Starting phenix.real_space_refine
on Wed Jul 23 13:56:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f63_31471/07_2025/7f63_31471.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f63_31471/07_2025/7f63_31471.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f63_31471/07_2025/7f63_31471.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f63_31471/07_2025/7f63_31471.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f63_31471/07_2025/7f63_31471.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f63_31471/07_2025/7f63_31471.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.031
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      15      5.16       5
     C    2149      2.51       5
     N     555      2.21       5
     O     656      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 3375
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1578
          Classifications: {'peptide': 199}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 187}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "H"
      Number of atoms: 945
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 945
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "L"
      Number of atoms: 852
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 852
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 4, 'TRANS': 105}
  Time building chain proxies: 3.47, per 1000 atoms: 1.03
  Number of scatterers: 3375
  At special positions: 0
  Unit cell: (67.1, 80.3, 115.5, 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      15     16.00
     O     656      8.00
     N     555      7.00
     C    2149      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=2.04
    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  88 " 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: 0.85
  Conformation dependent library (CDL) restraints added in 434.2 milliseconds
  

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  790

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 7 sheets defined
      8.6% alpha, 23.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 342
      removed outlier: 4.402A  pdb=" N   PHE A 342 " --> pdb=" O   PHE A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 371
      removed outlier: 4.479A  pdb=" N   TYR A 369 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   SER A 371 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 387
      removed outlier: 3.599A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 410
      removed outlier: 3.721A  pdb=" N   GLU A 406 " --> pdb=" O   ARG A 403 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   VAL A 407 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
      removed outlier: 5.509A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 439 through 442
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 5.006A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   GLU A 516 " --> pdb=" O   ASN A 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6
      removed outlier: 4.127A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   SER H  25 " --> pdb=" O   GLN H   3 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LYS H  23 " --> pdb=" O   GLN H   5 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.760A  pdb=" N   LYS H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.892A  pdb=" N   TRP H  47 " --> pdb=" O   LYS H  38 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.750A  pdb=" N   ALA L  34 " --> pdb=" O   GLN L  89 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   VAL L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 5.425A  pdb=" N   TYR L  49 " --> pdb=" O   VAL L  33 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 19 through 22
      removed outlier: 4.198A  pdb=" N   VAL L  19 " --> pdb=" O   ILE L  75 " (cutoff:3.500A)

    82 hydrogen bonds defined for protein.
    192 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: 0.75

  Time building geometry restraints manager: 1.03 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: 1061
        1.34 -     1.46: 912
        1.46 -     1.58: 1472
        1.58 -     1.70: 0
        1.70 -     1.82: 18
  Bond restraints: 3463
  Sorted by residual:
  bond pdb=" C   ALA A 520 "
       pdb=" N   PRO A 521 "
    ideal  model  delta    sigma   weight residual
    1.334  1.356 -0.022 2.34e-02 1.83e+03 9.23e-01
  bond pdb=" CA  ASN A 394 "
       pdb=" CB  ASN A 394 "
    ideal  model  delta    sigma   weight residual
    1.527  1.542 -0.015 1.61e-02 3.86e+03 8.66e-01
  bond pdb=" CB  CYS A 379 "
       pdb=" SG  CYS A 379 "
    ideal  model  delta    sigma   weight residual
    1.808  1.779  0.029 3.30e-02 9.18e+02 7.56e-01
  bond pdb=" N   ASN A 394 "
       pdb=" CA  ASN A 394 "
    ideal  model  delta    sigma   weight residual
    1.460  1.472 -0.012 1.42e-02 4.96e+03 7.05e-01
  bond pdb=" CA  ILE L  75 "
