Starting phenix.real_space_refine
on Wed Mar  5 18:31:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zpp_60351/03_2025/8zpp_60351.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zpp_60351/03_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_60351/03_2025/8zpp_60351.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zpp_60351/03_2025/8zpp_60351.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zpp_60351/03_2025/8zpp_60351.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zpp_60351/03_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-5624/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: 3.31, per 1000 atoms: 1.01
  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: 0.68
  Conformation dependent library (CDL) restraints added in 353.9 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: 0.45
  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: 0.84

  Time building geometry restraints manager: 0.83 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:             3.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.070
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.730
-------------------------------------------------------------------------------
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  : 0.354 
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: 0.1672
  time to fit residues: 22.6245
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  : 0.326 
-------------------------------------------------------------------------------
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 = 0.133229 restraints weight = 4656.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.136958 restraints weight = 2505.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.139354 restraints weight = 1614.111|
|-----------------------------------------------------------------------------|
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  : 0.323 
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: 0.8283 (tt0) cc_final: 0.7941 (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: 0.8703 (ttpp) cc_final: 0.8490 (ttpp)
  outliers start: 8
  outliers final: 5
  residues processed: 107
  average time/residue: 0.1827
  time to fit residues: 22.9857
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  : 0.354 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.5588

-------------------------------------------------------------------------------
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 = 0.3782 r_free = 0.3782 target = 0.153949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.136045 restraints weight = 4532.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.139581 restraints weight = 2509.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.142059 restraints weight = 1655.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3356  Z= 0.278
  Angle     :  0.625   6.055   4562  Z= 0.335
  Chirality :  0.047   0.149    478
  Planarity :  0.004   0.038    589
  Dihedral  :  5.332  24.577    462
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 23.08 %
    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: -0.32 (0.43), residues: 413
  helix: -2.49 (0.93), residues: 21
  sheet: -0.32 (0.39), residues: 173
  loop :  0.31 (0.45), residues: 219

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: 12
    poor density    : 99
  time to evaluate  : 0.369 
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: 0.8969 (tppp) cc_final: 0.8293 (tptp)
REVERT: A  420 ASP cc_start: 0.8404 (m-30) cc_final: 0.8171 (m-30)
REVERT: A  466 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6896 (ttt180)
REVERT: A  523 THR cc_start: 0.8098 (p) cc_final: 0.7846 (p)
REVERT: H    3 GLN cc_start: 0.8173 (pp30) cc_final: 0.7868 (pp30)
REVERT: H   34 MET cc_start: 0.7907 (tpt) cc_final: 0.7287 (tpt)
REVERT: H   46 GLU cc_start: 0.8067 (pt0) cc_final: 0.7840 (pt0)
REVERT: H  112 GLN cc_start: 0.8284 (pm20) cc_final: 0.8053 (pm20)
  outliers start: 12
  outliers final: 10
  residues processed: 103
  average time/residue: 0.1702
  time to fit residues: 20.7436
Evaluate side-chains
  104 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
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   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:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 4 optimal weight:    0.2980
   chunk 14 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 39 optimal weight:    0.4980
   chunk 34 optimal weight:    0.8980
   chunk 20 optimal weight:    6.9990
   chunk 37 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:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 GLN
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.151149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.133173 restraints weight = 4733.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.136755 restraints weight = 2615.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.139174 restraints weight = 1717.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.3147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3356  Z= 0.313
  Angle     :  0.623   6.012   4562  Z= 0.333
  Chirality :  0.046   0.150    478
  Planarity :  0.004   0.036    589
  Dihedral  :  5.426  22.742    462
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 23.08 %
    Favored  : 72.36 %
  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: -0.41 (0.43), residues: 413
  helix: -1.43 (1.44), residues: 13
  sheet: -0.55 (0.39), residues: 171
  loop :  0.20 (0.44), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 436 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.013   0.002   PHE A 429 
 TYR   0.011   0.002   TYR H  32 
 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
  113 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8970 (tppp) cc_final: 0.8276 (tptp)
REVERT: A  420 ASP cc_start: 0.8476 (m-30) cc_final: 0.8252 (m-30)
REVERT: A  466 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6838 (ttt180)
REVERT: A  523 THR cc_start: 0.8124 (p) cc_final: 0.7859 (p)
REVERT: H    3 GLN cc_start: 0.8094 (pp30) cc_final: 0.7829 (pp30)
REVERT: H   34 MET cc_start: 0.8039 (tpt) cc_final: 0.7414 (tpt)
REVERT: H   46 GLU cc_start: 0.8075 (pt0) cc_final: 0.7827 (pt0)
REVERT: H  114 THR cc_start: 0.9031 (m) cc_final: 0.8778 (p)
  outliers start: 16
  outliers final: 11
  residues processed: 103
  average time/residue: 0.1712
  time to fit residues: 20.8991
Evaluate side-chains
  104 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
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  500 THR
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   45 LEU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 4 optimal weight:    0.4980
   chunk 0 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0170
   chunk 22 optimal weight:    0.2980
   chunk 6 optimal weight:    0.5980
   chunk 14 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0370
   chunk 1 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.2896

