Starting phenix.real_space_refine
on Mon Feb 10 23:46:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yd1_33745/02_2025/7yd1_33745.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yd1_33745/02_2025/7yd1_33745.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yd1_33745/02_2025/7yd1_33745.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yd1_33745/02_2025/7yd1_33745.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yd1_33745/02_2025/7yd1_33745.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yd1_33745/02_2025/7yd1_33745.cif"
  }
  resolution = 2.99
  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=   0.011
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      16      5.16       5
     C    2104      2.51       5
     N     550      2.21       5
     O     635      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3305
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 1588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1588
          Classifications: {'peptide': 198}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 185}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 931
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 7, 'TRANS': 114}
    Chain: "B"
      Number of atoms: 786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 786
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
  Time building chain proxies: 3.00, per 1000 atoms: 0.91
  Number of scatterers: 3305
  At special positions: 0
  Unit cell: (84.056, 84.056, 92.568, 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      16     16.00
     O     635      8.00
     N     550      7.00
     C    2104      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  90 " distance=2.03

  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: 0.64
  Conformation dependent library (CDL) restraints added in 384.7 milliseconds
  

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  792

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 9 sheets defined
      6.8% alpha, 22.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 364 through 370
    Processing helix  chain 'C' and resid 406 through 410
    Processing helix  chain 'C' and resid 417 through 422
    Processing helix  chain 'B' and resid 81 through 85
      removed outlier: 3.523A  pdb=" N   ASP B  84 " --> pdb=" O   GLN B  81 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   GLU B  85 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 81 through 85'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.532A  pdb=" N   ALA C 397 " --> pdb=" O   LYS C 356 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   VAL C 433 " --> pdb=" O   LYS C 378 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362
      removed outlier: 6.542A  pdb=" N   CYS C 361 " --> pdb=" O   CYS C 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 473 through 474
      removed outlier: 3.508A  pdb=" N   TYR C 473 " --> pdb=" O   TYR C 489 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   TYR C 489 " --> pdb=" O   TYR C 473 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 3 through 6
    Processing sheet with id=AA5, first strand: chain 'A' and resid 11 through 12
    Processing sheet with id=AA6, first strand: chain 'A' and resid 37 through 40
      removed outlier: 6.657A  pdb=" N   TRP A  38 " --> pdb=" O   LEU A  50 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 12
    Processing sheet with id=AA8, first strand: chain 'B' and resid 18 through 23
    Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 50
      removed outlier: 6.771A  pdb=" N   TRP B  37 " --> pdb=" O   MET B  49 " (cutoff:3.500A)

    77 hydrogen bonds defined for protein.
    177 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: 0.84