       pdb=" C   ILE L  75 "
    ideal  model  delta    sigma   weight residual
    1.523  1.532 -0.009 1.16e-02 7.43e+03 6.11e-01
  ... (remaining 3458 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 4612
        1.66 -     3.33: 71
        3.33 -     4.99: 16
        4.99 -     6.65: 3
        6.65 -     8.31: 2
  Bond angle restraints: 4704
  Sorted by residual:
  angle pdb=" C   LEU H  70 "
        pdb=" N   THR H  71 "
        pdb=" CA  THR H  71 "
      ideal   model   delta    sigma   weight residual
     121.75  117.03    4.72 1.73e+00 3.34e-01 7.43e+00
  angle pdb=" C   TYR H  80 "
        pdb=" N   MET H  81 "
        pdb=" CA  MET H  81 "
      ideal   model   delta    sigma   weight residual
     122.65  126.43   -3.78 1.49e+00 4.50e-01 6.45e+00
  angle pdb=" C   THR A 393 "
        pdb=" N   ASN A 394 "
        pdb=" CA  ASN A 394 "
      ideal   model   delta    sigma   weight residual
     122.82  126.21   -3.39 1.42e+00 4.96e-01 5.72e+00
  angle pdb=" CA  LEU H  70 "
        pdb=" CB  LEU H  70 "
        pdb=" CG  LEU H  70 "
      ideal   model   delta    sigma   weight residual
     116.30  124.61   -8.31 3.50e+00 8.16e-02 5.64e+00
  angle pdb=" C   ASN A 331 "
        pdb=" N   ILE A 332 "
        pdb=" CA  ILE A 332 "
      ideal   model   delta    sigma   weight residual
     121.97  125.97   -4.00 1.80e+00 3.09e-01 4.94e+00
  ... (remaining 4699 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.04: 1824
       16.04 -    32.08: 153
       32.08 -    48.12: 47
       48.12 -    64.15: 8
       64.15 -    80.19: 4
  Dihedral angle restraints: 2036
    sinusoidal: 788
      harmonic: 1248
  Sorted by residual:
  dihedral pdb=" CB  CYS A 336 "
           pdb=" SG  CYS A 336 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   12.81   80.19     1      1.00e+01 1.00e-02 7.96e+01
  dihedral pdb=" CB  CYS A 480 "
           pdb=" SG  CYS A 480 "
           pdb=" SG  CYS A 488 "
           pdb=" CB  CYS A 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  154.13  -61.13     1      1.00e+01 1.00e-02 4.96e+01
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -46.16  -39.84     1      1.00e+01 1.00e-02 2.23e+01
  ... (remaining 2033 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 304
       0.032 -    0.064: 132
       0.064 -    0.096: 37
       0.096 -    0.128: 23
       0.128 -    0.160: 5
  Chirality restraints: 501
  Sorted by residual:
  chirality pdb=" CB  ILE A 332 "
            pdb=" CA  ILE A 332 "
            pdb=" CG1 ILE A 332 "
            pdb=" CG2 ILE A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.41e-01
  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   -2.45   -0.13 2.00e-01 2.50e+01 4.53e-01
  chirality pdb=" CA  ASN A 394 "
            pdb=" N   ASN A 394 "
            pdb=" C   ASN A 394 "
            pdb=" CB  ASN A 394 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.39e-01
  ... (remaining 498 not shown)

  Planarity restraints: 605
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H  64 "    0.014 2.00e-02 2.50e+03   2.31e-02 9.32e+00
        pdb=" CG  PHE H  64 "   -0.052 2.00e-02 2.50e+03
        pdb=" CD1 PHE H  64 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 PHE H  64 "    0.022 2.00e-02 2.50e+03
        pdb=" CE1 PHE H  64 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE H  64 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE H  64 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 336 "   -0.031 5.00e-02 4.00e+02   4.68e-02 3.50e+00
        pdb=" N   PRO A 337 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 337 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 337 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H  29 "    0.006 2.00e-02 2.50e+03   8.93e-03 1.40e+00
        pdb=" CG  PHE H  29 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 PHE H  29 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE H  29 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE H  29 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE H  29 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE H  29 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 602 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 92
        2.69 -     3.24: 3188
        3.24 -     3.79: 5100
        3.79 -     4.35: 6634
        4.35 -     4.90: 10708
  Nonbonded interactions: 25722
  Sorted by model distance:
  nonbonded pdb=" O   HIS L  61 "
            pdb=" OG  SER L  76 "
     model   vdw
     2.136 3.040
  nonbonded pdb=" O   ALA H 106 "
            pdb=" OH  TYR L  36 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" OG1 THR H  28 "
            pdb=" OE2 GLU H  31 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" O   CYS H  22 "
            pdb=" OG1 THR H  78 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" NH2 ARG A 346 "
            pdb=" OH  TYR A 451 "
