ARG F 385 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.466 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8516 (ptm-80) cc_final: 0.8266 (ttp-110)
REVERT: A   69 ILE cc_start: 0.7159 (tp) cc_final: 0.6945 (tp)
REVERT: A   74 LYS cc_start: 0.8613 (ttpt) cc_final: 0.8339 (ttpt)
REVERT: B  429 ASN cc_start: 0.8788 (t0) cc_final: 0.8468 (t0)
REVERT: B  572 TYR cc_start: 0.8061 (p90) cc_final: 0.7639 (p90)
REVERT: B  612 ARG cc_start: 0.8760 (ttt180) cc_final: 0.8154 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8702 (pt) cc_final: 0.8223 (mm)
REVERT: F  393 ASN cc_start: 0.7804 (t0) cc_final: 0.6930 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1509
  time to fit residues: 19.5263
Evaluate side-chains
  81 residues out of total 408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    0.0010
   chunk 16 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 13 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 461 GLN
F 369 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.4672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3588  Z= 0.191
  Angle     :  0.593  11.937   4885  Z= 0.299
  Chirality :  0.045   0.195    572
  Planarity :  0.003   0.028    615
  Dihedral  :  4.504  31.928    496
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.64 (0.41), residues: 433
  helix:  3.47 (0.51), residues: 96
  sheet:  0.82 (0.40), residues: 138
  loop :  0.14 (0.47), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 584 
 PHE   0.009   0.001   PHE F 334 
 TYR   0.013   0.001   TYR F 352 
 ARG   0.001   0.000   ARG F 385 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.446 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8500 (ptm-80) cc_final: 0.8264 (ttp-110)
REVERT: A   69 ILE cc_start: 0.7145 (tp) cc_final: 0.6938 (tp)
REVERT: A   74 LYS cc_start: 0.8609 (ttpt) cc_final: 0.8324 (ttpt)
REVERT: B  429 ASN cc_start: 0.8746 (t0) cc_final: 0.8430 (t0)
REVERT: B  572 TYR cc_start: 0.8106 (p90) cc_final: 0.7671 (p90)
REVERT: B  612 ARG cc_start: 0.8776 (ttt180) cc_final: 0.8153 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8735 (pt) cc_final: 0.8247 (mm)
REVERT: F  393 ASN cc_start: 0.7782 (t0) cc_final: 0.6660 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1656
  time to fit residues: 19.2838
Evaluate side-chains
  78 residues out of total 408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0370
   chunk 3 optimal weight:    0.0370
   chunk 13 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 39 optimal weight:    0.1980
   chunk 4 optimal weight:    0.9990
   chunk 23 optimal weight:    0.3980
   chunk 29 optimal weight:   10.0000
   overall best weight:    0.2736