  Time building geometry restraints manager: 0.78 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: 1045
        1.34 -     1.46: 849
        1.46 -     1.58: 1476
        1.58 -     1.69: 0
        1.69 -     1.81: 19
  Bond restraints: 3389
  Sorted by residual:
  bond pdb=" N   ASP B  52 "
       pdb=" CA  ASP B  52 "
    ideal  model  delta    sigma   weight residual
    1.457  1.467 -0.010 1.32e-02 5.74e+03 5.68e-01
  bond pdb=" C   SER A  67 "
       pdb=" N   SER A  68 "
    ideal  model  delta    sigma   weight residual
    1.332  1.323  0.009 1.40e-02 5.10e+03 4.49e-01
  bond pdb=" CA  PHE A 107 "
       pdb=" C   PHE A 107 "
    ideal  model  delta    sigma   weight residual
    1.531  1.524  0.007 1.08e-02 8.57e+03 4.23e-01
  bond pdb=" CG  PRO A  89 "
       pdb=" CD  PRO A  89 "
    ideal  model  delta    sigma   weight residual
    1.503  1.486  0.017 3.40e-02 8.65e+02 2.47e-01
  bond pdb=" C   TYR B  51 "
       pdb=" N   ASP B  52 "
    ideal  model  delta    sigma   weight residual
    1.332  1.339 -0.006 1.37e-02 5.33e+03 2.17e-01
  ... (remaining 3384 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 4552
        1.82 -     3.63: 63
        3.63 -     5.45: 3
        5.45 -     7.26: 0
        7.26 -     9.08: 1
  Bond angle restraints: 4619
  Sorted by residual:
  angle pdb=" N   VAL B  53 "
        pdb=" CA  VAL B  53 "
        pdb=" C   VAL B  53 "
      ideal   model   delta    sigma   weight residual
     109.34  113.82   -4.48 2.08e+00 2.31e-01 4.63e+00
  angle pdb=" CA  TYR B  51 "
        pdb=" CB  TYR B  51 "
        pdb=" CG  TYR B  51 "
      ideal   model   delta    sigma   weight residual
     113.90  117.74   -3.84 1.80e+00 3.09e-01 4.56e+00
  angle pdb=" C   ASP B  52 "
        pdb=" N   VAL B  53 "
        pdb=" CA  VAL B  53 "
      ideal   model   delta    sigma   weight residual
     121.97  125.50   -3.53 1.80e+00 3.09e-01 3.85e+00
  angle pdb=" CA  PHE A 107 "
        pdb=" C   PHE A 107 "
        pdb=" N   ASP A 108 "
      ideal   model   delta    sigma   weight residual
     114.17  117.17   -3.00 1.55e+00 4.16e-01 3.75e+00
  angle pdb=" C   TYR B  51 "
        pdb=" N   ASP B  52 "
        pdb=" CA  ASP B  52 "
      ideal   model   delta    sigma   weight residual
     121.31  124.15   -2.84 1.49e+00 4.50e-01 3.63e+00
  ... (remaining 4614 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.48: 1791
        9.48 -    18.96: 128
       18.96 -    28.44: 62
       28.44 -    37.93: 24
       37.93 -    47.41: 4
  Dihedral angle restraints: 2009
    sinusoidal: 766
      harmonic: 1243
  Sorted by residual:
  dihedral pdb=" CA  ASP B  52 "
           pdb=" C   ASP B  52 "
           pdb=" N   VAL B  53 "
           pdb=" CA  VAL B  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.24  -23.76     0      5.00e+00 4.00e-02 2.26e+01
  dihedral pdb=" CA  TYR B  51 "
           pdb=" C   TYR B  51 "
           pdb=" N   ASP B  52 "
           pdb=" CA  ASP B  52 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.50  -18.50     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  SER B  26 "
           pdb=" C   SER B  26 "
           pdb=" N   SER B  27 "
           pdb=" CA  SER B  27 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.42  -17.58     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 2006 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 279
       0.024 -    0.048: 143
       0.048 -    0.072: 48
       0.072 -    0.096: 26
       0.096 -    0.120: 20
  Chirality restraints: 516
  Sorted by residual:
  chirality pdb=" CA  ILE B  20 "
            pdb=" N   ILE B  20 "
            pdb=" C   ILE B  20 "
            pdb=" CB  ILE B  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.59e-01
  chirality pdb=" CA  VAL B  98 "
            pdb=" N   VAL B  98 "
            pdb=" C   VAL B  98 "
            pdb=" CB  VAL B  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.59e-01
  chirality pdb=" CA  ILE B  77 "
            pdb=" N   ILE B  77 "
            pdb=" C   ILE B  77 "
            pdb=" CB  ILE B  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.49e-01
  ... (remaining 513 not shown)

  Planarity restraints: 590
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 462 "    0.034 5.00e-02 4.00e+02   5.16e-02 4.26e+00
        pdb=" N   PRO C 463 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO C 463 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO C 463 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  88 "   -0.023 5.00e-02 4.00e+02   3.47e-02 1.92e+00
        pdb=" N   PRO A  89 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A  89 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A  89 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 383 "    0.019 5.00e-02 4.00e+02   2.88e-02 1.33e+00
        pdb=" N   PRO C 384 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO C 384 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 384 "    0.016 5.00e-02 4.00e+02
  ... (remaining 587 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 319
        2.75 -     3.29: 3186
        3.29 -     3.83: 5375
        3.83 -     4.36: 6403
        4.36 -     4.90: 11033
  Nonbonded interactions: 26316
  Sorted by model distance:
  nonbonded pdb=" OG  SER A   7 "
            pdb=" OG1 THR A  21 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OG1 THR B   5 "
            pdb=" OG1 THR B  23 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OG1 THR A  70 "
            pdb=" OG1 THR A  83 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   ILE A 106 "
            pdb=" OH  TYR B  38 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   THR C 393 "
            pdb=" OG1 THR C 523 "
     model   vdw
     2.310 3.040
  ... (remaining 26311 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             2.600
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.310
  Find NCS groups from input model:        0.060
  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:13.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7169
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      :  0.002   0.017   3389  Z= 0.104
  Angle     :  0.491   9.075   4619  Z= 0.261
  Chirality :  0.039   0.120    516
  Planarity :  0.004   0.052    590
  Dihedral  :  8.999  47.407   1199
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.95 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  :  5.19 %
    Favored  : 89.34 %
  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: -4.06 (0.37), residues: 422
  helix: -5.17 (0.22), residues: 20
  sheet: -1.77 (0.41), residues: 144
  loop : -3.20 (0.35), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 436 
 HIS   0.000   0.000   HIS B  41 
 PHE   0.007   0.001   PHE C 429 
 TYR   0.018   0.001   TYR B  51 
 ARG   0.002   0.000   ARG C 457 

