Starting phenix.real_space_refine
on Tue Feb  3 14:03:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k6y_62140/02_2026/9k6y_62140.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k6y_62140/02_2026/9k6y_62140.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k6y_62140/02_2026/9k6y_62140.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k6y_62140/02_2026/9k6y_62140.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k6y_62140/02_2026/9k6y_62140.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k6y_62140/02_2026/9k6y_62140.cif"
  }
  resolution = 2.67
  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=   0.008
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      20      5.16       5
     C    2152      2.51       5
     N     570      2.21       5
     O     652      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3394
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "L"
      Number of atoms: 859
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 859
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 8, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 970
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 4, 'TRANS': 118}
    Chain: "R"
      Number of atoms: 1537
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1537
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 0.96, per 1000 atoms: 0.28
  Number of scatterers: 3394
  At special positions: 0
  Unit cell: (60.6, 67.064, 108.272, 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      20     16.00
     O     652      8.00
     N     570      7.00
     C    2152      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 102 " - pdb=" SG  CYS H 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 336 " - pdb=" SG  CYS R 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 379 " - pdb=" SG  CYS R 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 391 " - pdb=" SG  CYS R 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 480 " - pdb=" SG  CYS R 488 " 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
  Links applied
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
    NAG-ASN
      " NAG A   1 " - " ASN R 343 "
  Time building additional restraints: 0.29
  Conformation dependent library (CDL) restraints added in 125.3 milliseconds
  

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  782

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 10 sheets defined
      6.5% alpha, 36.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'L' and resid 85 through 89
      removed outlier: 4.173A  pdb=" N   VAL L  89 " --> pdb=" O   ALA L  86 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 30
      No H-bonds generated for 'chain 'H' and resid 28 through 30'
    Processing helix  chain 'R' and resid 364 through 368
      removed outlier: 3.905A  pdb=" N   VAL R 367 " --> pdb=" O   ASP R 364 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 383 through 387
      removed outlier: 3.648A  pdb=" N   LEU R 387 " --> pdb=" O   PRO R 384 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 405 through 410
      removed outlier: 4.354A  pdb=" N   ARG R 408 " --> pdb=" O   ASP R 405 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 6
    Processing sheet with id=AA2, first strand: chain 'L' and resid 11 through 12
      removed outlier: 3.676A  pdb=" N   GLU L 111 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   LEU L  39 " --> pdb=" O   TYR L  55 " (cutoff:3.500A)
      removed outlier: 4.732A  pdb=" N   TYR L  55 " --> pdb=" O   LEU L  39 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 11 through 12
      removed outlier: 3.676A  pdb=" N   GLU L 111 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   THR L 103 " --> pdb=" O   GLN L  96 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 30 through 31
      removed outlier: 3.756A  pdb=" N   ASN L  36 " --> pdb=" O   ASP L  31 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA6, first strand: chain 'H' and resid 58 through 60
      removed outlier: 6.764A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   ARG H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   MET H  34 " --> pdb=" O   ARG H  50 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   LEU H 115 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60
      removed outlier: 6.764A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   ARG H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   MET H  34 " --> pdb=" O   ARG H  50 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'R' and resid 354 through 358
    Processing sheet with id=AA9, first strand: chain 'R' and resid 452 through 454
    Processing sheet with id=AB1, first strand: chain 'R' and resid 473 through 474

    122 hydrogen bonds defined for protein.
    288 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: 0.52