     model   vdw
     2.330 3.120
  ... (remaining 25717 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:             3.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.980
  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:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6102
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3469  Z= 0.107
  Angle     :  0.579   8.312   4716  Z= 0.300
  Chirality :  0.044   0.160    501
  Planarity :  0.004   0.047    605
  Dihedral  : 13.336  74.505   1228
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.31 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.31 (0.39), residues: 421
  helix: -3.88 (0.95), residues: 12
  sheet:  0.31 (0.48), residues: 132
  loop : -2.56 (0.33), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  36 
 HIS   0.000   0.000   HIS A 519 
 PHE   0.052   0.002   PHE H  64 
 TYR   0.016   0.001   TYR L  49 
 ARG   0.002   0.000   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17049 (   82)
  hydrogen bonds       : angle       7.15334 (  192)
  SS BOND              : bond        0.00293 (    6)
  SS BOND              : angle       1.44187 (   12)
  covalent geometry    : bond        0.00214 ( 3463)
  covalent geometry    : angle       0.57534 ( 4704)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  405 ASP cc_start: 0.7649 (m-30) cc_final: 0.6909 (m-30)
REVERT: A  406 GLU cc_start: 0.8120 (mp0) cc_final: 0.7712 (mp0)
REVERT: H  101 TYR cc_start: 0.6569 (t80) cc_final: 0.6301 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.2097
  time to fit residues: 28.2394
Evaluate side-chains
  67 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 21 optimal weight:    6.9990
   chunk 32 optimal weight:    0.5980
   chunk 12 optimal weight:    4.9990
   chunk 20 optimal weight:    0.2980
   chunk 24 optimal weight:    4.9990
   chunk 38 optimal weight:    0.2980
   chunk 11 optimal weight:    0.5980
   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
H  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.118951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.108347 restraints weight = 11744.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.110261 restraints weight = 7572.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.111578 restraints weight = 5331.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.4011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6648
moved from start:          0.3418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3469  Z= 0.138
  Angle     :  0.713  11.196   4716  Z= 0.367
  Chirality :  0.047   0.206    501
  Planarity :  0.004   0.036    605
  Dihedral  :  4.847  25.931    472
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  9.74 %
    Favored  : 89.79 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.21 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.34 (0.39), residues: 421
  helix: -2.95 (0.99), residues: 20
  sheet:  0.33 (0.48), residues: 131
  loop : -2.61 (0.33), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP L  35 
 HIS   0.002   0.001   HIS L  61 
 PHE   0.023   0.002   PHE H  29 
 TYR   0.012   0.001   TYR L  53 
 ARG   0.005   0.001   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03699 (   82)
  hydrogen bonds       : angle       6.17450 (  192)
  SS BOND              : bond        0.00676 (    6)
  SS BOND              : angle       1.49836 (   12)
  covalent geometry    : bond        0.00300 ( 3463)
  covalent geometry    : angle       0.71002 ( 4704)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  498 GLN cc_start: 0.8071 (mp10) cc_final: 0.7718 (mp10)
  outliers start: 7
  outliers final: 2
  residues processed: 86
  average time/residue: 0.2141
  time to fit residues: 21.9535
Evaluate side-chains
  63 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  443 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 14 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 370 ASN
H   5 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.111554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.100560 restraints weight = 11340.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.102398 restraints weight = 7387.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.103663 restraints weight = 5285.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6947
moved from start:          0.5002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3469  Z= 0.152
  Angle     :  0.703  11.488   4716  Z= 0.370
  Chirality :  0.048   0.204    501
  Planarity :  0.004   0.037    605
  Dihedral  :  5.258  17.630    472
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 10.93 %
    Favored  : 88.60 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 17.25 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.40), residues: 421
  helix: -3.18 (0.91), residues: 20
  sheet:  0.21 (0.49), residues: 136