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.369 
Fit side-chains
REVERT: C  346 ARG cc_start: 0.6893 (tpt90) cc_final: 0.6617 (tpt90)
REVERT: C  392 PHE cc_start: 0.8236 (m-80) cc_final: 0.8025 (m-80)
REVERT: C  395 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8421 (m)
REVERT: C  399 SER cc_start: 0.8317 (m) cc_final: 0.7941 (p)
REVERT: C  429 PHE cc_start: 0.7342 (t80) cc_final: 0.7096 (t80)
REVERT: C  437 ASN cc_start: 0.7918 (t0) cc_final: 0.7672 (t0)
REVERT: C  438 SER cc_start: 0.8450 (p) cc_final: 0.8188 (p)
REVERT: C  455 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7534 (tm)
REVERT: C  456 PHE cc_start: 0.6700 (m-80) cc_final: 0.6210 (m-80)
REVERT: C  494 SER cc_start: 0.8374 (t) cc_final: 0.8150 (p)
REVERT: C  515 PHE cc_start: 0.8611 (m-10) cc_final: 0.8263 (m-10)
REVERT: A   18 LEU cc_start: 0.8044 (mt) cc_final: 0.7368 (mp)
REVERT: A   47 LEU cc_start: 0.8403 (mt) cc_final: 0.8120 (mt)
REVERT: A   52 LEU cc_start: 0.8743 (tp) cc_final: 0.8466 (tp)
REVERT: A   61 TYR cc_start: 0.8444 (m-80) cc_final: 0.7757 (m-80)
REVERT: A   87 MET cc_start: 0.6147 (mmm) cc_final: 0.5527 (mmm)
REVERT: A  107 PHE cc_start: 0.8136 (m-10) cc_final: 0.7886 (m-10)
REVERT: A  112 GLN cc_start: 0.6423 (pp30) cc_final: 0.6127 (pp30)
  outliers start: 20
  outliers final: 5
  residues processed: 124
  average time/residue: 0.5125
  time to fit residues: 67.5292
Evaluate side-chains
  107 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  455 LEU
Chi-restraints excluded: chain A residue   92 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 16 optimal weight:    0.4980
   chunk 32 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0980
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0770
   chunk 37 optimal weight:    0.0060
   overall best weight:    0.2954

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 460 ASN
C 506 GLN
A  16 GLN
A  78 ASN
A  79 GLN
B  39 GLN
B  81 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.135347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.123618 restraints weight = 5122.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 2.39
r_work: 0.3537 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3381 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3389  Z= 0.209
  Angle     :  0.596  10.594   4619  Z= 0.296
  Chirality :  0.043   0.199    516
  Planarity :  0.005   0.054    590
  Dihedral  :  5.466  43.874    479
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.95 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 12.30 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.48 (0.38), residues: 422
  helix: -5.05 (0.25), residues: 20
  sheet: -1.35 (0.41), residues: 144
  loop : -2.78 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  49 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.011   0.001   PHE A  24 
 TYR   0.017   0.001   TYR B  51 
 ARG   0.002   0.000   ARG C 457 

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.355 
Fit side-chains
REVERT: C  346 ARG cc_start: 0.7600 (tpt90) cc_final: 0.7239 (tpt90)
REVERT: C  392 PHE cc_start: 0.8422 (m-80) cc_final: 0.8076 (m-80)
REVERT: C  395 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8492 (m)
REVERT: C  399 SER cc_start: 0.8668 (m) cc_final: 0.8394 (p)
REVERT: C  407 VAL cc_start: 0.8767 (t) cc_final: 0.8552 (p)
REVERT: C  429 PHE cc_start: 0.7824 (t80) cc_final: 0.7458 (t80)
REVERT: C  438 SER cc_start: 0.8665 (p) cc_final: 0.8393 (p)
REVERT: C  445 VAL cc_start: 0.8636 (t) cc_final: 0.8412 (m)
REVERT: C  456 PHE cc_start: 0.7339 (m-80) cc_final: 0.7100 (m-80)
REVERT: C  473 TYR cc_start: 0.6938 (t80) cc_final: 0.6613 (t80)
REVERT: C  494 SER cc_start: 0.8451 (t) cc_final: 0.8226 (p)
REVERT: A   18 LEU cc_start: 0.7747 (mt) cc_final: 0.7273 (mp)
REVERT: A   41 GLN cc_start: 0.8367 (tt0) cc_final: 0.8005 (tt0)
REVERT: A   52 LEU cc_start: 0.8999 (tp) cc_final: 0.8777 (tp)
REVERT: A   96 TYR cc_start: 0.8656 (m-80) cc_final: 0.8400 (m-80)
REVERT: A  107 PHE cc_start: 0.8185 (m-10) cc_final: 0.7954 (m-10)
REVERT: B   63 ARG cc_start: 0.8516 (mtp180) cc_final: 0.8261 (mtp180)
REVERT: B   83 GLU cc_start: 0.7767 (mp0) cc_final: 0.7364 (mp0)
  outliers start: 18
  outliers final: 7
  residues processed: 111
  average time/residue: 0.4744
  time to fit residues: 56.3534
Evaluate side-chains
  107 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue   92 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0770
   chunk 30 optimal weight:    0.8980
   chunk 34 optimal weight:    0.4980
   chunk 28 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0370
   chunk 0 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.3616

