Starting phenix.real_space_refine
on Tue Mar  3 11:40:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f63_31471/03_2026/7f63_31471.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f63_31471/03_2026/7f63_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f63_31471/03_2026/7f63_31471.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f63_31471/03_2026/7f63_31471.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f63_31471/03_2026/7f63_31471.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f63_31471/03_2026/7f63_31471.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.99, per 1000 atoms: 0.29
  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: 0.26
  Conformation dependent library (CDL) restraints added in 151.1 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: 0.11
  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: 0.43

  Time building geometry restraints manager: 0.37 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:             5.000
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.490
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.890
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.002   0.000   ARG A 346 
 TYR   0.016   0.001   TYR L  49 
 PHE   0.052   0.002   PHE H  64 
 TRP   0.014   0.001   TRP H  36 
 HIS   0.000   0.000   HIS A 519 

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

*********************** 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  : 0.095 
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: 0.0975
  time to fit residues: 13.0519
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  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.1980
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A 370 ASN
A 487 ASN
H  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.110894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.099776 restraints weight = 11436.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.101608 restraints weight = 7456.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.102787 restraints weight = 5342.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.103717 restraints weight = 4165.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.104257 restraints weight = 3402.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6948
moved from start:          0.4831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3469  Z= 0.222
  Angle     :  0.823  11.416   4716  Z= 0.435
  Chirality :  0.050   0.221    501
  Planarity :  0.005   0.042    605
  Dihedral  :  5.765  27.619    472
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 12.35 %
    Favored  : 87.17 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 13.48 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.44 (0.39), residues: 421
  helix: -3.17 (0.94), residues: 20
  sheet:  0.36 (0.49), residues: 129
  loop : -2.71 (0.33), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  98 
 TYR   0.018   0.002   TYR H 103 
 PHE   0.020   0.002   PHE A 392 
 TRP   0.015   0.003   TRP L  35 
 HIS   0.001   0.001   HIS L  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 3463)
  covalent geometry    : angle       0.81909 ( 4704)
  SS BOND              : bond        0.01170 (    6)
  SS BOND              : angle       1.81600 (   12)
  hydrogen bonds       : bond        0.04732 (   82)
  hydrogen bonds       : angle       6.46141 (  192)

*********************** 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: 11
    poor density    : 77
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  493 GLN cc_start: 0.8130 (mp10) cc_final: 0.7738 (mp10)
REVERT: A  498 GLN cc_start: 0.7879 (mp10) cc_final: 0.7388 (mp10)
REVERT: H   33 THR cc_start: 0.9367 (OUTLIER) cc_final: 0.9075 (t)
REVERT: H   35 TYR cc_start: 0.8664 (m-80) cc_final: 0.8388 (m-80)
  outliers start: 11
  outliers final: 4
  residues processed: 85
  average time/residue: 0.0839
  time to fit residues: 8.4783
Evaluate side-chains
  62 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain H residue   33 THR
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain L residue   15 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0270
   chunk 21 optimal weight:    7.9990
   chunk 38 optimal weight:    0.7980
   chunk 6 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 19 optimal weight:    9.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.7038

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.111016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.100475 restraints weight = 11547.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.102289 restraints weight = 7273.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.103549 restraints weight = 5114.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.104416 restraints weight = 3895.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.105051 restraints weight = 3164.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6923
moved from start:          0.5238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3469  Z= 0.137
  Angle     :  0.708  12.250   4716  Z= 0.367
  Chirality :  0.047   0.207    501
  Planarity :  0.004   0.035    605
  Dihedral  :  5.402  19.570    472
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  9.98 %
    Favored  : 89.55 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 18.33 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.38 (0.39), residues: 421
  helix: -3.13 (0.99), residues: 20
  sheet:  0.20 (0.49), residues: 126
  loop : -2.51 (0.34), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  98 
 TYR   0.016   0.001   TYR H  80 
 PHE   0.018   0.001   PHE H  29 
 TRP   0.008   0.001   TRP L  35 
 HIS   0.003   0.001   HIS L  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3463)
  covalent geometry    : angle       0.70629 ( 4704)
  SS BOND              : bond        0.00244 (    6)
  SS BOND              : angle       1.25905 (   12)
  hydrogen bonds       : bond        0.03693 (   82)
  hydrogen bonds       : angle       6.18353 (  192)