-------------------------------------------------------------------------------
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 = 0.3787 r_free = 0.3787 target = 0.154811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.136609 restraints weight = 4653.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.140181 restraints weight = 2571.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.142723 restraints weight = 1689.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.3604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3356  Z= 0.191
  Angle     :  0.572   6.051   4562  Z= 0.304
  Chirality :  0.045   0.135    478
  Planarity :  0.004   0.033    589
  Dihedral  :  5.055  22.880    462
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 25.36 %
    Favored  : 71.79 %
  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: -0.35 (0.43), residues: 413
  helix: -1.57 (1.34), residues: 14
  sheet: -0.46 (0.39), residues: 171
  loop :  0.22 (0.45), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H 110 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.011   0.001   PHE A 377 
 TYR   0.010   0.001   TYR H  32 
 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
  116 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.355 
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: 0.8243 (tptp)
REVERT: A  462 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7674 (ttpp)
REVERT: A  523 THR cc_start: 0.7941 (p) cc_final: 0.7726 (p)
REVERT: H   46 GLU cc_start: 0.8101 (pt0) cc_final: 0.7877 (pt0)
REVERT: L  104 LYS cc_start: 0.8625 (ttpp) cc_final: 0.8199 (ttpt)
  outliers start: 10
  outliers final: 7
  residues processed: 111
  average time/residue: 0.1671
  time to fit residues: 22.1079
Evaluate side-chains
  103 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 0 optimal weight:    0.2980
   chunk 31 optimal weight:    0.2980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 422 ASN
A 460 ASN
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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.152775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.134070 restraints weight = 4853.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.137711 restraints weight = 2685.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.140222 restraints weight = 1769.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.3593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3356  Z= 0.258
  Angle     :  0.608   6.061   4562  Z= 0.321
  Chirality :  0.045   0.145    478
  Planarity :  0.004   0.033    589
  Dihedral  :  5.130  21.594    462
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 26.78 %
    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: -0.43 (0.43), residues: 413
  helix: -1.60 (1.32), residues: 13
  sheet: -0.52 (0.39), residues: 171
  loop :  0.16 (0.45), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 353 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.012   0.001   PHE A 374 
 TYR   0.009   0.001   TYR H  32 
 ARG   0.004   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
  111 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.325 
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: 0.8919 (tppp) cc_final: 0.8203 (tptp)
REVERT: A  466 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6753 (ttt180)
REVERT: A  523 THR cc_start: 0.8023 (p) cc_final: 0.7742 (p)
REVERT: H    3 GLN cc_start: 0.8049 (pp30) cc_final: 0.7634 (pp30)
REVERT: H   40 ARG cc_start: 0.8291 (mtp85) cc_final: 0.7723 (ttm-80)
REVERT: L  104 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8366 (ttpt)
  outliers start: 16
  outliers final: 11
  residues processed: 103
  average time/residue: 0.1697
  time to fit residues: 20.7826
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  : 0.277 
-------------------------------------------------------------------------------
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  493 GLN
Chi-restraints excluded: chain H residue   45 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 5 optimal weight:    0.1980
   chunk 0 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   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 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 = 0.3763 r_free = 0.3763 target = 0.152235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.133512 restraints weight = 4694.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.137117 restraints weight = 2649.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.139594 restraints weight = 1768.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.3688

