Starting phenix.real_space_refine
on Mon Jan 13 16:29:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zpp_60351/01_2025/8zpp_60351.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zpp_60351/01_2025/8zpp_60351.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zpp_60351/01_2025/8zpp_60351.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zpp_60351/01_2025/8zpp_60351.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zpp_60351/01_2025/8zpp_60351.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zpp_60351/01_2025/8zpp_60351.cif"
  }
  resolution = 3.6
  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=  -0.001 sd=   0.051
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    2082      2.51       5
     N     540      2.21       5
     O     628      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 3266
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1532
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1532
          Classifications: {'peptide': 192}
          Link IDs: {'PTRANS': 11, 'TRANS': 180}
    Chain: "H"
      Number of atoms: 928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 928
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "L"
      Number of atoms: 806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 806
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 6, 'TRANS': 101}
  Time building chain proxies: 3.46, per 1000 atoms: 1.06
  Number of scatterers: 3266
  At special positions: 0
  Unit cell: (70.3, 68.4, 95, 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     628      8.00
     N     540      7.00
     C    2082      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " 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 492.3 milliseconds
  

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  760

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 7 sheets defined
      11.2% alpha, 33.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 343
    Processing helix  chain 'A' and resid 365 through 372
      removed outlier: 4.076A  pdb=" N   TYR A 369 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ASN A 370 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ALA A 372 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 407
      No H-bonds generated for 'chain 'A' and resid 405 through 407'
    Processing helix  chain 'A' and resid 417 through 422
    Processing helix  chain 'A' and resid 438 through 443
      removed outlier: 3.521A  pdb=" N   SER A 443 " --> pdb=" O   ASN A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 505
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'L' and resid 30 through 32
      No H-bonds generated for 'chain 'L' and resid 30 through 32'
    Processing helix  chain 'L' and resid 80 through 84
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.623A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.726A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   LYS H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   TRP H  47 " --> pdb=" O   LYS H  38 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.893A  pdb=" N   TYR H 109 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6
      removed outlier: 5.524A  pdb=" N   THR L  70 " --> pdb=" O   VAL L  25 " (cutoff:3.500A)
      removed outlier: 10.577A  pdb=" N   SER L  27 " --> pdb=" O   SER L  68 " (cutoff:3.500A)
      removed outlier: 10.555A  pdb=" N   SER L  68 " --> pdb=" O   SER L  27 " (cutoff:3.500A)
      removed outlier: 10.911A  pdb=" N   ILE L  29 " --> pdb=" O   SER L  66 " (cutoff:3.500A)
      removed outlier: 11.591A  pdb=" N   SER L  66 " --> pdb=" O   ILE L  29 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13
      removed outlier: 5.525A  pdb=" N   MET L  11 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   TYR L  87 " --> pdb=" O   THR L 103 " (cutoff:3.500A)
      removed outlier: 5.499A  pdb=" N   GLN L  38 " --> pdb=" O   PRO L  47 " (cutoff:3.500A)

    95 hydrogen bonds defined for protein.
    225 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: 0.81