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 369 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.4865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3588  Z= 0.151
  Angle     :  0.565  10.023   4885  Z= 0.286
  Chirality :  0.044   0.172    572
  Planarity :  0.003   0.026    615
  Dihedral  :  4.432  33.804    496
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.52 (0.41), residues: 433
  helix:  3.11 (0.52), residues: 102
  sheet:  0.88 (0.43), residues: 127
  loop :  0.04 (0.45), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 584 
 PHE   0.007   0.001   PHE F 348 
 TYR   0.010   0.001   TYR F 352 
 ARG   0.001   0.000   ARG F 419 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.423 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8469 (ptm-80) cc_final: 0.8225 (ttp-110)
REVERT: A   74 LYS cc_start: 0.8599 (ttpt) cc_final: 0.8365 (ttpt)
REVERT: B  429 ASN cc_start: 0.8743 (t0) cc_final: 0.8438 (t0)
REVERT: B  442 LYS cc_start: 0.8884 (pttt) cc_final: 0.8678 (pttp)
REVERT: B  453 GLN cc_start: 0.8691 (pt0) cc_final: 0.8164 (pm20)
REVERT: B  612 ARG cc_start: 0.8711 (ttt180) cc_final: 0.8110 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7699 (t0) cc_final: 0.6814 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1557
  time to fit residues: 19.3199
Evaluate side-chains
  84 residues out of total 408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 461 GLN
** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.4927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3588  Z= 0.227
  Angle     :  0.590   8.862   4885  Z= 0.302
  Chirality :  0.045   0.204    572
  Planarity :  0.003   0.027    615
  Dihedral  :  4.529  30.820    496
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.66 (0.41), residues: 433
  helix:  3.42 (0.50), residues: 96
  sheet:  0.98 (0.41), residues: 138
  loop :  0.07 (0.47), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 447 
 HIS   0.004   0.001   HIS B 465 
 PHE   0.010   0.001   PHE F 348 
 TYR   0.015   0.001   TYR A  82 
 ARG   0.001   0.000   ARG F 398 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.8494 (ptm-80) cc_final: 0.8256 (ttp-110)
REVERT: A   69 ILE cc_start: 0.7139 (tp) cc_final: 0.6918 (tp)
REVERT: A   74 LYS cc_start: 0.8669 (ttpt) cc_final: 0.8388 (ttpt)
REVERT: B  429 ASN cc_start: 0.8732 (t0) cc_final: 0.8452 (t0)
REVERT: B  453 GLN cc_start: 0.8790 (pt0) cc_final: 0.8153 (pm20)
REVERT: B  553 LYS cc_start: 0.8088 (ptmm) cc_final: 0.7810 (pttm)
REVERT: B  612 ARG cc_start: 0.8774 (ttt180) cc_final: 0.8215 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7769 (t0) cc_final: 0.6856 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1547
  time to fit residues: 18.4291
Evaluate side-chains
  81 residues out of total 408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0020
   chunk 22 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0670
   chunk 29 optimal weight:    8.9990
   chunk 11 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.5328

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 369 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.5100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3588  Z= 0.182
  Angle     :  0.574   8.093   4885  Z= 0.293
  Chirality :  0.045   0.197    572
  Planarity :  0.003   0.031    615
  Dihedral  :  4.550  34.520    496
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.58 (0.41), residues: 433
  helix:  3.07 (0.52), residues: 102
  sheet:  1.07 (0.44), residues: 127
  loop :  0.01 (0.46), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.013   0.001   PHE F 348 
 TYR   0.008   0.001   TYR F 424 
 ARG   0.001   0.000   ARG F 398 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.8500 (ptm-80) cc_final: 0.8251 (ttp-110)
REVERT: A   69 ILE cc_start: 0.6755 (tp) cc_final: 0.6366 (tp)
REVERT: A   74 LYS cc_start: 0.8579 (ttpt) cc_final: 0.8294 (ttpt)
REVERT: B  429 ASN cc_start: 0.8723 (t0) cc_final: 0.8446 (t0)
REVERT: B  453 GLN cc_start: 0.8794 (pt0) cc_final: 0.8146 (pm20)
REVERT: B  540 ASN cc_start: 0.8762 (t0) cc_final: 0.8387 (t0)
REVERT: B  553 LYS cc_start: 0.8061 (ptmm) cc_final: 0.7738 (mtmm)
REVERT: B  612 ARG cc_start: 0.8779 (ttt180) cc_final: 0.8235 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7758 (t0) cc_final: 0.6859 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1574
  time to fit residues: 18.8133
Evaluate side-chains
  81 residues out of total 408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0270
   chunk 24 optimal weight:    0.0470
   chunk 39 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0470
   chunk 27 optimal weight:    0.7980
   chunk 41 optimal weight:    0.3980
   chunk 38 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.2234