  Time building geometry restraints manager: 0.39 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.20 -     1.32: 566
        1.32 -     1.45: 1038
        1.45 -     1.57: 1852
        1.57 -     1.70: 0
        1.70 -     1.82: 26
  Bond restraints: 3482
  Sorted by residual:
  bond pdb=" CA  SER R 494 "
       pdb=" CB  SER R 494 "
    ideal  model  delta    sigma   weight residual
    1.532  1.470  0.062 1.74e-02 3.30e+03 1.29e+01
  bond pdb=" N   VAL H   2 "
       pdb=" CA  VAL H   2 "
    ideal  model  delta    sigma   weight residual
    1.462  1.500 -0.038 1.25e-02 6.40e+03 9.04e+00
  bond pdb=" N   ILE L  98 "
       pdb=" CA  ILE L  98 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.28e-02 6.10e+03 7.41e+00
  bond pdb=" C   PRO L   8 "
       pdb=" O   PRO L   8 "
    ideal  model  delta    sigma   weight residual
    1.233  1.196  0.037 1.39e-02 5.18e+03 7.27e+00
  bond pdb=" CA  SER L  10 "
       pdb=" CB  SER L  10 "
    ideal  model  delta    sigma   weight residual
    1.530  1.488  0.043 1.69e-02 3.50e+03 6.34e+00
  ... (remaining 3477 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 4565
        1.89 -     3.78: 130
        3.78 -     5.67: 25
        5.67 -     7.56: 8
        7.56 -     9.45: 2
  Bond angle restraints: 4730
  Sorted by residual:
  angle pdb=" CB  GLN H   1 "
        pdb=" CG  GLN H   1 "
        pdb=" CD  GLN H   1 "
      ideal   model   delta    sigma   weight residual
     112.60  121.69   -9.09 1.70e+00 3.46e-01 2.86e+01
  angle pdb=" C   GLN H   1 "
        pdb=" CA  GLN H   1 "
        pdb=" CB  GLN H   1 "
      ideal   model   delta    sigma   weight residual
     110.10  119.55   -9.45 1.90e+00 2.77e-01 2.47e+01
  angle pdb=" CA  PHE L 104 "
        pdb=" CB  PHE L 104 "
        pdb=" CG  PHE L 104 "
      ideal   model   delta    sigma   weight residual
     113.80  118.64   -4.84 1.00e+00 1.00e+00 2.34e+01
  angle pdb=" CA  PHE L 100 "
        pdb=" CB  PHE L 100 "
        pdb=" CG  PHE L 100 "
      ideal   model   delta    sigma   weight residual
     113.80  109.03    4.77 1.00e+00 1.00e+00 2.27e+01
  angle pdb=" CA  SER L   7 "
        pdb=" C   SER L   7 "
        pdb=" N   PRO L   8 "
      ideal   model   delta    sigma   weight residual
     118.44  125.48   -7.04 1.59e+00 3.96e-01 1.96e+01
  ... (remaining 4725 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.60: 1879
       13.60 -    27.21: 153
       27.21 -    40.81: 33
       40.81 -    54.41: 20
       54.41 -    68.02: 1
  Dihedral angle restraints: 2086
    sinusoidal: 848
      harmonic: 1238
  Sorted by residual:
  dihedral pdb=" CA  SER L   7 "
           pdb=" C   SER L   7 "
           pdb=" N   PRO L   8 "
           pdb=" CA  PRO L   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.97  -25.03     0      5.00e+00 4.00e-02 2.51e+01
  dihedral pdb=" C   ASN R 487 "
           pdb=" N   ASN R 487 "
           pdb=" CA  ASN R 487 "
           pdb=" CB  ASN R 487 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.13   10.53     0      2.50e+00 1.60e-01 1.77e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   61.63   31.37     1      1.00e+01 1.00e-02 1.40e+01
  ... (remaining 2083 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 427
       0.065 -    0.130: 72
       0.130 -    0.196: 5
       0.196 -    0.261: 1
       0.261 -    0.326: 2
  Chirality restraints: 507
  Sorted by residual:
  chirality pdb=" CA  PHE L 100 "
            pdb=" N   PHE L 100 "
            pdb=" C   PHE L 100 "
            pdb=" CB  PHE L 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.66e+00
  chirality pdb=" CA  ASN R 487 "
            pdb=" N   ASN R 487 "
            pdb=" C   ASN R 487 "
            pdb=" CB  ASN R 487 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" CA  VAL H   2 "
            pdb=" N   VAL H   2 "
            pdb=" C   VAL H   2 "
            pdb=" CB  VAL H   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.23 2.00e-01 2.50e+01 1.28e+00
  ... (remaining 504 not shown)