  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:
        1.22 -     1.34: 1022
        1.34 -     1.46: 775
        1.46 -     1.57: 1539
        1.57 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 3356
  Sorted by residual:
  bond pdb=" CG  MET L  79 "
       pdb=" SD  MET L  79 "
    ideal  model  delta    sigma   weight residual
    1.803  1.707  0.096 2.50e-02 1.60e+03 1.48e+01
  bond pdb=" SD  MET L  79 "
       pdb=" CE  MET L  79 "
    ideal  model  delta    sigma   weight residual
    1.791  1.697  0.094 2.50e-02 1.60e+03 1.43e+01
  bond pdb=" CG  LEU H  70 "
       pdb=" CD2 LEU H  70 "
    ideal  model  delta    sigma   weight residual
    1.521  1.400  0.121 3.30e-02 9.18e+02 1.34e+01
  bond pdb=" CA  LEU H  70 "
       pdb=" C   LEU H  70 "
    ideal  model  delta    sigma   weight residual
    1.524  1.559 -0.035 1.23e-02 6.61e+03 8.19e+00
  bond pdb=" C   MET L  11 "
       pdb=" N   ALA L  12 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.32e-02 5.74e+03 6.61e+00
  ... (remaining 3351 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 4251
        1.28 -     2.55: 243
        2.55 -     3.83: 42
        3.83 -     5.11: 18
        5.11 -     6.39: 8
  Bond angle restraints: 4562
  Sorted by residual:
  angle pdb=" N   LEU H  70 "
        pdb=" CA  LEU H  70 "
        pdb=" C   LEU H  70 "
      ideal   model   delta    sigma   weight residual
     108.73  114.63   -5.90 1.63e+00 3.76e-01 1.31e+01
  angle pdb=" C   VAL A 486 "
        pdb=" N   ASN A 487 "
        pdb=" CA  ASN A 487 "
      ideal   model   delta    sigma   weight residual
     121.54  127.93   -6.39 1.91e+00 2.74e-01 1.12e+01
  angle pdb=" C   PRO H  53 "
        pdb=" CA  PRO H  53 "
        pdb=" CB  PRO H  53 "
      ideal   model   delta    sigma   weight residual
     111.85  115.90   -4.05 1.42e+00 4.96e-01 8.14e+00
  angle pdb=" CA  TYR L  95 "
        pdb=" CB  TYR L  95 "
        pdb=" CG  TYR L  95 "
      ideal   model   delta    sigma   weight residual
     113.90  109.00    4.90 1.80e+00 3.09e-01 7.43e+00
  angle pdb=" C   PHE A 371 "
        pdb=" N   ALA A 372 "
        pdb=" CA  ALA A 372 "
      ideal   model   delta    sigma   weight residual
     123.11  118.40    4.71 1.79e+00 3.12e-01 6.93e+00
  ... (remaining 4557 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.81: 1794
       16.81 -    33.63: 123
       33.63 -    50.44: 35
       50.44 -    67.25: 4
       67.25 -    84.06: 1
  Dihedral angle restraints: 1957
    sinusoidal: 750
      harmonic: 1207
  Sorted by residual:
  dihedral pdb=" CA  GLY L  94 "
           pdb=" C   GLY L  94 "
           pdb=" N   TYR L  95 "
           pdb=" CA  TYR L  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.22  -21.78     0      5.00e+00 4.00e-02 1.90e+01
  dihedral pdb=" CA  PHE A 490 "
           pdb=" C   PHE A 490 "
           pdb=" N   PRO A 491 "
           pdb=" CA  PRO A 491 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.87  -18.13     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CA  LEU A 461 "
           pdb=" C   LEU A 461 "
           pdb=" N   LYS A 462 "
           pdb=" CA  LYS A 462 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.09   17.91     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 1954 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 409
       0.069 -    0.139: 63
       0.139 -    0.208: 2
       0.208 -    0.278: 2
       0.278 -    0.347: 2
  Chirality restraints: 478
  Sorted by residual:
  chirality pdb=" CG  LEU H  70 "
            pdb=" CB  LEU H  70 "
            pdb=" CD1 LEU H  70 "
            pdb=" CD2 LEU H  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.24   -0.35 2.00e-01 2.50e+01 3.01e+00
  chirality pdb=" CA  PRO H  53 "
            pdb=" N   PRO H  53 "
            pdb=" C   PRO H  53 "
            pdb=" CB  PRO H  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.43    0.29 2.00e-01 2.50e+01 2.04e+00
  chirality pdb=" CA  THR H  71 "
            pdb=" N   THR H  71 "
            pdb=" C   THR H  71 "
            pdb=" CB  THR H  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.26    0.26 2.00e-01 2.50e+01 1.74e+00
  ... (remaining 475 not shown)