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= 0.295
  Angle     :  0.624   6.219   4562  Z= 0.329
  Chirality :  0.046   0.145    478
  Planarity :  0.004   0.033    589
  Dihedral  :  5.254  21.386    462
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 25.36 %
    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: -0.53 (0.43), residues: 413
  helix: -1.66 (1.32), residues: 13
  sheet: -0.59 (0.39), residues: 171
  loop :  0.09 (0.44), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 353 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.012   0.001   PHE A 429 
 TYR   0.013   0.001   TYR A 473 
 ARG   0.005   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: 19
    poor density    : 93
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8934 (tppp) cc_final: 0.8199 (tptp)
REVERT: A  420 ASP cc_start: 0.8538 (m-30) cc_final: 0.8275 (m-30)
REVERT: A  523 THR cc_start: 0.8055 (p) cc_final: 0.7763 (p)
REVERT: H    3 GLN cc_start: 0.8054 (pp30) cc_final: 0.7630 (pp30)
REVERT: H   40 ARG cc_start: 0.8302 (mtp85) cc_final: 0.7806 (ttm-80)
REVERT: L  104 LYS cc_start: 0.8612 (ttpp) cc_final: 0.8350 (ttpt)
  outliers start: 19
  outliers final: 14
  residues processed: 103
  average time/residue: 0.1658
  time to fit residues: 20.3316
Evaluate side-chains
  105 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
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  493 GLN
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  115 THR
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:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 9 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 460 ASN
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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.150046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.130704 restraints weight = 4816.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.134475 restraints weight = 2694.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.136946 restraints weight = 1775.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.3705

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= 0.336
  Angle     :  0.651   6.263   4562  Z= 0.342
  Chirality :  0.047   0.147    478
  Planarity :  0.004   0.033    589
  Dihedral  :  5.358  21.313    462
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  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: -0.69 (0.42), residues: 413
  helix: -2.04 (1.17), residues: 13
  sheet: -0.73 (0.39), residues: 172
  loop :  0.03 (0.44), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 353 
 HIS   0.002   0.001   HIS L  35 
 PHE   0.013   0.001   PHE A 429 
 TYR   0.021   0.002   TYR A 473 
 ARG   0.004   0.001   ARG A 357 

*********************** 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: 18
    poor density    : 94
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8941 (tppp) cc_final: 0.8166 (tptp)
REVERT: A  462 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7726 (ttpp)
REVERT: A  523 THR cc_start: 0.8234 (p) cc_final: 0.7918 (p)
REVERT: H    3 GLN cc_start: 0.8116 (pp30) cc_final: 0.7646 (pp30)
REVERT: H   40 ARG cc_start: 0.8346 (mtp85) cc_final: 0.7845 (ttm-80)
REVERT: H   46 GLU cc_start: 0.8349 (pt0) cc_final: 0.8120 (pt0)
REVERT: L  104 LYS cc_start: 0.8640 (ttpp) cc_final: 0.8364 (ttpt)
  outliers start: 18
  outliers final: 15
  residues processed: 101
  average time/residue: 0.1709
  time to fit residues: 20.6334
Evaluate side-chains
  107 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
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  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   78 THR
Chi-restraints excluded: chain H residue  115 THR
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:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 29 optimal weight:    0.2980
   chunk 23 optimal weight:    0.4980
   chunk 22 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0970
   chunk 32 optimal weight:    0.1980
   chunk 30 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.3578