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 461 GLN
** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 369 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.5213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3588  Z= 0.145
  Angle     :  0.554   7.465   4885  Z= 0.285
  Chirality :  0.044   0.187    572
  Planarity :  0.004   0.034    615
  Dihedral  :  4.540  37.096    496
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.58 (0.41), residues: 433
  helix:  2.85 (0.51), residues: 108
  sheet:  1.11 (0.44), residues: 127
  loop :  0.02 (0.46), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 367 
 HIS   0.003   0.001   HIS B 584 
 PHE   0.012   0.001   PHE F 348 
 TYR   0.010   0.001   TYR A  82 
 ARG   0.001   0.000   ARG F 398 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.426 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8488 (ptm-80) cc_final: 0.8185 (ttp-110)
REVERT: A   69 ILE cc_start: 0.6767 (tp) cc_final: 0.6375 (tp)
REVERT: A   74 LYS cc_start: 0.8520 (ttpt) cc_final: 0.8222 (ttpt)
REVERT: B  429 ASN cc_start: 0.8712 (t0) cc_final: 0.8462 (t0)
REVERT: B  453 GLN cc_start: 0.8790 (pt0) cc_final: 0.8200 (pm20)
REVERT: B  540 ASN cc_start: 0.8673 (t0) cc_final: 0.8416 (t0)
REVERT: B  542 LYS cc_start: 0.8514 (mmtm) cc_final: 0.8248 (mmtm)
REVERT: B  553 LYS cc_start: 0.8031 (ptmm) cc_final: 0.7719 (mtmm)
REVERT: B  612 ARG cc_start: 0.8763 (ttt180) cc_final: 0.8204 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7638 (t0) cc_final: 0.6762 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1662
  time to fit residues: 20.7272
Evaluate side-chains
  82 residues out of total 408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 10 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0010
   chunk 4 optimal weight:    0.0010
   chunk 9 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0870
   chunk 34 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0970
   overall best weight:    0.1968

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 369 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.5332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3588  Z= 0.140
  Angle     :  0.554   6.648   4885  Z= 0.285
  Chirality :  0.044   0.208    572
  Planarity :  0.003   0.029    615
  Dihedral  :  4.364  35.454    496
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.62 (0.41), residues: 433
  helix:  2.91 (0.51), residues: 108
  sheet:  1.20 (0.44), residues: 127
  loop : -0.03 (0.45), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 366 
 HIS   0.004   0.001   HIS B 584 
 PHE   0.012   0.001   PHE F 348 
 TYR   0.013   0.001   TYR B 572 
 ARG   0.002   0.000   ARG F 398 

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.8465 (ptm-80) cc_final: 0.8187 (ttp-110)
REVERT: B  429 ASN cc_start: 0.8748 (t0) cc_final: 0.8522 (t0)
REVERT: B  453 GLN cc_start: 0.8791 (pt0) cc_final: 0.8222 (pm20)
REVERT: B  553 LYS cc_start: 0.8065 (ptmm) cc_final: 0.7778 (mtmm)
REVERT: B  612 ARG cc_start: 0.8654 (ttt180) cc_final: 0.8123 (ttt-90)
REVERT: F  355 GLU cc_start: 0.8406 (pm20) cc_final: 0.8164 (pm20)
REVERT: F  393 ASN cc_start: 0.7492 (t0) cc_final: 0.6610 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1469
  time to fit residues: 18.5095
Evaluate side-chains
  80 residues out of total 408 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 24 optimal weight:    0.3980
   chunk 38 optimal weight:    4.9990
   chunk 22 optimal weight:    0.1980
   chunk 28 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0870
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 461 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.113493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.093040 restraints weight = 8025.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.095763 restraints weight = 4903.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.097654 restraints weight = 3416.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.5427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3588  Z= 0.163
  Angle     :  0.568   6.404   4885  Z= 0.290
  Chirality :  0.045   0.226    572
  Planarity :  0.003   0.029    615
  Dihedral  :  4.332  34.416    496
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.55 (0.42), residues: 433
  helix:  2.85 (0.52), residues: 108
  sheet:  0.90 (0.44), residues: 136
  loop :  0.11 (0.47), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 366 
 HIS   0.003   0.001   HIS B 584 
 PHE   0.011   0.001   PHE F 348 
 TYR   0.018   0.001   TYR A  82 
 ARG   0.001   0.000   ARG F 398 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1592.25 seconds
wall clock time: 29 minutes 8.65 seconds (1748.65 seconds total)