*********************** 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
  82 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  493 GLN cc_start: 0.7899 (mp10) cc_final: 0.7573 (mp10)
REVERT: H   33 THR cc_start: 0.9242 (OUTLIER) cc_final: 0.9000 (t)
  outliers start: 9
  outliers final: 2
  residues processed: 79
  average time/residue: 0.0676
  time to fit residues: 6.5232
Evaluate side-chains
  61 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain H residue   33 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    0.0970
   chunk 33 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 26 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.7578

-------------------------------------------------------------------------------
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 = 0.3980 r_free = 0.3980 target = 0.110231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.099747 restraints weight = 11510.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.101509 restraints weight = 7282.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.102746 restraints weight = 5122.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.103599 restraints weight = 3919.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.104140 restraints weight = 3206.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6964
moved from start:          0.5847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3469  Z= 0.147
  Angle     :  0.730  11.660   4716  Z= 0.384
  Chirality :  0.047   0.208    501
  Planarity :  0.005   0.064    605
  Dihedral  :  5.608  20.192    472
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 11.88 %
    Favored  : 87.65 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.95 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.59 (0.39), residues: 421
  helix: -3.38 (0.65), residues: 26
  sheet:  0.05 (0.49), residues: 128
  loop : -2.63 (0.34), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  54 
 TYR   0.027   0.002   TYR H 104 
 PHE   0.018   0.002   PHE H  64 
 TRP   0.007   0.001   TRP H  36 
 HIS   0.001   0.000   HIS L  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 3463)
  covalent geometry    : angle       0.72443 ( 4704)
  SS BOND              : bond        0.00709 (    6)
  SS BOND              : angle       1.90694 (   12)
  hydrogen bonds       : bond        0.03662 (   82)
  hydrogen bonds       : angle       6.72795 (  192)

*********************** 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
  77 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 ARG cc_start: 0.8093 (tpt170) cc_final: 0.7864 (tpt90)
REVERT: A  493 GLN cc_start: 0.7890 (mp10) cc_final: 0.7532 (mp10)
REVERT: H   62 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7438 (tm-30)
REVERT: L   91 TYR cc_start: 0.8412 (p90) cc_final: 0.8025 (p90)
  outliers start: 10
  outliers final: 6
  residues processed: 76
  average time/residue: 0.0685
  time to fit residues: 6.3503
Evaluate side-chains
  65 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   99 ASP
Chi-restraints excluded: chain H residue  104 TYR
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 23 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0050
   chunk 37 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0060
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.4610

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

Flipped N/Q/H residues before XYZ refinement:
A 370 ASN
A 414 GLN
H  55 ASN
** L  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.111513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.101287 restraints weight = 11520.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.103070 restraints weight = 7154.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.104345 restraints weight = 4962.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.105220 restraints weight = 3729.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.105759 restraints weight = 2998.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6928
moved from start:          0.6084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3469  Z= 0.132
  Angle     :  0.708  11.547   4716  Z= 0.369
  Chirality :  0.047   0.200    501
  Planarity :  0.004   0.044    605
  Dihedral  :  5.432  20.383    472
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 10.45 %
    Favored  : 89.07 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 21.02 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.64 (0.39), residues: 421
  helix: -3.84 (0.57), residues: 26
  sheet:  0.16 (0.49), residues: 130
  loop : -2.73 (0.33), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  98 
 TYR   0.020   0.001   TYR H 104 
 PHE   0.016   0.001   PHE H  29 
 TRP   0.006   0.001   TRP H  36 
 HIS   0.002   0.001   HIS L  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 3463)
  covalent geometry    : angle       0.70491 ( 4704)
  SS BOND              : bond        0.00345 (    6)
  SS BOND              : angle       1.49014 (   12)
  hydrogen bonds       : bond        0.03326 (   82)
  hydrogen bonds       : angle       6.18211 (  192)