  loop : -2.54 (0.34), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H  36 
 HIS   0.003   0.001   HIS L  61 
 PHE   0.017   0.002   PHE H  29 
 TYR   0.014   0.001   TYR H 103 
 ARG   0.005   0.001   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03865 (   82)
  hydrogen bonds       : angle       6.12095 (  192)
  SS BOND              : bond        0.00628 (    6)
  SS BOND              : angle       1.29590 (   12)
  covalent geometry    : bond        0.00324 ( 3463)
  covalent geometry    : angle       0.70046 ( 4704)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 ARG cc_start: 0.8158 (tmt-80) cc_final: 0.7916 (tpt90)
REVERT: H   33 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.8952 (t)
REVERT: H   62 GLN cc_start: 0.7457 (tm-30) cc_final: 0.7117 (tm-30)
REVERT: L   83 LEU cc_start: 0.6862 (tt) cc_final: 0.6634 (pp)
REVERT: L   91 TYR cc_start: 0.8462 (p90) cc_final: 0.7957 (p90)
  outliers start: 13
  outliers final: 10
  residues processed: 83
  average time/residue: 0.2742
  time to fit residues: 26.9263
Evaluate side-chains
  70 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  364 ASP
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain H residue   99 ASP
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   55 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 29 optimal weight:    0.4980
   chunk 33 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 8 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.110993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.100146 restraints weight = 11512.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.102003 restraints weight = 7373.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.103279 restraints weight = 5264.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6998
moved from start:          0.5548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3469  Z= 0.147
  Angle     :  0.718  11.547   4716  Z= 0.374
  Chirality :  0.048   0.214    501
  Planarity :  0.004   0.038    605
  Dihedral  :  5.443  19.180    472
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 11.16 %
    Favored  : 88.36 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 20.49 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.39), residues: 421
  helix: -3.17 (0.66), residues: 26
  sheet:  0.10 (0.49), residues: 133
  loop : -2.60 (0.34), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  36 
 HIS   0.003   0.001   HIS L  61 
 PHE   0.016   0.001   PHE H  29 
 TYR   0.013   0.001   TYR H  60 
 ARG   0.003   0.000   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03646 (   82)
  hydrogen bonds       : angle       6.65639 (  192)
  SS BOND              : bond        0.00479 (    6)
  SS BOND              : angle       1.98556 (   12)
  covalent geometry    : bond        0.00329 ( 3463)
  covalent geometry    : angle       0.71149 ( 4704)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 ARG cc_start: 0.8061 (tmt-80) cc_final: 0.7802 (tpt90)
REVERT: H   33 THR cc_start: 0.9237 (OUTLIER) cc_final: 0.8936 (t)
REVERT: L   83 LEU cc_start: 0.6987 (tt) cc_final: 0.6581 (pp)
REVERT: L   91 TYR cc_start: 0.8571 (p90) cc_final: 0.8140 (p90)
  outliers start: 9
  outliers final: 5
  residues processed: 73
  average time/residue: 0.3156
  time to fit residues: 28.9302
Evaluate side-chains
  64 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   99 ASP
Chi-restraints excluded: chain H residue  107 LEU
Chi-restraints excluded: chain L residue   15 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 21 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 370 ASN
** L  42 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 = 0.3946 r_free = 0.3946 target = 0.107939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.097605 restraints weight = 11617.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.099328 restraints weight = 7506.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.100534 restraints weight = 5370.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.6339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3469  Z= 0.170
  Angle     :  0.741  11.364   4716  Z= 0.394
  Chirality :  0.048   0.199    501
  Planarity :  0.005   0.074    605
  Dihedral  :  5.762  21.105    472
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 11.64 %
    Favored  : 87.89 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 19.68 %
    Favored  : 75.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.60 (0.40), residues: 421
  helix: -3.46 (0.61), residues: 26
  sheet:  0.07 (0.50), residues: 133
  loop : -2.70 (0.34), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP H  36 
 HIS   0.003   0.001   HIS L  61 
 PHE   0.012   0.002   PHE H 109 
 TYR   0.020   0.002   TYR L  55 
 ARG   0.004   0.001   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04100 (   82)