  Planarity restraints: 589
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 429 "    0.014 2.00e-02 2.50e+03   1.00e-02 1.75e+00
        pdb=" CG  PHE A 429 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 429 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 429 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 429 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 429 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 429 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 524 "    0.007 2.00e-02 2.50e+03   1.30e-02 1.68e+00
        pdb=" C   VAL A 524 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   VAL A 524 "    0.008 2.00e-02 2.50e+03
        pdb=" N   CYS A 525 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  95 "    0.010 2.00e-02 2.50e+03   7.59e-03 1.15e+00
        pdb=" CG  TYR L  95 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  95 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  95 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  95 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  95 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  95 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR L  95 "    0.001 2.00e-02 2.50e+03
  ... (remaining 586 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 737
        2.77 -     3.30: 3078
        3.30 -     3.84: 5522
        3.84 -     4.37: 6617
        4.37 -     4.90: 11471
  Nonbonded interactions: 27425
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 398 "
            pdb=" OH  TYR A 423 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   ASP L  83 "
            pdb=" OH  TYR L  87 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OD2 ASP H  73 "
            pdb=" N   SER H  76 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" O   ILE L  29 "
            pdb=" OH  TYR L  72 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   GLY L  51 "
            pdb=" OG1 THR L  52 "
     model   vdw
     2.317 3.040
  ... (remaining 27420 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 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:             2.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.950
  Find NCS groups from input model:        0.030
  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:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
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      :  0.008   0.121   3356  Z= 0.531
  Angle     :  0.754   6.386   4562  Z= 0.412
  Chirality :  0.052   0.347    478
  Planarity :  0.004   0.032    589
  Dihedral  : 12.662  84.065   1179
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.25 %
    Favored  : 87.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.42), residues: 413
  helix: -3.07 (0.75), residues: 27
  sheet: -0.13 (0.40), residues: 172
  loop :  0.39 (0.44), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  47 
 HIS   0.004   0.002   HIS L  35 
 PHE   0.022   0.002   PHE A 429 
 TYR   0.018   0.002   TYR L  95 
 ARG   0.002   0.000   ARG L  62 

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8881 (tppp) cc_final: 0.8149 (tptp)
REVERT: A  455 LEU cc_start: 0.9002 (tp) cc_final: 0.8713 (tp)
REVERT: A  523 THR cc_start: 0.8257 (p) cc_final: 0.7957 (p)
REVERT: H    3 GLN cc_start: 0.8447 (pp30) cc_final: 0.8028 (pp30)
REVERT: H  114 THR cc_start: 0.9027 (m) cc_final: 0.8514 (m)
REVERT: L  104 LYS cc_start: 0.8695 (ttpp) cc_final: 0.8423 (ttpp)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1853
  time to fit residues: 25.3171
Evaluate side-chains
  93 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.1980
   chunk 30 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN
H  50 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.151779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.133228 restraints weight = 4656.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.136965 restraints weight = 2505.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.139355 restraints weight = 1613.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   3356  Z= 0.304
  Angle     :  0.657   5.722   4562  Z= 0.354
  Chirality :  0.048   0.179    478
  Planarity :  0.004   0.033    589
  Dihedral  :  5.498  25.689    462
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 20.80 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.20 (0.43), residues: 413
  helix: -2.77 (0.86), residues: 21
  sheet: -0.21 (0.41), residues: 173
  loop :  0.42 (0.45), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 436 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.018   0.002   PHE H  64 
 TYR   0.019   0.002   TYR A 365 
 ARG   0.003   0.000   ARG L  62 