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

Flipped N/Q/H residues before XYZ refinement:
C 388 ASN
C 409 GLN
C 506 GLN
B  33 ASN
B  41 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.133076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.121882 restraints weight = 5071.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 2.32
r_work: 0.3514 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3359 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3389  Z= 0.248
  Angle     :  0.615  10.439   4619  Z= 0.300
  Chirality :  0.044   0.228    516
  Planarity :  0.005   0.056    590
  Dihedral  :  5.453  44.871    477
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 15.30 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.07 (0.39), residues: 422
  helix: -4.98 (0.27), residues: 20
  sheet: -0.99 (0.42), residues: 142
  loop : -2.53 (0.38), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  49 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.021   0.001   PHE A  24 
 TYR   0.024   0.002   TYR C 380 
 ARG   0.002   0.000   ARG C 457 

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.364 
Fit side-chains
REVERT: C  395 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8478 (m)
REVERT: C  396 TYR cc_start: 0.7919 (m-80) cc_final: 0.7693 (m-80)
REVERT: C  399 SER cc_start: 0.8703 (m) cc_final: 0.8416 (p)
REVERT: C  407 VAL cc_start: 0.8740 (t) cc_final: 0.8513 (p)
REVERT: C  429 PHE cc_start: 0.7863 (t80) cc_final: 0.7579 (t80)
REVERT: C  438 SER cc_start: 0.8686 (p) cc_final: 0.8425 (p)
REVERT: C  456 PHE cc_start: 0.7629 (m-80) cc_final: 0.7397 (m-80)
REVERT: C  473 TYR cc_start: 0.6979 (t80) cc_final: 0.6679 (t80)
REVERT: C  494 SER cc_start: 0.8543 (t) cc_final: 0.8308 (p)
REVERT: A   18 LEU cc_start: 0.7812 (mt) cc_final: 0.7295 (mp)
REVERT: A   52 LEU cc_start: 0.9004 (tp) cc_final: 0.8793 (tp)
REVERT: A   92 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8588 (p)
REVERT: A   96 TYR cc_start: 0.8676 (m-80) cc_final: 0.8414 (m-80)
REVERT: A  107 PHE cc_start: 0.8223 (m-10) cc_final: 0.8011 (m-10)
REVERT: B   20 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7780 (mm)
REVERT: B   55 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6918 (mptp)
REVERT: B   83 GLU cc_start: 0.7919 (mp0) cc_final: 0.7467 (mp0)
  outliers start: 18
  outliers final: 8
  residues processed: 107
  average time/residue: 0.5350
  time to fit residues: 60.8714
Evaluate side-chains
  111 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   55 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0870
   chunk 21 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0970
   chunk 22 optimal weight:    0.4980
   chunk 9 optimal weight:    0.0980
   chunk 19 optimal weight:    0.2980
   overall best weight:    0.2156

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 414 GLN
C 506 GLN
A  78 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.134431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.122934 restraints weight = 5170.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 2.41
r_work: 0.3524 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3365 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3389  Z= 0.171
  Angle     :  0.584   9.868   4619  Z= 0.280
  Chirality :  0.042   0.182    516
  Planarity :  0.005   0.056    590
  Dihedral  :  5.363  42.699    477
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 17.49 %
    Favored  : 78.42 %
  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: -2.78 (0.40), residues: 422
  helix: -4.95 (0.27), residues: 20
  sheet: -0.72 (0.43), residues: 141
  loop : -2.36 (0.38), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 436 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.018   0.001   PHE A  24 
 TYR   0.016   0.001   TYR B  51 
 ARG   0.001   0.000   ARG C 408 