*********************** 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
  75 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  493 GLN cc_start: 0.7839 (mp10) cc_final: 0.7515 (mp10)
REVERT: H   62 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7367 (tm-30)
REVERT: L    9 LYS cc_start: 0.4504 (tmtt) cc_final: 0.3865 (mmpt)
REVERT: L   24 LYS cc_start: 0.3251 (OUTLIER) cc_final: 0.2274 (tmtt)
REVERT: L   55 TYR cc_start: 0.3272 (OUTLIER) cc_final: 0.2336 (m-10)
  outliers start: 13
  outliers final: 5
  residues processed: 73
  average time/residue: 0.0578
  time to fit residues: 5.2639
Evaluate side-chains
  64 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  414 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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 38 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0970
   chunk 22 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0020
   chunk 21 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN
H  55 ASN
** L  42 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 = 0.4005 r_free = 0.4005 target = 0.111289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.101118 restraints weight = 11489.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.102932 restraints weight = 7057.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.104200 restraints weight = 4868.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.105061 restraints weight = 3663.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.105645 restraints weight = 2955.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6935
moved from start:          0.6330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3469  Z= 0.135
  Angle     :  0.742  11.892   4716  Z= 0.384
  Chirality :  0.047   0.208    501
  Planarity :  0.005   0.044    605
  Dihedral  :  5.593  24.039    472
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 11.16 %
    Favored  : 88.36 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 21.56 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.73 (0.39), residues: 421
  helix: -4.01 (0.59), residues: 26
  sheet:  0.02 (0.48), residues: 132
  loop : -2.74 (0.34), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  98 
 TYR   0.026   0.002   TYR H 104 
 PHE   0.035   0.002   PHE L  87 
 TRP   0.006   0.001   TRP A 436 
 HIS   0.003   0.001   HIS L  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3463)
  covalent geometry    : angle       0.73758 ( 4704)
  SS BOND              : bond        0.00195 (    6)
  SS BOND              : angle       1.81298 (   12)
  hydrogen bonds       : bond        0.03539 (   82)
  hydrogen bonds       : angle       6.36333 (  192)

*********************** 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
  79 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  493 GLN cc_start: 0.7800 (mp10) cc_final: 0.7498 (mp10)
REVERT: A  498 GLN cc_start: 0.8221 (mp10) cc_final: 0.7611 (mp10)
REVERT: H   62 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7320 (tm-30)
REVERT: L    9 LYS cc_start: 0.4450 (tmtt) cc_final: 0.3772 (mmpt)
REVERT: L   24 LYS cc_start: 0.3061 (OUTLIER) cc_final: 0.2118 (tmtt)
REVERT: L   55 TYR cc_start: 0.3539 (OUTLIER) cc_final: 0.2237 (m-10)
  outliers start: 13
  outliers final: 6
  residues processed: 77
  average time/residue: 0.0675
  time to fit residues: 6.2897
Evaluate side-chains
  64 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  414 GLN
Chi-restraints excluded: chain H residue   55 ASN
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   65 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    0.0470
   chunk 9 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 2 optimal weight:    0.0030
   chunk 41 optimal weight:    0.3980
   chunk 17 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.3888

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN
** 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 = 0.4015 r_free = 0.4015 target = 0.111770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.101512 restraints weight = 11606.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.103322 restraints weight = 7189.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.104588 restraints weight = 4974.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.105452 restraints weight = 3745.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.106055 restraints weight = 3020.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6917
moved from start:          0.6411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3469  Z= 0.134
  Angle     :  0.757  12.099   4716  Z= 0.389
  Chirality :  0.047   0.219    501
  Planarity :  0.005   0.067    605
  Dihedral  :  5.644  23.998    472
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 10.21 %
    Favored  : 89.31 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 22.10 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.77 (0.39), residues: 421
  helix: -4.10 (0.57), residues: 26
  sheet: -0.01 (0.49), residues: 132
  loop : -2.76 (0.34), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 408 
 TYR   0.024   0.001   TYR H 104 
 PHE   0.014   0.001   PHE H  29 
 TRP   0.005   0.001   TRP A 436 
 HIS   0.003   0.001   HIS L  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 3463)
  covalent geometry    : angle       0.75012 ( 4704)
  SS BOND              : bond        0.00269 (    6)
  SS BOND              : angle       2.16424 (   12)
  hydrogen bonds       : bond        0.03476 (   82)
  hydrogen bonds       : angle       6.40914 (  192)