  Planarity restraints: 612
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L  97 "    0.279 9.50e-02 1.11e+02   1.25e-01 9.62e+00
        pdb=" NE  ARG L  97 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG L  97 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG L  97 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG L  97 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY R 485 "   -0.013 2.00e-02 2.50e+03   2.56e-02 6.54e+00
        pdb=" C   GLY R 485 "    0.044 2.00e-02 2.50e+03
        pdb=" O   GLY R 485 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   PHE R 486 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR L   5 "    0.012 2.00e-02 2.50e+03   2.36e-02 5.55e+00
        pdb=" C   THR L   5 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   THR L   5 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLN L   6 "    0.014 2.00e-02 2.50e+03
  ... (remaining 609 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 331
        2.75 -     3.29: 3065
        3.29 -     3.82: 5405
        3.82 -     4.36: 6602
        4.36 -     4.90: 11366
  Nonbonded interactions: 26769
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 438 "
            pdb=" OD1 ASP R 442 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   THR R 393 "
            pdb=" OG1 THR R 523 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OD2 ASP R 442 "
            pdb=" OH  TYR R 451 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OD2 ASP L  34 "
            pdb=" OH  TYR L  38 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OG1 THR R 393 "
            pdb=" O   GLU R 516 "
     model   vdw
     2.306 3.040
  ... (remaining 26764 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             15.650
  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:                    0.010
  Process input model:                     5.410
  Find NCS groups from input model:        0.160
  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:6.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
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      :  0.004   0.062   3491  Z= 0.260
  Angle     :  0.782   9.448   4750  Z= 0.489
  Chirality :  0.052   0.326    507
  Planarity :  0.006   0.125    611
  Dihedral  : 11.155  68.017   1283
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.49 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.26 %
  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:  0.08 (0.42), residues: 423
  helix: -3.84 (0.81), residues: 20
  sheet:  0.77 (0.41), residues: 153
  loop :  0.01 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  72 
 TYR   0.012   0.001   TYR H  60 
 PHE   0.026   0.001   PHE L 100 
 TRP   0.011   0.001   TRP R 436 
 HIS   0.003   0.001   HIS H 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 3482)
  covalent geometry    : angle       0.77463 ( 4730)
  SS BOND              : bond        0.00479 (    7)
  SS BOND              : angle       1.58418 (   14)
  hydrogen bonds       : bond        0.11524 (  104)
  hydrogen bonds       : angle       6.45873 (  288)
  link_BETA1-4         : bond        0.00177 (    1)
  link_BETA1-4         : angle       1.93344 (    3)
  link_NAG-ASN         : bond        0.00103 (    1)
  link_NAG-ASN         : angle       2.38150 (    3)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
REVERT: L    4 MET cc_start: 0.7536 (mmm) cc_final: 0.6975 (mmm)
REVERT: L   22 SER cc_start: 0.7960 (m) cc_final: 0.7726 (t)
REVERT: H   30 THR cc_start: 0.8668 (p) cc_final: 0.8414 (t)
REVERT: H   90 ASP cc_start: 0.8217 (m-30) cc_final: 0.7999 (m-30)
REVERT: R  354 ASN cc_start: 0.6940 (t0) cc_final: 0.6542 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.2688
  time to fit residues: 20.4407
Evaluate side-chains
  72 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.4980
   chunk 16 optimal weight:    0.0870
   chunk 32 optimal weight:    0.0970
   chunk 31 optimal weight:    0.1980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0270
   chunk 22 optimal weight:    0.0370
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.0892