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: C  357 ARG cc_start: 0.8287 (ptp-170) cc_final: 0.8046 (ptp-170)
REVERT: C  392 PHE cc_start: 0.8439 (m-80) cc_final: 0.8070 (m-80)
REVERT: C  395 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8485 (m)
REVERT: C  396 TYR cc_start: 0.8041 (m-80) cc_final: 0.7612 (m-80)
REVERT: C  399 SER cc_start: 0.8711 (m) cc_final: 0.8488 (p)
REVERT: C  407 VAL cc_start: 0.8743 (t) cc_final: 0.8510 (p)
REVERT: C  438 SER cc_start: 0.8669 (p) cc_final: 0.8359 (p)
REVERT: C  456 PHE cc_start: 0.7650 (m-80) cc_final: 0.7377 (m-80)
REVERT: C  494 SER cc_start: 0.8501 (t) cc_final: 0.8281 (p)
REVERT: A   18 LEU cc_start: 0.7782 (mt) cc_final: 0.7304 (mp)
REVERT: A   52 LEU cc_start: 0.9011 (tp) cc_final: 0.8766 (tp)
REVERT: A   96 TYR cc_start: 0.8681 (m-80) cc_final: 0.8412 (m-80)
REVERT: B   20 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7733 (mm)
REVERT: B   55 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6860 (mptp)
REVERT: B   63 ARG cc_start: 0.8587 (mtp180) cc_final: 0.8105 (mtp180)
REVERT: B   83 GLU cc_start: 0.7955 (mp0) cc_final: 0.7396 (mp0)
  outliers start: 15
  outliers final: 8
  residues processed: 105
  average time/residue: 0.5345
  time to fit residues: 59.6527
Evaluate side-chains
  107 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   55 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0770
   chunk 3 optimal weight:    0.7980
   chunk 21 optimal weight:    0.1980
   chunk 37 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0870
   overall best weight:    0.3116

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 506 GLN
A  78 ASN
B  40 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.133036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.121562 restraints weight = 5157.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 2.39
r_work: 0.3514 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3355 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.2724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3389  Z= 0.220
  Angle     :  0.604  10.964   4619  Z= 0.290
  Chirality :  0.043   0.194    516
  Planarity :  0.005   0.056    590
  Dihedral  :  5.498  42.869    477
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 19.13 %
    Favored  : 77.05 %
  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: -2.55 (0.40), residues: 422
  helix: -4.85 (0.31), residues: 20
  sheet: -0.54 (0.43), residues: 139
  loop : -2.20 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  49 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.008   0.001   PHE C 400 
 TYR   0.023   0.001   TYR C 380 
 ARG   0.001   0.000   ARG C 408 

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.295 
Fit side-chains
REVERT: C  357 ARG cc_start: 0.8261 (ptp-170) cc_final: 0.8023 (ptp-170)
REVERT: C  367 VAL cc_start: 0.8119 (OUTLIER) cc_final: 0.7900 (m)
REVERT: C  395 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8480 (m)
REVERT: C  396 TYR cc_start: 0.8038 (m-80) cc_final: 0.7477 (m-80)
REVERT: C  399 SER cc_start: 0.8726 (m) cc_final: 0.8466 (p)
REVERT: C  407 VAL cc_start: 0.8749 (t) cc_final: 0.8527 (p)
REVERT: C  414 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7944 (mm-40)
REVERT: C  438 SER cc_start: 0.8669 (p) cc_final: 0.8374 (p)
REVERT: C  445 VAL cc_start: 0.8625 (t) cc_final: 0.8389 (m)
REVERT: C  456 PHE cc_start: 0.7676 (m-80) cc_final: 0.7450 (m-80)
REVERT: C  473 TYR cc_start: 0.6889 (t80) cc_final: 0.6373 (t80)
REVERT: C  494 SER cc_start: 0.8564 (t) cc_final: 0.8303 (p)
REVERT: A   18 LEU cc_start: 0.7856 (mt) cc_final: 0.7327 (mp)
REVERT: A   52 LEU cc_start: 0.9019 (tp) cc_final: 0.8786 (tp)
REVERT: A   92 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8605 (p)
REVERT: A   96 TYR cc_start: 0.8692 (m-80) cc_final: 0.8404 (m-80)
REVERT: B   55 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.6953 (mptp)
REVERT: B   63 ARG cc_start: 0.8600 (mtp180) cc_final: 0.8352 (mtp180)
REVERT: B   83 GLU cc_start: 0.8039 (mp0) cc_final: 0.7455 (mp0)
  outliers start: 14
  outliers final: 7
  residues processed: 107
  average time/residue: 0.5362
  time to fit residues: 60.8625
Evaluate side-chains
  106 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   55 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0170
   chunk 28 optimal weight:    0.9990
   chunk 2 optimal weight:    0.1980
   chunk 30 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0870
   chunk 1 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.3196