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  361 CYS cc_start: 0.5290 (OUTLIER) cc_final: 0.5082 (t)
REVERT: A  378 LYS cc_start: 0.8914 (tppp) cc_final: 0.8130 (tptp)
REVERT: A  523 THR cc_start: 0.8104 (p) cc_final: 0.7836 (p)
REVERT: H    3 GLN cc_start: 0.8251 (pp30) cc_final: 0.7699 (pp30)
REVERT: H    6 GLN cc_start: 0.8282 (tt0) cc_final: 0.7942 (tt0)
REVERT: H   46 GLU cc_start: 0.8069 (pt0) cc_final: 0.7796 (pt0)
REVERT: H  112 GLN cc_start: 0.8322 (pm20) cc_final: 0.8033 (pm20)
REVERT: H  114 THR cc_start: 0.9069 (m) cc_final: 0.8490 (m)
REVERT: L   54 ASN cc_start: 0.8446 (m110) cc_final: 0.8203 (m110)
REVERT: L  104 LYS cc_start: 0.8702 (ttpp) cc_final: 0.8490 (ttpp)
  outliers start: 8
  outliers final: 5
  residues processed: 107
  average time/residue: 0.1801
  time to fit residues: 22.7456
Evaluate side-chains
  99 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   28 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0020
   chunk 33 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   6 GLN
H  39 GLN
L  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.153428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.135385 restraints weight = 4533.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.138966 restraints weight = 2501.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.141287 restraints weight = 1644.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.2875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3356  Z= 0.288
  Angle     :  0.628   6.043   4562  Z= 0.337
  Chirality :  0.047   0.150    478
  Planarity :  0.004   0.037    589
  Dihedral  :  5.354  24.436    462
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 22.79 %
    Favored  : 73.50 %
  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: -0.33 (0.43), residues: 413
  helix: -2.49 (0.93), residues: 21
  sheet: -0.31 (0.39), residues: 172
  loop :  0.28 (0.45), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  47 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.014   0.001   PHE A 377 
 TYR   0.012   0.001   TYR L  95 
 ARG   0.004   0.001   ARG A 357 

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8978 (tppp) cc_final: 0.8284 (tptp)
REVERT: A  420 ASP cc_start: 0.8411 (m-30) cc_final: 0.8164 (m-30)
REVERT: A  466 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6839 (ttt180)
REVERT: A  523 THR cc_start: 0.8125 (p) cc_final: 0.7866 (p)
REVERT: H    3 GLN cc_start: 0.8161 (pp30) cc_final: 0.7847 (pp30)
REVERT: H   34 MET cc_start: 0.7918 (tpt) cc_final: 0.7278 (tpt)
REVERT: H   38 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7722 (ttmp)
REVERT: H   46 GLU cc_start: 0.8086 (pt0) cc_final: 0.7849 (pt0)
REVERT: H  112 GLN cc_start: 0.8295 (pm20) cc_final: 0.8058 (pm20)
REVERT: L  104 LYS cc_start: 0.8698 (ttpp) cc_final: 0.8495 (ttpp)
  outliers start: 13
  outliers final: 10
  residues processed: 103
  average time/residue: 0.1797
  time to fit residues: 21.8938
Evaluate side-chains
  105 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   38 LYS
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9990
   chunk 23 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9980
   chunk 4 optimal weight:    0.4980
   chunk 14 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 39 optimal weight:    0.3980
   chunk 34 optimal weight:    0.7980
   chunk 20 optimal weight:    5.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 GLN
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN
H  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.152881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.134707 restraints weight = 4716.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.138381 restraints weight = 2589.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.140850 restraints weight = 1693.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.3216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3356  Z= 0.242
  Angle     :  0.591   6.259   4562  Z= 0.314
  Chirality :  0.046   0.143    478
  Planarity :  0.004   0.035    589
  Dihedral  :  5.185  23.057    462
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 23.93 %
    Favored  : 72.93 %
  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: -0.27 (0.43), residues: 413
  helix: -1.31 (1.47), residues: 13
  sheet: -0.40 (0.39), residues: 171
  loop :  0.24 (0.44), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 436 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.013   0.001   PHE A 377 
 TYR   0.014   0.001   TYR A 365 
 ARG   0.004   0.000   ARG A 357 

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8952 (tppp) cc_final: 0.8256 (tptp)
REVERT: A  420 ASP cc_start: 0.8449 (m-30) cc_final: 0.8204 (m-30)
REVERT: A  523 THR cc_start: 0.8050 (p) cc_final: 0.7823 (p)
REVERT: H   34 MET cc_start: 0.7980 (tpt) cc_final: 0.7369 (tpt)
REVERT: H   46 GLU cc_start: 0.8111 (pt0) cc_final: 0.7873 (pt0)
REVERT: H  114 THR cc_start: 0.9013 (m) cc_final: 0.8766 (p)
REVERT: L  104 LYS cc_start: 0.8659 (ttpp) cc_final: 0.8425 (ttpp)
  outliers start: 11
  outliers final: 9
  residues processed: 104
  average time/residue: 0.1656
  time to fit residues: 20.6436
Evaluate side-chains
  104 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  448 ASN
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   76 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 32 optimal weight:    0.0470
   chunk 4 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 33 optimal weight:    0.2980
   chunk 29 optimal weight:    0.0870
   overall best weight:    0.3256