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
L  44 GLN
H   1 GLN
H  39 GLN
R 409 GLN
R 422 ASN
R 440 ASN
R 498 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.149981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.137119 restraints weight = 4998.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3941 rms_B_bonded: 2.40
r_work: 0.3842 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3692 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   3491  Z= 0.107
  Angle     :  0.533   7.063   4750  Z= 0.279
  Chirality :  0.044   0.233    507
  Planarity :  0.004   0.030    611
  Dihedral  :  5.427  50.272    521
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 11.41 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.21 (0.42), residues: 423
  helix: -3.56 (0.95), residues: 20
  sheet:  0.96 (0.41), residues: 151
  loop :  0.01 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H 118 
 TYR   0.012   0.001   TYR R 380 
 PHE   0.032   0.002   PHE L 100 
 TRP   0.013   0.001   TRP R 436 
 HIS   0.004   0.001   HIS H 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 3482)
  covalent geometry    : angle       0.52878 ( 4730)
  SS BOND              : bond        0.00345 (    7)
  SS BOND              : angle       0.92779 (   14)
  hydrogen bonds       : bond        0.03229 (  104)
  hydrogen bonds       : angle       5.28034 (  288)
  link_BETA1-4         : bond        0.00275 (    1)
  link_BETA1-4         : angle       1.77439 (    3)
  link_NAG-ASN         : bond        0.00181 (    1)
  link_NAG-ASN         : angle       1.15128 (    3)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.134 
Fit side-chains
REVERT: H   30 THR cc_start: 0.8566 (p) cc_final: 0.8353 (t)
REVERT: R  354 ASN cc_start: 0.7046 (t0) cc_final: 0.6664 (t0)
  outliers start: 4
  outliers final: 2
  residues processed: 76
  average time/residue: 0.2532
  time to fit residues: 20.5185
Evaluate side-chains
  74 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain R residue  483 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0050
   chunk 17 optimal weight:    0.0030
   chunk 18 optimal weight:    0.7980
   chunk 10 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0970
   overall best weight:    0.2002

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

Flipped N/Q/H residues before XYZ refinement:
R 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.147983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.135017 restraints weight = 4993.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3929 rms_B_bonded: 2.38
r_work: 0.3831 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3681 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3491  Z= 0.154
  Angle     :  0.568   7.223   4750  Z= 0.292
  Chirality :  0.045   0.227    507
  Planarity :  0.004   0.048    611
  Dihedral  :  5.363  45.090    521
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.32 %
    Favored  : 84.51 %
  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:  0.11 (0.42), residues: 423
  helix: -3.55 (0.98), residues: 20
  sheet:  0.79 (0.42), residues: 152
  loop :  0.00 (0.41), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 118 
 TYR   0.016   0.002   TYR R 351 
 PHE   0.021   0.002   PHE L 100 
 TRP   0.011   0.001   TRP R 353 
 HIS   0.006   0.002   HIS H 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 3482)
  covalent geometry    : angle       0.55793 ( 4730)
  SS BOND              : bond        0.00634 (    7)
  SS BOND              : angle       1.67760 (   14)
  hydrogen bonds       : bond        0.03381 (  104)
  hydrogen bonds       : angle       5.05687 (  288)
  link_BETA1-4         : bond        0.00301 (    1)
  link_BETA1-4         : angle       2.18772 (    3)
  link_NAG-ASN         : bond        0.00041 (    1)
  link_NAG-ASN         : angle       1.49818 (    3)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.117 
Fit side-chains
REVERT: R  354 ASN cc_start: 0.7100 (t0) cc_final: 0.6715 (t0)
REVERT: R  418 ILE cc_start: 0.8427 (tt) cc_final: 0.8208 (tt)
REVERT: R  460 ASN cc_start: 0.8592 (m-40) cc_final: 0.8362 (t0)
  outliers start: 8
  outliers final: 6
  residues processed: 76
  average time/residue: 0.2804
  time to fit residues: 22.5768
Evaluate side-chains
  80 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  483 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 31 optimal weight:    0.0570
   chunk 4 optimal weight:    0.5980
   chunk 30 optimal weight:    0.2980
   chunk 18 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   chunk 39 optimal weight:    0.4980
   chunk 41 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.3898