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 506 GLN
A  78 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.132462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.121126 restraints weight = 5268.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 2.36
r_work: 0.3510 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3355 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3389  Z= 0.227
  Angle     :  0.612  11.676   4619  Z= 0.292
  Chirality :  0.044   0.212    516
  Planarity :  0.005   0.057    590
  Dihedral  :  5.220  35.228    475
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.95 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.39 (0.40), residues: 422
  helix: -4.81 (0.33), residues: 20
  sheet: -0.46 (0.43), residues: 139
  loop : -2.05 (0.39), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  49 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.016   0.001   PHE A  24 
 TYR   0.018   0.001   TYR C 380 
 ARG   0.001   0.000   ARG C 457 

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.310 
Fit side-chains
REVERT: C  357 ARG cc_start: 0.8243 (ptp-170) cc_final: 0.8003 (ptp-170)
REVERT: C  367 VAL cc_start: 0.8081 (OUTLIER) cc_final: 0.7870 (m)
REVERT: C  395 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8499 (m)
REVERT: C  396 TYR cc_start: 0.8043 (m-80) cc_final: 0.7536 (m-80)
REVERT: C  399 SER cc_start: 0.8742 (m) cc_final: 0.8464 (p)
REVERT: C  407 VAL cc_start: 0.8759 (t) cc_final: 0.8531 (p)
REVERT: C  414 GLN cc_start: 0.8260 (mm-40) cc_final: 0.7947 (mm-40)
REVERT: C  438 SER cc_start: 0.8682 (p) cc_final: 0.8365 (p)
REVERT: C  445 VAL cc_start: 0.8633 (t) cc_final: 0.8401 (m)
REVERT: C  456 PHE cc_start: 0.7674 (m-80) cc_final: 0.7469 (m-80)
REVERT: C  473 TYR cc_start: 0.6791 (t80) cc_final: 0.6381 (t80)
REVERT: C  494 SER cc_start: 0.8617 (t) cc_final: 0.8359 (p)
REVERT: C  503 VAL cc_start: 0.8574 (t) cc_final: 0.8148 (p)
REVERT: A   52 LEU cc_start: 0.9027 (tp) cc_final: 0.8822 (tp)
REVERT: A   92 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8634 (p)
REVERT: A   96 TYR cc_start: 0.8675 (m-80) cc_final: 0.8376 (m-80)
REVERT: B   55 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7014 (mptp)
REVERT: B   63 ARG cc_start: 0.8602 (mtp180) cc_final: 0.8346 (mtp180)
REVERT: B   83 GLU cc_start: 0.8055 (mp0) cc_final: 0.7456 (mp0)
  outliers start: 12
  outliers final: 7
  residues processed: 110
  average time/residue: 0.5216
  time to fit residues: 60.9631
Evaluate side-chains
  109 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   55 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 23 optimal weight:    0.4980
   chunk 17 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 1 optimal weight:    0.4980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 506 GLN
A  78 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.129556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.118338 restraints weight = 5144.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 2.30
r_work: 0.3485 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.3148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   3389  Z= 0.340
  Angle     :  0.663  12.642   4619  Z= 0.324
  Chirality :  0.045   0.215    516
  Planarity :  0.005   0.059    590
  Dihedral  :  5.515  35.513    475
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.90 %
    Favored  : 89.10 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 20.77 %
    Favored  : 75.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -2.35 (0.41), residues: 422
  helix: -4.80 (0.33), residues: 20
  sheet: -0.41 (0.44), residues: 138
  loop : -2.03 (0.39), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  49 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.010   0.001   PHE C 400 
 TYR   0.020   0.002   TYR C 380 
 ARG   0.002   0.000   ARG C 457 

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.359 
Fit side-chains
REVERT: C  357 ARG cc_start: 0.8259 (ptp-170) cc_final: 0.8017 (ptp-170)
REVERT: C  367 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7898 (m)
REVERT: C  395 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8512 (m)
REVERT: C  396 TYR cc_start: 0.8052 (m-80) cc_final: 0.7581 (m-80)
REVERT: C  399 SER cc_start: 0.8735 (m) cc_final: 0.8464 (p)
REVERT: C  407 VAL cc_start: 0.8794 (t) cc_final: 0.8560 (p)
REVERT: C  414 GLN cc_start: 0.8301 (mm-40) cc_final: 0.8053 (mm110)
REVERT: C  438 SER cc_start: 0.8704 (p) cc_final: 0.8420 (p)
REVERT: C  445 VAL cc_start: 0.8623 (t) cc_final: 0.8399 (m)
REVERT: C  473 TYR cc_start: 0.6799 (t80) cc_final: 0.6394 (t80)
REVERT: C  494 SER cc_start: 0.8643 (t) cc_final: 0.8407 (p)
REVERT: C  503 VAL cc_start: 0.8674 (t) cc_final: 0.8285 (p)
REVERT: C  512 VAL cc_start: 0.8510 (m) cc_final: 0.8226 (p)
REVERT: A   52 LEU cc_start: 0.9026 (tp) cc_final: 0.8784 (tp)
REVERT: A   92 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8635 (p)
REVERT: A   96 TYR cc_start: 0.8678 (m-80) cc_final: 0.8460 (m-80)
REVERT: B   18 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7954 (pt)
REVERT: B   55 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7098 (mptp)
REVERT: B   78 SER cc_start: 0.7932 (t) cc_final: 0.7474 (p)
REVERT: B   83 GLU cc_start: 0.8189 (mp0) cc_final: 0.7600 (mp0)
  outliers start: 15
  outliers final: 8
  residues processed: 114
  average time/residue: 0.4945
  time to fit residues: 60.0322
Evaluate side-chains
  116 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   55 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 6 optimal weight:    0.0570
   chunk 36 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0870
   chunk 3 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.4276