*********************** 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
  73 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  493 GLN cc_start: 0.7791 (mp10) cc_final: 0.7512 (mp10)
REVERT: A  498 GLN cc_start: 0.8153 (mp10) cc_final: 0.7592 (mp10)
REVERT: H   39 GLN cc_start: 0.6809 (mm110) cc_final: 0.6498 (mm110)
REVERT: H   62 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7246 (tm-30)
REVERT: L    9 LYS cc_start: 0.4488 (tmtt) cc_final: 0.3837 (mmpt)
REVERT: L   24 LYS cc_start: 0.3098 (OUTLIER) cc_final: 0.2205 (tmtt)
REVERT: L   55 TYR cc_start: 0.3622 (OUTLIER) cc_final: 0.2183 (m-10)
REVERT: L   91 TYR cc_start: 0.8402 (p90) cc_final: 0.8183 (p90)
  outliers start: 13
  outliers final: 9
  residues processed: 72
  average time/residue: 0.0510
  time to fit residues: 4.8273
Evaluate side-chains
  65 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
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  382 VAL
Chi-restraints excluded: chain A residue  414 GLN
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain H residue   99 ASP
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   65 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 17 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.3954 r_free = 0.3954 target = 0.108622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.098343 restraints weight = 11850.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.100061 restraints weight = 7591.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.101281 restraints weight = 5382.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.102115 restraints weight = 4110.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.102710 restraints weight = 3355.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.6899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3469  Z= 0.168
  Angle     :  0.805  12.479   4716  Z= 0.420
  Chirality :  0.048   0.222    501
  Planarity :  0.005   0.067    605
  Dihedral  :  6.031  26.672    472
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 14.01 %
    Favored  : 85.51 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 21.83 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.94 (0.39), residues: 421
  helix: -4.19 (0.59), residues: 26
  sheet: -0.13 (0.49), residues: 133
  loop : -2.90 (0.34), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 408 
 TYR   0.030   0.002   TYR H 104 
 PHE   0.011   0.002   PHE H 109 
 TRP   0.009   0.002   TRP A 436 
 HIS   0.003   0.001   HIS L  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 3463)
  covalent geometry    : angle       0.79000 ( 4704)
  SS BOND              : bond        0.00369 (    6)
  SS BOND              : angle       3.16526 (   12)
  hydrogen bonds       : bond        0.04033 (   82)
  hydrogen bonds       : angle       6.65525 (  192)

*********************** 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
  81 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  493 GLN cc_start: 0.7904 (mp10) cc_final: 0.7609 (mp10)
REVERT: A  498 GLN cc_start: 0.7977 (mp10) cc_final: 0.7377 (mp10)
REVERT: H   62 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7351 (tm-30)
REVERT: L    9 LYS cc_start: 0.4675 (tmtt) cc_final: 0.4052 (mmpt)
REVERT: L   24 LYS cc_start: 0.3341 (OUTLIER) cc_final: 0.2269 (tmtt)
REVERT: L   55 TYR cc_start: 0.3791 (OUTLIER) cc_final: 0.2259 (m-10)
  outliers start: 17
  outliers final: 10
  residues processed: 77
  average time/residue: 0.0513
  time to fit residues: 5.0075
Evaluate side-chains
  68 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
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  382 VAL
Chi-restraints excluded: chain A residue  414 GLN
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain H residue   99 ASP
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   65 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 19 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 GLN ** 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 = 0.3942 r_free = 0.3942 target = 0.107573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.097359 restraints weight = 11670.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.099078 restraints weight = 7499.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.100262 restraints weight = 5296.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.101073 restraints weight = 4081.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.101657 restraints weight = 3351.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7100
moved from start:          0.7435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3469  Z= 0.189
  Angle     :  0.881  12.661   4716  Z= 0.460
  Chirality :  0.049   0.230    501
  Planarity :  0.006   0.066    605
  Dihedral  :  6.427  29.027    472
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 15.49
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 13.78 %
    Favored  : 85.75 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 23.99 %
    Favored  : 73.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.06 (0.39), residues: 421
  helix: -4.38 (0.47), residues: 26
  sheet: -0.17 (0.49), residues: 133
  loop : -3.00 (0.34), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG H  98 
 TYR   0.029   0.002   TYR H 104 
 PHE   0.020   0.002   PHE L  87 
 TRP   0.008   0.002   TRP H  36 
 HIS   0.003   0.001   HIS L  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 3463)
  covalent geometry    : angle       0.86547 ( 4704)
  SS BOND              : bond        0.00286 (    6)
  SS BOND              : angle       3.41863 (   12)
  hydrogen bonds       : bond        0.04503 (   82)
  hydrogen bonds       : angle       6.86915 (  192)