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

Flipped N/Q/H residues before XYZ refinement:
R 409 GLN
R 422 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.146328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.133667 restraints weight = 4827.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 2.28
r_work: 0.3800 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3650 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   3491  Z= 0.262
  Angle     :  0.647   7.903   4750  Z= 0.337
  Chirality :  0.048   0.259    507
  Planarity :  0.005   0.045    611
  Dihedral  :  6.049  39.586    521
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 14.13 %
    Favored  : 82.88 %
  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:  0.04 (0.42), residues: 423
  helix: -3.88 (1.13), residues: 12
  sheet:  0.87 (0.42), residues: 150
  loop : -0.25 (0.40), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H 118 
 TYR   0.016   0.002   TYR L  55 
 PHE   0.023   0.002   PHE L 100 
 TRP   0.015   0.002   TRP R 436 
 HIS   0.005   0.002   HIS H 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00582 ( 3482)
  covalent geometry    : angle       0.63367 ( 4730)
  SS BOND              : bond        0.00708 (    7)
  SS BOND              : angle       1.89726 (   14)
  hydrogen bonds       : bond        0.03823 (  104)
  hydrogen bonds       : angle       5.34414 (  288)
  link_BETA1-4         : bond        0.00044 (    1)
  link_BETA1-4         : angle       3.09856 (    3)
  link_NAG-ASN         : bond        0.00069 (    1)
  link_NAG-ASN         : angle       1.85124 (    3)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
REVERT: L   97 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7809 (ptm-80)
REVERT: R  354 ASN cc_start: 0.7221 (t0) cc_final: 0.6816 (t0)
REVERT: R  457 ARG cc_start: 0.8690 (ttt90) cc_final: 0.8460 (ttt90)
REVERT: R  461 LEU cc_start: 0.8416 (mt) cc_final: 0.8171 (mt)
  outliers start: 11
  outliers final: 6
  residues processed: 80
  average time/residue: 0.2770
  time to fit residues: 23.3376
Evaluate side-chains
  80 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue   97 ARG
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  422 ASN
Chi-restraints excluded: chain R residue  503 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0970
   chunk 2 optimal weight:    0.0980
   chunk 16 optimal weight:    0.1980
   chunk 23 optimal weight:    0.0000
   chunk 40 optimal weight:    0.2980
   chunk 19 optimal weight:    0.9990
   chunk 39 optimal weight:    0.1980
   chunk 27 optimal weight:    0.2980
   chunk 33 optimal weight:    0.0970
   chunk 4 optimal weight:    0.0970
   overall best weight:    0.0778

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

Flipped N/Q/H residues before XYZ refinement:
R 409 GLN
R 422 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.148657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.135649 restraints weight = 4896.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3936 rms_B_bonded: 2.35
r_work: 0.3839 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3692 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   3491  Z= 0.107
  Angle     :  0.539   6.434   4750  Z= 0.281
  Chirality :  0.043   0.192    507
  Planarity :  0.004   0.050    611
  Dihedral  :  5.569  48.559    521
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 16.58 %
    Favored  : 82.07 %
  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:  0.06 (0.41), residues: 423
  helix: -4.09 (0.92), residues: 12
  sheet:  0.83 (0.43), residues: 142
  loop : -0.16 (0.39), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H 118 
 TYR   0.017   0.001   TYR R 489 
 PHE   0.021   0.002   PHE L 100 
 TRP   0.014   0.001   TRP R 436 
 HIS   0.009   0.003   HIS H 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 3482)
  covalent geometry    : angle       0.53527 ( 4730)
  SS BOND              : bond        0.00370 (    7)
  SS BOND              : angle       1.04932 (   14)
  hydrogen bonds       : bond        0.02955 (  104)
  hydrogen bonds       : angle       4.96374 (  288)
  link_BETA1-4         : bond        0.00343 (    1)
  link_BETA1-4         : angle       1.68772 (    3)
  link_NAG-ASN         : bond        0.00135 (    1)
  link_NAG-ASN         : angle       1.02037 (    3)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.079 
Fit side-chains
   revert: symmetry clash
REVERT: R  354 ASN cc_start: 0.7191 (t0) cc_final: 0.6824 (t0)
REVERT: R  460 ASN cc_start: 0.8512 (m-40) cc_final: 0.8301 (t0)
  outliers start: 5
  outliers final: 4
  residues processed: 73
  average time/residue: 0.2313
  time to fit residues: 18.0216
Evaluate side-chains
  75 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  513 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 13 optimal weight:    0.1980
   chunk 5 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0010
   chunk 10 optimal weight:    0.1980
   chunk 29 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 19 optimal weight:    0.3980
   chunk 22 optimal weight:    0.0980
   overall best weight:    0.1786