  hydrogen bonds       : angle       6.39914 (  192)
  SS BOND              : bond        0.00460 (    6)
  SS BOND              : angle       1.64136 (   12)
  covalent geometry    : bond        0.00387 ( 3463)
  covalent geometry    : angle       0.73742 ( 4704)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  498 GLN cc_start: 0.7990 (mp10) cc_final: 0.7384 (mp10)
REVERT: L   55 TYR cc_start: 0.3407 (OUTLIER) cc_final: 0.2013 (m-10)
REVERT: L   83 LEU cc_start: 0.7067 (tt) cc_final: 0.6644 (pp)
  outliers start: 18
  outliers final: 8
  residues processed: 79
  average time/residue: 0.2149
  time to fit residues: 21.1073
Evaluate side-chains
  64 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  364 ASP
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  414 GLN
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain H residue   99 ASP
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   55 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0870
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** L  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.109431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.099355 restraints weight = 11719.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.101099 restraints weight = 7433.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.102272 restraints weight = 5234.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.6555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3469  Z= 0.141
  Angle     :  0.733  12.034   4716  Z= 0.383
  Chirality :  0.048   0.214    501
  Planarity :  0.005   0.054    605
  Dihedral  :  5.705  25.768    472
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 11.40 %
    Favored  : 88.12 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 22.10 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.74 (0.39), residues: 421
  helix: -3.66 (0.64), residues: 26
  sheet: -0.05 (0.49), residues: 132
  loop : -2.76 (0.34), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  36 
 HIS   0.004   0.002   HIS L  61 
 PHE   0.013   0.001   PHE H  29 
 TYR   0.036   0.002   TYR H 103 
 ARG   0.003   0.000   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03577 (   82)
  hydrogen bonds       : angle       6.81330 (  192)
  SS BOND              : bond        0.00373 (    6)
  SS BOND              : angle       1.88006 (   12)
  covalent geometry    : bond        0.00319 ( 3463)
  covalent geometry    : angle       0.72804 ( 4704)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 ARG cc_start: 0.7985 (tmt-80) cc_final: 0.7499 (tpt90)
REVERT: L   24 LYS cc_start: 0.3185 (OUTLIER) cc_final: 0.2065 (tmtt)
REVERT: L   83 LEU cc_start: 0.6683 (tt) cc_final: 0.6352 (pp)
  outliers start: 10
  outliers final: 4
  residues processed: 70
  average time/residue: 0.2934
  time to fit residues: 25.1075
Evaluate side-chains
  58 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 1.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain H residue   99 ASP
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   24 LYS
Chi-restraints excluded: chain L residue   55 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   chunk 11 optimal weight:    0.0010
   chunk 2 optimal weight:    0.1980
   chunk 27 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.110449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.100473 restraints weight = 11582.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.102152 restraints weight = 7389.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.103199 restraints weight = 5279.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7019
moved from start:          0.6707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3469  Z= 0.140
  Angle     :  0.747  12.052   4716  Z= 0.391
  Chirality :  0.048   0.211    501
  Planarity :  0.005   0.047    605
  Dihedral  :  5.612  25.786    472
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 11.16 %
    Favored  : 88.36 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 23.45 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.39), residues: 421
  helix: -3.93 (0.60), residues: 26
  sheet: -0.19 (0.48), residues: 134
  loop : -2.79 (0.34), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  36 
 HIS   0.003   0.001   HIS L  61 
 PHE   0.016   0.001   PHE H 109 
 TYR   0.036   0.002   TYR H 103 
 ARG   0.003   0.000   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03761 (   82)
  hydrogen bonds       : angle       6.55618 (  192)
  SS BOND              : bond        0.00283 (    6)
  SS BOND              : angle       2.04446 (   12)
  covalent geometry    : bond        0.00317 ( 3463)
  covalent geometry    : angle       0.74087 ( 4704)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   74 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7925 (mtmt)
REVERT: L   24 LYS cc_start: 0.3367 (OUTLIER) cc_final: 0.2274 (tmtt)