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

Flipped N/Q/H residues before XYZ refinement:
A 422 ASN
A 493 GLN
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   1 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.154376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.135143 restraints weight = 4651.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.138919 restraints weight = 2586.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.141584 restraints weight = 1708.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.3531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3356  Z= 0.194
  Angle     :  0.570   6.011   4562  Z= 0.299
  Chirality :  0.045   0.138    478
  Planarity :  0.004   0.033    589
  Dihedral  :  4.919  22.808    462
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 23.08 %
    Favored  : 72.93 %
  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: -0.27 (0.43), residues: 413
  helix: -1.52 (1.35), residues: 14
  sheet: -0.35 (0.39), residues: 171
  loop :  0.23 (0.44), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H 110 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.012   0.001   PHE A 377 
 TYR   0.014   0.001   TYR A 365 
 ARG   0.004   0.001   ARG A 357 

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8931 (tppp) cc_final: 0.8166 (tptp)
REVERT: A  466 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6709 (ttt180)
REVERT: A  523 THR cc_start: 0.7992 (p) cc_final: 0.7714 (p)
REVERT: H    3 GLN cc_start: 0.8088 (pp30) cc_final: 0.7674 (pp30)
REVERT: H   46 GLU cc_start: 0.8137 (pt0) cc_final: 0.7917 (pt0)
REVERT: L  104 LYS cc_start: 0.8697 (ttpp) cc_final: 0.8426 (ttpp)
  outliers start: 14
  outliers final: 10
  residues processed: 110
  average time/residue: 0.1850
  time to fit residues: 23.9501
Evaluate side-chains
  109 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  448 ASN
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain L residue   11 MET
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   27 SER
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   76 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 20 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   1 GLN
H   6 GLN
H  31 ASN
H  39 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.148936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.129744 restraints weight = 4910.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.133447 restraints weight = 2732.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.135990 restraints weight = 1800.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.3423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   3356  Z= 0.366
  Angle     :  0.659   6.001   4562  Z= 0.350
  Chirality :  0.047   0.148    478
  Planarity :  0.004   0.032    589
  Dihedral  :  5.405  21.311    462
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  5.98 %
    Allowed  : 24.22 %
    Favored  : 69.80 %
  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: -0.45 (0.43), residues: 413
  helix: -1.74 (1.29), residues: 13
  sheet: -0.57 (0.39), residues: 171
  loop :  0.19 (0.45), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H 110 
 HIS   0.003   0.001   HIS L  35 
 PHE   0.013   0.002   PHE A 429 
 TYR   0.014   0.002   TYR A 365 
 ARG   0.005   0.000   ARG A 357 