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

Flipped N/Q/H residues before XYZ refinement:
R 409 GLN
** R 422 ASN ** 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 = 0.4066 r_free = 0.4066 target = 0.147776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.134552 restraints weight = 4917.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3922 rms_B_bonded: 2.38
r_work: 0.3823 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3673 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3491  Z= 0.142
  Angle     :  0.549   6.946   4750  Z= 0.284
  Chirality :  0.044   0.208    507
  Planarity :  0.004   0.051    611
  Dihedral  :  5.557  46.680    521
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 16.58 %
    Favored  : 80.16 %
  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: -0.03 (0.41), residues: 423
  helix: -4.54 (0.63), residues: 18
  sheet:  0.87 (0.42), residues: 150
  loop : -0.17 (0.40), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 118 
 TYR   0.021   0.001   TYR R 489 
 PHE   0.018   0.002   PHE L 100 
 TRP   0.012   0.001   TRP R 436 
 HIS   0.006   0.002   HIS H 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 3482)
  covalent geometry    : angle       0.54249 ( 4730)
  SS BOND              : bond        0.00455 (    7)
  SS BOND              : angle       1.28629 (   14)
  hydrogen bonds       : bond        0.03039 (  104)
  hydrogen bonds       : angle       4.94950 (  288)
  link_BETA1-4         : bond        0.00183 (    1)
  link_BETA1-4         : angle       2.05674 (    3)
  link_NAG-ASN         : bond        0.00031 (    1)
  link_NAG-ASN         : angle       1.32347 (    3)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.079 
Fit side-chains
   revert: symmetry clash
REVERT: L   97 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8355 (mtm180)
REVERT: R  354 ASN cc_start: 0.7177 (t0) cc_final: 0.6804 (t0)
  outliers start: 12
  outliers final: 6
  residues processed: 70
  average time/residue: 0.2709
  time to fit residues: 19.9777
Evaluate side-chains
  69 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   32 SER
Chi-restraints excluded: chain L residue   97 ARG
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  518 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 2 optimal weight:    0.1980
   chunk 10 optimal weight:    0.2980
   chunk 1 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0570
   chunk 9 optimal weight:    0.4980
   chunk 41 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0980
   chunk 34 optimal weight:    0.0970
   overall best weight:    0.1496

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

Flipped N/Q/H residues before XYZ refinement:
R 409 GLN
** R 422 ASN ** 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 = 0.4069 r_free = 0.4069 target = 0.148050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.134694 restraints weight = 5021.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3922 rms_B_bonded: 2.41
r_work: 0.3823 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3674 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3491  Z= 0.127
  Angle     :  0.539   6.672   4750  Z= 0.279
  Chirality :  0.044   0.195    507
  Planarity :  0.004   0.052    611
  Dihedral  :  5.510  47.995    521
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 16.03 %
    Favored  : 80.71 %
  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: -0.01 (0.41), residues: 423
  helix: -4.55 (0.60), residues: 18
  sheet:  0.86 (0.43), residues: 142
  loop : -0.11 (0.39), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 118 
 TYR   0.026   0.001   TYR R 489 
 PHE   0.017   0.002   PHE L 100 
 TRP   0.012   0.001   TRP R 436 
 HIS   0.004   0.002   HIS H 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 3482)
  covalent geometry    : angle       0.53378 ( 4730)
  SS BOND              : bond        0.00425 (    7)
  SS BOND              : angle       1.19982 (   14)
  hydrogen bonds       : bond        0.02909 (  104)
  hydrogen bonds       : angle       4.86766 (  288)
  link_BETA1-4         : bond        0.00235 (    1)
  link_BETA1-4         : angle       1.79213 (    3)
  link_NAG-ASN         : bond        0.00090 (    1)
  link_NAG-ASN         : angle       1.22784 (    3)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.077 
Fit side-chains
   revert: symmetry clash
REVERT: R  354 ASN cc_start: 0.7160 (t0) cc_final: 0.6796 (t0)
  outliers start: 12
  outliers final: 7
  residues processed: 69
  average time/residue: 0.2208
  time to fit residues: 16.2650
Evaluate side-chains
  69 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   32 SER
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  418 ILE
Chi-restraints excluded: chain R residue  524 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.2980
   chunk 8 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 33 optimal weight:    0.1980
   chunk 19 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0270
   chunk 7 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0970
   chunk 4 optimal weight:    0.4980
   overall best weight:    0.2236