REVERT: L   83 LEU cc_start: 0.6712 (tt) cc_final: 0.6363 (pp)
REVERT: L   85 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7172 (tm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 69
  average time/residue: 0.1921
  time to fit residues: 16.2648
Evaluate side-chains
  63 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   24 LYS
Chi-restraints excluded: chain L residue   55 TYR
Chi-restraints excluded: chain L residue   73 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 14 optimal weight:    8.9990
   chunk 30 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 5 optimal weight:    0.2980
   chunk 9 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0570
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.110879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.101123 restraints weight = 11726.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.102821 restraints weight = 7387.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.103993 restraints weight = 5206.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6994
moved from start:          0.6846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3469  Z= 0.141
  Angle     :  0.764  12.533   4716  Z= 0.398
  Chirality :  0.048   0.203    501
  Planarity :  0.005   0.046    605
  Dihedral  :  5.697  25.606    472
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 11.40 %
    Favored  : 88.12 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 25.07 %
    Favored  : 72.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.92 (0.39), residues: 421
  helix: -4.21 (0.53), residues: 26
  sheet: -0.27 (0.48), residues: 135
  loop : -2.80 (0.34), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  36 
 HIS   0.002   0.001   HIS L  61 
 PHE   0.017   0.001   PHE H 109 
 TYR   0.018   0.001   TYR L  91 
 ARG   0.003   0.000   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03786 (   82)
  hydrogen bonds       : angle       6.67973 (  192)
  SS BOND              : bond        0.00233 (    6)
  SS BOND              : angle       2.41597 (   12)
  covalent geometry    : bond        0.00320 ( 3463)
  covalent geometry    : angle       0.75480 ( 4704)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   74 LYS cc_start: 0.8133 (mmtt) cc_final: 0.7870 (mtmt)
REVERT: L   24 LYS cc_start: 0.3364 (OUTLIER) cc_final: 0.2280 (tmtt)
REVERT: L   79 GLN cc_start: 0.2109 (OUTLIER) cc_final: 0.1825 (mm-40)
REVERT: L   83 LEU cc_start: 0.6721 (tt) cc_final: 0.6352 (pp)
REVERT: L   85 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7270 (tm-30)
  outliers start: 9
  outliers final: 7
  residues processed: 71
  average time/residue: 0.2339
  time to fit residues: 20.5462
Evaluate side-chains
  66 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   24 LYS
Chi-restraints excluded: chain L residue   55 TYR
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   79 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    0.0370
   chunk 0 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 14 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  42 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 = 0.4000 r_free = 0.4000 target = 0.111061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.101250 restraints weight = 11433.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.102920 restraints weight = 7219.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.104058 restraints weight = 5117.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.6997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3469  Z= 0.145
  Angle     :  0.796  12.625   4716  Z= 0.412
  Chirality :  0.048   0.181    501
  Planarity :  0.005   0.046    605
  Dihedral  :  5.726  25.316    472
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 11.40 %
    Favored  : 88.12 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 22.37 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.01 (0.39), residues: 421
  helix: -4.25 (0.53), residues: 26
  sheet: -0.33 (0.48), residues: 135
  loop : -2.86 (0.33), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 436 
 HIS   0.003   0.001   HIS L  61 
 PHE   0.012   0.001   PHE H  29 
 TYR   0.019   0.001   TYR H 103 
 ARG   0.002   0.000   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03729 (   82)
  hydrogen bonds       : angle       6.82172 (  192)
  SS BOND              : bond        0.00316 (    6)
  SS BOND              : angle       3.30669 (   12)
  covalent geometry    : bond        0.00332 ( 3463)
  covalent geometry    : angle       0.77911 ( 4704)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   74 LYS cc_start: 0.8087 (mmtt) cc_final: 0.7787 (mtmt)
REVERT: L   24 LYS cc_start: 0.3242 (OUTLIER) cc_final: 0.2306 (tmtt)
REVERT: L   83 LEU cc_start: 0.6797 (tt) cc_final: 0.6404 (pp)
REVERT: L   85 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7357 (tm-30)