*********************** 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
  73 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  391 CYS cc_start: 0.2664 (p) cc_final: 0.2460 (p)
REVERT: A  493 GLN cc_start: 0.7875 (mp10) cc_final: 0.7601 (mp10)
REVERT: A  498 GLN cc_start: 0.8016 (mp10) cc_final: 0.7591 (mp10)
REVERT: H   62 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7799 (tm-30)
REVERT: H  109 PHE cc_start: 0.6873 (t80) cc_final: 0.6640 (t80)
REVERT: L   24 LYS cc_start: 0.3066 (OUTLIER) cc_final: 0.1885 (tmtt)
REVERT: L   55 TYR cc_start: 0.3352 (OUTLIER) cc_final: 0.1876 (m-10)
REVERT: L   85 GLU cc_start: 0.7469 (tm-30) cc_final: 0.6767 (tm-30)
  outliers start: 11
  outliers final: 8
  residues processed: 71
  average time/residue: 0.0439
  time to fit residues: 4.0191
Evaluate side-chains
  66 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
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  364 ASP
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain H residue   99 ASP
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   65 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
L  37 GLN
** 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 = 0.3970 r_free = 0.3970 target = 0.109210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.099200 restraints weight = 11643.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.100896 restraints weight = 7459.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.102105 restraints weight = 5297.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.102921 restraints weight = 4044.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.103454 restraints weight = 3295.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
moved from start:          0.7523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3469  Z= 0.159
  Angle     :  0.856  13.116   4716  Z= 0.443
  Chirality :  0.049   0.226    501
  Planarity :  0.005   0.057    605
  Dihedral  :  6.107  29.036    472
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 15.33
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 13.06 %
    Favored  : 86.46 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 24.80 %
    Favored  : 72.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.06 (0.39), residues: 421
  helix: -4.43 (0.46), residues: 26
  sheet: -0.20 (0.48), residues: 133
  loop : -2.96 (0.34), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 457 
 TYR   0.026   0.002   TYR H 104 
 PHE   0.016   0.002   PHE L  87 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.002   0.001   HIS L  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 3463)
  covalent geometry    : angle       0.84267 ( 4704)
  SS BOND              : bond        0.00289 (    6)
  SS BOND              : angle       3.15182 (   12)
  hydrogen bonds       : bond        0.04079 (   82)
  hydrogen bonds       : angle       6.75174 (  192)

********************** 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: 11
    poor density    : 61
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  391 CYS cc_start: 0.3004 (p) cc_final: 0.2654 (p)
REVERT: A  493 GLN cc_start: 0.7736 (mp10) cc_final: 0.7449 (mp10)
REVERT: A  498 GLN cc_start: 0.7897 (mp10) cc_final: 0.7369 (mp10)
REVERT: H   62 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7767 (tm-30)
REVERT: H  109 PHE cc_start: 0.6810 (t80) cc_final: 0.6449 (t80)
REVERT: L    9 LYS cc_start: 0.4805 (tmtt) cc_final: 0.4159 (mmpt)
REVERT: L   24 LYS cc_start: 0.3046 (OUTLIER) cc_final: 0.1803 (tmtt)
REVERT: L   55 TYR cc_start: 0.3258 (OUTLIER) cc_final: 0.2127 (m-10)
REVERT: L   85 GLU cc_start: 0.7417 (tm-30) cc_final: 0.6898 (tm-30)
REVERT: L  104 LEU cc_start: 0.7621 (tp) cc_final: 0.7345 (tp)
  outliers start: 11
  outliers final: 8
  residues processed: 70
  average time/residue: 0.0565
  time to fit residues: 5.0290
Evaluate side-chains
  65 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
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  382 VAL
Chi-restraints excluded: chain H residue   99 ASP
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   65 SER
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 38 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3972 r_free = 0.3972 target = 0.109262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.099190 restraints weight = 11914.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.100874 restraints weight = 7625.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.102085 restraints weight = 5432.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.102907 restraints weight = 4164.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.103489 restraints weight = 3402.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.7689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3469  Z= 0.166
  Angle     :  0.870  13.002   4716  Z= 0.453
  Chirality :  0.049   0.217    501
  Planarity :  0.005   0.055    605
  Dihedral  :  6.159  29.029    472
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 13.54 %
    Favored  : 85.99 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 24.80 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.09 (0.39), residues: 421
  helix: -4.43 (0.47), residues: 26
  sheet: -0.26 (0.48), residues: 133
  loop : -2.97 (0.34), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 408 
 TYR   0.025   0.002   TYR H 104 
 PHE   0.015   0.002   PHE L  87 
 TRP   0.010   0.002   TRP H  36 
 HIS   0.002   0.001   HIS L  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 3463)
  covalent geometry    : angle       0.85555 ( 4704)
  SS BOND              : bond        0.00178 (    6)
  SS BOND              : angle       3.29016 (   12)
  hydrogen bonds       : bond        0.04345 (   82)
  hydrogen bonds       : angle       6.85718 (  192)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 862.74 seconds
wall clock time: 15 minutes 27.04 seconds (927.04 seconds total)