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

Flipped N/Q/H residues before XYZ refinement:
R 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.146616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.133311 restraints weight = 4995.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3909 rms_B_bonded: 2.40
r_work: 0.3809 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3656 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3491  Z= 0.165
  Angle     :  0.578   6.992   4750  Z= 0.298
  Chirality :  0.046   0.207    507
  Planarity :  0.004   0.052    611
  Dihedral  :  5.626  45.783    521
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 15.22 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.17 (0.41), residues: 423
  helix: -4.52 (0.63), residues: 18
  sheet:  0.82 (0.42), residues: 150
  loop : -0.31 (0.40), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 118 
 TYR   0.024   0.002   TYR R 489 
 PHE   0.018   0.002   PHE L 100 
 TRP   0.012   0.002   TRP R 436 
 HIS   0.003   0.002   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 3482)
  covalent geometry    : angle       0.57103 ( 4730)
  SS BOND              : bond        0.00547 (    7)
  SS BOND              : angle       1.38168 (   14)
  hydrogen bonds       : bond        0.03138 (  104)
  hydrogen bonds       : angle       4.88085 (  288)
  link_BETA1-4         : bond        0.00127 (    1)
  link_BETA1-4         : angle       2.17523 (    3)
  link_NAG-ASN         : bond        0.00032 (    1)
  link_NAG-ASN         : angle       1.45963 (    3)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
REVERT: L   97 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8342 (mtm180)
REVERT: R  354 ASN cc_start: 0.7097 (t0) cc_final: 0.6715 (t0)
REVERT: R  418 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7812 (mt)
  outliers start: 12
  outliers final: 7
  residues processed: 71
  average time/residue: 0.2699
  time to fit residues: 20.3407
Evaluate side-chains
  75 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   32 SER
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue   97 ARG
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  418 ILE
Chi-restraints excluded: chain R residue  518 LEU
Chi-restraints excluded: chain R residue  524 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0670
   chunk 10 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0980
   chunk 32 optimal weight:    0.5980
   chunk 1 optimal weight:    0.0970
   chunk 30 optimal weight:    0.2980
   overall best weight:    0.2316

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

Flipped N/Q/H residues before XYZ refinement:
R 409 GLN
** R 422 ASN ** 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 = 0.4047 r_free = 0.4047 target = 0.146350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.133314 restraints weight = 5022.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3903 rms_B_bonded: 2.37
r_work: 0.3803 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3652 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3491  Z= 0.169
  Angle     :  0.579   7.010   4750  Z= 0.297
  Chirality :  0.045   0.211    507
  Planarity :  0.004   0.052    611
  Dihedral  :  5.692  46.102    521
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 15.76 %
    Favored  : 81.25 %
  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: -0.19 (0.41), residues: 423
  helix: -4.51 (0.63), residues: 18
  sheet:  0.88 (0.42), residues: 148
  loop : -0.37 (0.40), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 118 
 TYR   0.022   0.002   TYR R 489 
 PHE   0.018   0.002   PHE L 100 
 TRP   0.013   0.002   TRP R 436 
 HIS   0.004   0.002   HIS H 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 3482)
  covalent geometry    : angle       0.57109 ( 4730)
  SS BOND              : bond        0.00540 (    7)
  SS BOND              : angle       1.43077 (   14)
  hydrogen bonds       : bond        0.03163 (  104)
  hydrogen bonds       : angle       4.95375 (  288)
  link_BETA1-4         : bond        0.00075 (    1)
  link_BETA1-4         : angle       2.10054 (    3)
  link_NAG-ASN         : bond        0.00031 (    1)
  link_NAG-ASN         : angle       1.44166 (    3)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
REVERT: L   97 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8334 (mtm180)
REVERT: R  354 ASN cc_start: 0.7108 (t0) cc_final: 0.6728 (t0)
REVERT: R  418 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7819 (mt)
  outliers start: 11
  outliers final: 7
  residues processed: 73
  average time/residue: 0.2166
  time to fit residues: 16.7892
Evaluate side-chains
  77 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   32 SER
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue   97 ARG
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  418 ILE
Chi-restraints excluded: chain R residue  518 LEU
Chi-restraints excluded: chain R residue  524 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0070
   chunk 32 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0020
   chunk 5 optimal weight:    0.0670
   chunk 27 optimal weight:    0.0770
   chunk 12 optimal weight:    0.4980
   chunk 40 optimal weight:    0.0970
   chunk 39 optimal weight:    0.1980
   overall best weight:    0.0500