  outliers start: 15
  outliers final: 8
  residues processed: 73
  average time/residue: 0.1999
  time to fit residues: 18.4269
Evaluate side-chains
  66 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   24 LYS
Chi-restraints excluded: chain L residue   55 TYR
Chi-restraints excluded: chain L residue   73 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 17 optimal weight:    0.4980
   chunk 11 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0670
   chunk 31 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.3918

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

Flipped N/Q/H residues before XYZ refinement:
** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.113060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.103250 restraints weight = 11736.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.105038 restraints weight = 7286.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.106241 restraints weight = 5068.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6949
moved from start:          0.7082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3469  Z= 0.145
  Angle     :  0.818  12.754   4716  Z= 0.423
  Chirality :  0.048   0.188    501
  Planarity :  0.005   0.041    605
  Dihedral  :  5.677  26.694    472
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 10.93 %
    Favored  : 88.60 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 23.72 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.39), residues: 421
  helix: -4.39 (0.47), residues: 26
  sheet: -0.30 (0.48), residues: 134
  loop : -2.84 (0.34), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 436 
 HIS   0.002   0.001   HIS L  61 
 PHE   0.019   0.001   PHE H 109 
 TYR   0.010   0.001   TYR L  91 
 ARG   0.003   0.000   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03673 (   82)
  hydrogen bonds       : angle       6.73705 (  192)
  SS BOND              : bond        0.00315 (    6)
  SS BOND              : angle       3.18472 (   12)
  covalent geometry    : bond        0.00335 ( 3463)
  covalent geometry    : angle       0.80300 ( 4704)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 ARG cc_start: 0.7735 (tpt170) cc_final: 0.7449 (tpt90)
REVERT: H   74 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7747 (mtmt)
REVERT: L   24 LYS cc_start: 0.3443 (OUTLIER) cc_final: 0.2456 (tmtt)
REVERT: L   83 LEU cc_start: 0.6754 (tt) cc_final: 0.6359 (pp)
REVERT: L   85 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7274 (tm-30)
  outliers start: 7
  outliers final: 6
  residues processed: 71
  average time/residue: 0.1777
  time to fit residues: 15.7242
Evaluate side-chains
  67 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain L residue   15 VAL
Chi-restraints excluded: chain L residue   24 LYS
Chi-restraints excluded: chain L residue   55 TYR
Chi-restraints excluded: chain L residue   73 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 14 optimal weight:    0.2980
   chunk 22 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   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 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  37 GLN
** L  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  93 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.110535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.100315 restraints weight = 11742.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.102181 restraints weight = 7161.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.103500 restraints weight = 4965.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.7313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3469  Z= 0.161
  Angle     :  0.829  12.715   4716  Z= 0.432
  Chirality :  0.049   0.171    501
  Planarity :  0.006   0.080    605
  Dihedral  :  5.827  28.593    472
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 15.49
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 12.11 %
    Favored  : 87.41 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 24.53 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.02 (0.39), residues: 421
  helix: -4.30 (0.53), residues: 26
  sheet: -0.39 (0.48), residues: 135
  loop : -2.83 (0.34), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  36 
 HIS   0.003   0.001   HIS L  61 
 PHE   0.026   0.002   PHE A 392 
 TYR   0.022   0.001   TYR H 103 
 ARG   0.003   0.000   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04005 (   82)
  hydrogen bonds       : angle       6.88607 (  192)
  SS BOND              : bond        0.00257 (    6)
  SS BOND              : angle       2.22553 (   12)
  covalent geometry    : bond        0.00376 ( 3463)
  covalent geometry    : angle       0.82212 ( 4704)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2370.45 seconds
wall clock time: 44 minutes 30.30 seconds (2670.30 seconds total)