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 450 ASN
C 506 GLN
A  78 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.131159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.120007 restraints weight = 5174.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 2.33
r_work: 0.3494 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3337 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.3186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   3389  Z= 0.293
  Angle     :  0.656  12.088   4619  Z= 0.315
  Chirality :  0.045   0.215    516
  Planarity :  0.005   0.058    590
  Dihedral  :  5.573  39.824    475
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.48 %
    Favored  : 90.52 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 21.31 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.24 (0.41), residues: 422
  helix: -4.80 (0.33), residues: 20
  sheet: -0.32 (0.44), residues: 138
  loop : -1.95 (0.39), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 436 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.016   0.001   PHE A  24 
 TYR   0.015   0.002   TYR C 380 
 ARG   0.002   0.000   ARG C 457 

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: C  357 ARG cc_start: 0.8252 (ptp-170) cc_final: 0.8006 (ptp-170)
REVERT: C  367 VAL cc_start: 0.8038 (OUTLIER) cc_final: 0.7830 (m)
REVERT: C  395 VAL cc_start: 0.8863 (OUTLIER) cc_final: 0.8518 (m)
REVERT: C  396 TYR cc_start: 0.8024 (m-80) cc_final: 0.7558 (m-80)
REVERT: C  399 SER cc_start: 0.8745 (m) cc_final: 0.8451 (p)
REVERT: C  407 VAL cc_start: 0.8766 (t) cc_final: 0.8537 (p)
REVERT: C  438 SER cc_start: 0.8679 (p) cc_final: 0.8380 (p)
REVERT: C  473 TYR cc_start: 0.6807 (t80) cc_final: 0.6399 (t80)
REVERT: C  494 SER cc_start: 0.8625 (t) cc_final: 0.8400 (p)
REVERT: C  503 VAL cc_start: 0.8635 (t) cc_final: 0.8228 (p)
REVERT: C  512 VAL cc_start: 0.8506 (m) cc_final: 0.8215 (p)
REVERT: C  523 THR cc_start: 0.8094 (p) cc_final: 0.7719 (t)
REVERT: A   52 LEU cc_start: 0.9034 (tp) cc_final: 0.8800 (tp)
REVERT: A   92 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8638 (p)
REVERT: A   96 TYR cc_start: 0.8689 (m-80) cc_final: 0.8407 (m-80)
REVERT: B   55 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7079 (mptp)
REVERT: B   63 ARG cc_start: 0.8619 (mtp180) cc_final: 0.8145 (mtp180)
REVERT: B   78 SER cc_start: 0.7839 (t) cc_final: 0.7419 (p)
REVERT: B   83 GLU cc_start: 0.8151 (mp0) cc_final: 0.7565 (mp0)
  outliers start: 16
  outliers final: 8
  residues processed: 115
  average time/residue: 0.5202
  time to fit residues: 63.6945
Evaluate side-chains
  115 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   55 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 1 optimal weight:    0.2980
   chunk 17 optimal weight:    0.2980
   chunk 5 optimal weight:    0.2980
   chunk 16 optimal weight:    0.7980
   chunk 30 optimal weight:    0.3980
   chunk 33 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0970
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.2778

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 506 GLN
A  78 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.131254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.119961 restraints weight = 5167.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 2.34
r_work: 0.3510 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3355 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3389  Z= 0.214
  Angle     :  0.647  12.391   4619  Z= 0.305
  Chirality :  0.044   0.199    516
  Planarity :  0.005   0.057    590
  Dihedral  :  5.466  39.363    475
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 22.95 %
    Favored  : 73.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -2.14 (0.41), residues: 422
  helix: -4.76 (0.35), residues: 20
  sheet: -0.29 (0.45), residues: 139
  loop : -1.87 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 436 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.010   0.001   PHE C 456 
 TYR   0.015   0.001   TYR C 453 
 ARG   0.003   0.000   ARG C 408 