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8965 (tppp) cc_final: 0.8222 (tptp)
REVERT: A  420 ASP cc_start: 0.8504 (m-30) cc_final: 0.8237 (m-30)
REVERT: A  466 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6802 (ttt180)
REVERT: A  523 THR cc_start: 0.8237 (p) cc_final: 0.7928 (p)
REVERT: H    3 GLN cc_start: 0.8094 (pp30) cc_final: 0.7644 (pp30)
REVERT: H   46 GLU cc_start: 0.8061 (pt0) cc_final: 0.7858 (pt0)
REVERT: L  104 LYS cc_start: 0.8751 (ttpp) cc_final: 0.8486 (ttpp)
  outliers start: 21
  outliers final: 14
  residues processed: 105
  average time/residue: 0.1784
  time to fit residues: 22.3357
Evaluate side-chains
  107 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  448 ASN
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain L residue   11 MET
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   27 SER
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue   76 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 5 optimal weight:    0.2980
   chunk 0 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 460 ASN
A 493 GLN
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   1 GLN
H  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.150050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.131129 restraints weight = 4713.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.134764 restraints weight = 2652.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.137229 restraints weight = 1765.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.3585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3356  Z= 0.299
  Angle     :  0.630   6.260   4562  Z= 0.334
  Chirality :  0.046   0.144    478
  Planarity :  0.004   0.030    589
  Dihedral  :  5.316  21.745    462
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 25.07 %
    Favored  : 69.23 %
  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: -0.55 (0.43), residues: 413
  helix: -1.86 (1.25), residues: 13
  sheet: -0.66 (0.39), residues: 171
  loop :  0.14 (0.45), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP H  47 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.016   0.001   PHE A 374 
 TYR   0.016   0.001   TYR A 365 
 ARG   0.004   0.001   ARG A 357 

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8948 (tppp) cc_final: 0.8186 (tptp)
REVERT: A  462 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7925 (ttpp)
REVERT: A  466 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6734 (ttt180)
REVERT: A  523 THR cc_start: 0.8203 (p) cc_final: 0.7892 (p)
REVERT: H    3 GLN cc_start: 0.8111 (pp30) cc_final: 0.7691 (pp30)
REVERT: L  104 LYS cc_start: 0.8714 (ttpp) cc_final: 0.8445 (ttpp)
  outliers start: 20
  outliers final: 15
  residues processed: 101
  average time/residue: 0.1893
  time to fit residues: 22.6690
Evaluate side-chains
  109 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   35 ASN
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain L residue   11 MET
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   27 SER
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue   76 ILE
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    0.4980
   chunk 33 optimal weight:    0.9980
   chunk 39 optimal weight:    0.2980
   chunk 1 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 GLN
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   1 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.149392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.130134 restraints weight = 4810.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.133813 restraints weight = 2739.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.136342 restraints weight = 1836.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.3630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3356  Z= 0.332
  Angle     :  0.656   6.260   4562  Z= 0.346
  Chirality :  0.047   0.147    478
  Planarity :  0.004   0.029    589
  Dihedral  :  5.361  21.301    462
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 25.64 %
    Favored  : 68.95 %
  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: -0.66 (0.43), residues: 413
  helix: -2.17 (1.16), residues: 13
  sheet: -0.74 (0.39), residues: 171
  loop :  0.08 (0.44), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 436 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.013   0.001   PHE A 429 
 TYR   0.015   0.002   TYR A 365 
 ARG   0.004   0.001   ARG A 457 

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8963 (tppp) cc_final: 0.8196 (tptp)
REVERT: A  420 ASP cc_start: 0.8321 (m-30) cc_final: 0.7985 (m-30)
REVERT: A  462 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7909 (ttpp)
REVERT: A  466 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6699 (ttt180)
REVERT: A  523 THR cc_start: 0.8268 (p) cc_final: 0.7941 (p)
REVERT: H    3 GLN cc_start: 0.8161 (pp30) cc_final: 0.7736 (pp30)
REVERT: L  104 LYS cc_start: 0.8736 (ttpp) cc_final: 0.8417 (ttpp)
  outliers start: 19
  outliers final: 17
  residues processed: 101
  average time/residue: 0.1860
  time to fit residues: 22.1586
Evaluate side-chains
  111 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   35 ASN
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain L residue   11 MET
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   27 SER
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue   76 ILE
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   chunk 36 optimal weight:    0.1980
   chunk 29 optimal weight:    0.0050
   chunk 23 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.4194

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 GLN
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.151696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.132632 restraints weight = 4723.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.136392 restraints weight = 2653.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.138991 restraints weight = 1754.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.3840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3356  Z= 0.229
  Angle     :  0.626   6.435   4562  Z= 0.327
  Chirality :  0.046   0.144    478
  Planarity :  0.004   0.028    589
  Dihedral  :  5.187  21.757    462
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 26.21 %
    Favored  : 68.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.68 (0.42), residues: 413
  helix: -2.31 (1.15), residues: 13
  sheet: -0.73 (0.39), residues: 170
  loop :  0.05 (0.44), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 353 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.019   0.001   PHE H  64 
 TYR   0.014   0.001   TYR A 473 
 ARG   0.005   0.001   ARG A 457 