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.153328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.133806 restraints weight = 4721.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.137624 restraints weight = 2687.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.140002 restraints weight = 1785.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.3921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3356  Z= 0.211
  Angle     :  0.604   6.538   4562  Z= 0.317
  Chirality :  0.046   0.140    478
  Planarity :  0.004   0.032    589
  Dihedral  :  5.152  21.961    462
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 27.35 %
    Favored  : 67.81 %
  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: -2.18 (1.15), residues: 13
  sheet: -0.68 (0.39), residues: 171
  loop :  0.01 (0.44), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 353 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.020   0.002   PHE H  64 
 TYR   0.017   0.001   TYR A 473 
 ARG   0.004   0.001   ARG A 357 

*********************** 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
  109 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8915 (tppp) cc_final: 0.8150 (tptp)
REVERT: A  420 ASP cc_start: 0.8336 (m-30) cc_final: 0.7719 (t0)
REVERT: A  462 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7696 (ttpp)
REVERT: H    3 GLN cc_start: 0.8049 (pp30) cc_final: 0.7594 (pp30)
REVERT: H   46 GLU cc_start: 0.8384 (pt0) cc_final: 0.8153 (pt0)
REVERT: L  104 LYS cc_start: 0.8583 (ttpp) cc_final: 0.8271 (ttpt)
  outliers start: 17
  outliers final: 14
  residues processed: 101
  average time/residue: 0.1677
  time to fit residues: 20.2527
Evaluate side-chains
  104 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
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  367 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain H residue   35 ASN
Chi-restraints excluded: chain H residue  115 THR
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:    0.9980
   chunk 17 optimal weight:    0.1980
   chunk 37 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 487 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 = 0.3734 r_free = 0.3734 target = 0.150612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.131489 restraints weight = 4628.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.135109 restraints weight = 2617.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.137752 restraints weight = 1739.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.3920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3356  Z= 0.263
  Angle     :  0.628   6.422   4562  Z= 0.328
  Chirality :  0.046   0.145    478
  Planarity :  0.004   0.032    589
  Dihedral  :  5.197  21.944    462
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 26.21 %
    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: -0.74 (0.42), residues: 413
  helix: -2.48 (1.11), residues: 13
  sheet: -0.74 (0.39), residues: 171
  loop :  0.00 (0.44), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 353 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.022   0.002   PHE H  64 
 TYR   0.016   0.001   TYR A 473 
 ARG   0.005   0.001   ARG A 357 

********************** 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
  110 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8930 (tppp) cc_final: 0.8131 (tptp)
REVERT: A  462 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7751 (ttpp)
REVERT: H    3 GLN cc_start: 0.8045 (pp30) cc_final: 0.7588 (pp30)
REVERT: H   46 GLU cc_start: 0.8418 (pt0) cc_final: 0.8206 (pt0)
REVERT: L  104 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8322 (ttpt)
  outliers start: 19
  outliers final: 16
  residues processed: 100
  average time/residue: 0.1575
  time to fit residues: 19.0525
Evaluate side-chains
  106 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
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  367 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  462 LYS
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   78 THR
Chi-restraints excluded: chain H residue  115 THR
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:    0.0370
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.6658

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

Flipped N/Q/H residues before XYZ refinement:
A 460 ASN
** A 487 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.148879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.129686 restraints weight = 4662.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.133361 restraints weight = 2635.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.135917 restraints weight = 1751.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.3914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3356  Z= 0.307
  Angle     :  0.641   6.448   4562  Z= 0.337
  Chirality :  0.047   0.148    478
  Planarity :  0.004   0.049    589
  Dihedral  :  5.332  21.852    462
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 27.35 %
    Favored  : 67.52 %
  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: -0.79 (0.42), residues: 413
  helix: -3.07 (0.98), residues: 13
  sheet: -0.76 (0.39), residues: 172
  loop :  0.00 (0.44), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 353 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.023   0.002   PHE H  64 
 TYR   0.014   0.001   TYR A 473 
 ARG   0.005   0.001   ARG A 357 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1656.24 seconds
wall clock time: 29 minutes 24.78 seconds (1764.78 seconds total)