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
REVERT: C  395 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8501 (m)
REVERT: C  396 TYR cc_start: 0.8038 (m-80) cc_final: 0.7588 (m-80)
REVERT: C  399 SER cc_start: 0.8716 (m) cc_final: 0.8423 (p)
REVERT: C  407 VAL cc_start: 0.8762 (t) cc_final: 0.8546 (p)
REVERT: C  414 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7890 (mm-40)
REVERT: C  438 SER cc_start: 0.8646 (p) cc_final: 0.8329 (p)
REVERT: C  473 TYR cc_start: 0.6779 (t80) cc_final: 0.6406 (t80)
REVERT: C  503 VAL cc_start: 0.8579 (t) cc_final: 0.8164 (p)
REVERT: C  523 THR cc_start: 0.8045 (p) cc_final: 0.7667 (t)
REVERT: A   52 LEU cc_start: 0.9018 (tp) cc_final: 0.8807 (tp)
REVERT: A   92 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8669 (p)
REVERT: A   96 TYR cc_start: 0.8665 (m-80) cc_final: 0.8424 (m-80)
REVERT: B   55 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.6939 (mptp)
REVERT: B   83 GLU cc_start: 0.8124 (mp0) cc_final: 0.7528 (mp0)
  outliers start: 12
  outliers final: 7
  residues processed: 106
  average time/residue: 0.5251
  time to fit residues: 59.1413
Evaluate side-chains
  109 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   55 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 16 optimal weight:    0.4980
   chunk 8 optimal weight:    0.4980
   chunk 13 optimal weight:    0.3980
   chunk 15 optimal weight:    0.0060
   chunk 5 optimal weight:    0.2980
   chunk 7 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0050
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.2410

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 506 GLN
A  78 ASN
A  86 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.131813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.120593 restraints weight = 5114.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 2.30
r_work: 0.3524 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3371 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.3249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3389  Z= 0.194
  Angle     :  0.644  12.465   4619  Z= 0.301
  Chirality :  0.043   0.181    516
  Planarity :  0.005   0.057    590
  Dihedral  :  5.215  40.661    473
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 23.50 %
    Favored  : 73.77 %
  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 (0.41), residues: 422
  helix: -4.78 (0.34), residues: 20
  sheet: -0.40 (0.43), residues: 150
  loop : -1.74 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 436 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.013   0.001   PHE A  24 
 TYR   0.015   0.001   TYR C 453 
 ARG   0.004   0.000   ARG C 408 

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: C  395 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8494 (m)
REVERT: C  396 TYR cc_start: 0.8043 (m-80) cc_final: 0.7554 (m-80)
REVERT: C  399 SER cc_start: 0.8713 (m) cc_final: 0.8424 (p)
REVERT: C  438 SER cc_start: 0.8640 (p) cc_final: 0.8325 (p)
REVERT: C  473 TYR cc_start: 0.6763 (t80) cc_final: 0.6389 (t80)
REVERT: C  523 THR cc_start: 0.8027 (p) cc_final: 0.7652 (t)
REVERT: A   52 LEU cc_start: 0.8994 (tp) cc_final: 0.8766 (tp)
REVERT: A   87 MET cc_start: 0.6374 (mmm) cc_final: 0.5630 (mmm)
REVERT: A   92 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8665 (p)
REVERT: A   96 TYR cc_start: 0.8646 (m-80) cc_final: 0.8383 (m-80)
REVERT: B   55 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6896 (mptp)
REVERT: B   83 GLU cc_start: 0.8103 (mp0) cc_final: 0.7493 (mp0)
  outliers start: 10
  outliers final: 7
  residues processed: 106
  average time/residue: 0.5256
  time to fit residues: 59.0821
Evaluate side-chains
  108 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   55 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 16 optimal weight:    0.2980
   chunk 20 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 460 ASN
C 506 GLN
A  78 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.128842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.117485 restraints weight = 5156.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 2.29
r_work: 0.3470 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.080   3389  Z= 0.442
  Angle     :  0.742  13.635   4619  Z= 0.356
  Chirality :  0.047   0.158    516
  Planarity :  0.005   0.060    590
  Dihedral  :  5.622  37.454    473
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.61 %
    Favored  : 88.39 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 23.22 %
    Favored  : 73.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -2.18 (0.41), residues: 422
  helix: -4.92 (0.32), residues: 20
  sheet: -0.45 (0.43), residues: 149
  loop : -1.84 (0.40), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  49 
 HIS   0.001   0.000   HIS C 519 
 PHE   0.011   0.002   PHE A 107 
 TYR   0.023   0.002   TYR C 380 
 ARG   0.003   0.001   ARG C 457 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3012.04 seconds
wall clock time: 54 minutes 11.01 seconds (3251.01 seconds total)