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

Flipped N/Q/H residues before XYZ refinement:
H 108 HIS
R 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.149431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.136537 restraints weight = 5001.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3947 rms_B_bonded: 2.37
r_work: 0.3850 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3703 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.2876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3491  Z= 0.093
  Angle     :  0.517   6.048   4750  Z= 0.266
  Chirality :  0.043   0.157    507
  Planarity :  0.004   0.052    611
  Dihedral  :  5.432  53.011    521
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 16.30 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.01 (0.41), residues: 423
  helix: -4.61 (0.56), residues: 18
  sheet:  1.11 (0.43), residues: 136
  loop : -0.24 (0.39), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 118 
 TYR   0.020   0.001   TYR R 489 
 PHE   0.015   0.001   PHE H  64 
 TRP   0.012   0.001   TRP R 436 
 HIS   0.005   0.002   HIS H 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 3482)
  covalent geometry    : angle       0.51432 ( 4730)
  SS BOND              : bond        0.00349 (    7)
  SS BOND              : angle       0.90280 (   14)
  hydrogen bonds       : bond        0.02700 (  104)
  hydrogen bonds       : angle       4.62122 (  288)
  link_BETA1-4         : bond        0.00427 (    1)
  link_BETA1-4         : angle       1.27061 (    3)
  link_NAG-ASN         : bond        0.00117 (    1)
  link_NAG-ASN         : angle       1.02062 (    3)

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.082 
Fit side-chains
REVERT: L   97 ARG cc_start: 0.8480 (ptm-80) cc_final: 0.8252 (mtm180)
REVERT: R  418 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7626 (mt)
  outliers start: 8
  outliers final: 6
  residues processed: 65
  average time/residue: 0.2960
  time to fit residues: 20.3409
Evaluate side-chains
  67 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   32 SER
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  418 ILE
Chi-restraints excluded: chain R residue  518 LEU
Chi-restraints excluded: chain R residue  524 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 9 optimal weight:    0.3980
   chunk 11 optimal weight:    0.0020
   chunk 13 optimal weight:    0.3980
   chunk 26 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0010
   chunk 6 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 10 optimal weight:    0.1980
   chunk 2 optimal weight:    0.3980
   overall best weight:    0.1994

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

Flipped N/Q/H residues before XYZ refinement:
R 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.146809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.133839 restraints weight = 5071.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3913 rms_B_bonded: 2.39
r_work: 0.3815 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3666 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3491  Z= 0.156
  Angle     :  0.562   6.833   4750  Z= 0.288
  Chirality :  0.045   0.197    507
  Planarity :  0.004   0.054    611
  Dihedral  :  5.442  44.849    521
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.93 %
    Favored  : 79.89 %
  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: -0.18 (0.41), residues: 423
  helix: -4.56 (0.59), residues: 18
  sheet:  0.78 (0.42), residues: 151
  loop : -0.30 (0.40), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 118 
 TYR   0.023   0.002   TYR R 489 
 PHE   0.018   0.002   PHE L 100 
 TRP   0.013   0.001   TRP R 436 
 HIS   0.006   0.002   HIS H 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 3482)
  covalent geometry    : angle       0.55398 ( 4730)
  SS BOND              : bond        0.00480 (    7)
  SS BOND              : angle       1.41053 (   14)
  hydrogen bonds       : bond        0.03058 (  104)
  hydrogen bonds       : angle       4.78101 (  288)
  link_BETA1-4         : bond        0.00097 (    1)
  link_BETA1-4         : angle       2.12235 (    3)
  link_NAG-ASN         : bond        0.00064 (    1)
  link_NAG-ASN         : angle       1.35255 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1730.89 seconds
wall clock time: 30 minutes 19.08 seconds (1819.08 seconds total)