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8946 (tppp) cc_final: 0.8178 (tptp)
REVERT: A  457 ARG cc_start: 0.8316 (ttp80) cc_final: 0.7766 (ttp80)
REVERT: A  462 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7845 (ttpp)
REVERT: A  466 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.6666 (ttt180)
REVERT: A  523 THR cc_start: 0.8120 (p) cc_final: 0.7797 (p)
REVERT: H    3 GLN cc_start: 0.8123 (pp30) cc_final: 0.7617 (pp30)
REVERT: L  104 LYS cc_start: 0.8709 (ttpp) cc_final: 0.8456 (ttpp)
  outliers start: 18
  outliers final: 15
  residues processed: 102
  average time/residue: 0.1924
  time to fit residues: 23.1485
Evaluate side-chains
  107 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   35 ASN
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain L residue   11 MET
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   27 SER
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue   76 ILE
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 29 optimal weight:    0.0870
   chunk 17 optimal weight:    0.3980
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 18 optimal weight:    0.2980
   chunk 23 optimal weight:    0.3980
   chunk 34 optimal weight:    0.3980
   chunk 30 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.3158

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 GLN
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.152582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.134231 restraints weight = 4637.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.137860 restraints weight = 2624.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.140424 restraints weight = 1744.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.4029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3356  Z= 0.202
  Angle     :  0.615   6.521   4562  Z= 0.322
  Chirality :  0.046   0.142    478
  Planarity :  0.004   0.028    589
  Dihedral  :  5.050  22.243    462
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 26.78 %
    Favored  : 68.38 %
  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: -0.64 (0.42), residues: 413
  helix: -2.46 (1.13), residues: 13
  sheet: -0.66 (0.40), residues: 170
  loop :  0.06 (0.44), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 353 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.009   0.001   PHE A 429 
 TYR   0.023   0.001   TYR A 473 
 ARG   0.005   0.001   ARG A 457 

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8938 (tppp) cc_final: 0.8157 (tptp)
REVERT: A  462 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7857 (ttpp)
REVERT: A  466 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6585 (ttt180)
REVERT: H    3 GLN cc_start: 0.8084 (pp30) cc_final: 0.7587 (pp30)
REVERT: L  104 LYS cc_start: 0.8724 (ttpp) cc_final: 0.8482 (ttpp)
  outliers start: 17
  outliers final: 14
  residues processed: 102
  average time/residue: 0.1824
  time to fit residues: 22.0864
Evaluate side-chains
  110 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain H residue   35 ASN
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain L residue   11 MET
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   27 SER
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue   76 ILE
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 12 optimal weight:    0.4980
   chunk 3 optimal weight:    0.0870
   chunk 24 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0050
   chunk 32 optimal weight:    0.9990
   chunk 29 optimal weight:    0.1980
   overall best weight:    0.2772

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 GLN
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN
H  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.153955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.134999 restraints weight = 4597.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.138698 restraints weight = 2570.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.141277 restraints weight = 1695.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.4192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3356  Z= 0.196
  Angle     :  0.630   6.531   4562  Z= 0.328
  Chirality :  0.046   0.150    478
  Planarity :  0.004   0.028    589
  Dihedral  :  5.023  22.404    462
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 27.07 %
    Favored  : 68.38 %
  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: -0.62 (0.42), residues: 413
  helix: -2.88 (1.02), residues: 13
  sheet: -0.61 (0.40), residues: 170
  loop :  0.06 (0.44), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 353 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.008   0.001   PHE A 429 
 TYR   0.021   0.001   TYR A 473 
 ARG   0.005   0.001   ARG A 457 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1633.30 seconds
wall clock time: 30 minutes 12.04 seconds (1812.04 seconds total)