Starting phenix.real_space_refine
on Fri Aug 22 18:29:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ijz_60646/08_2025/9ijz_60646_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ijz_60646/08_2025/9ijz_60646.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ijz_60646/08_2025/9ijz_60646.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ijz_60646/08_2025/9ijz_60646.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ijz_60646/08_2025/9ijz_60646_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ijz_60646/08_2025/9ijz_60646_trim.cif"
  }
  resolution = 2.91
  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=   0.058
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: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      32      5.16       5
     C    4474      2.51       5
     N    1054      2.21       5
     O    1090      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6654
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3270
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 392, 3270
          Classifications: {'peptide': 392}
          Link IDs: {'PTRANS': 13, 'TRANS': 378}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 57
          Unusual residues: {'6PL': 1, 'PO4': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.35, per 1000 atoms: 0.35
  Number of scatterers: 6654
  At special positions: 0
  Unit cell: (69.9, 123.956, 77.356, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     P       4     15.00
     O    1090      8.00
     N    1054      7.00
     C    4474      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 415 " - pdb=" SG  CYS A 440 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 415 " - pdb=" SG  CYS B 440 " 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: 0.61
  Conformation dependent library (CDL) restraints added in 374.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1488

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 0 sheets defined
      77.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 230 through 257
    Processing helix  chain 'A' and resid 265 through 296
    Processing helix  chain 'A' and resid 298 through 303
    Processing helix  chain 'A' and resid 312 through 336
    Processing helix  chain 'A' and resid 345 through 361
      removed outlier: 3.802A  pdb=" N   LEU A 349 " --> pdb=" O   TYR A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 383
      removed outlier: 3.591A  pdb=" N   PHE A 382 " --> pdb=" O   LEU A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 403
    Processing helix  chain 'A' and resid 403 through 420
      removed outlier: 3.757A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 470
      Proline residue:  A 455  - end of helix
    Processing helix  chain 'A' and resid 472 through 503
      removed outlier: 4.130A  pdb=" N   HIS A 476 " --> pdb=" O   ARG A 472 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   VAL A 478 " --> pdb=" O   PHE A 474 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   GLU A 501 " --> pdb=" O   SER A 497 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ARG A 502 " --> pdb=" O   THR A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 532
      removed outlier: 4.403A  pdb=" N   VAL A 509 " --> pdb=" O   SER A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 571
      removed outlier: 4.104A  pdb=" N   TYR A 559 " --> pdb=" O   GLN A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 583
      removed outlier: 3.820A  pdb=" N   ILE A 575 " --> pdb=" O   PHE A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 618
      Proline residue:  A 598  - end of helix
      removed outlier: 3.835A  pdb=" N   PHE A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   PHE A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 257
    Processing helix  chain 'B' and resid 265 through 296
    Processing helix  chain 'B' and resid 298 through 303
    Processing helix  chain 'B' and resid 312 through 336
    Processing helix  chain 'B' and resid 345 through 361
      removed outlier: 3.802A  pdb=" N   LEU B 349 " --> pdb=" O   TYR B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 383
      removed outlier: 3.591A  pdb=" N   PHE B 382 " --> pdb=" O   LEU B 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 403
    Processing helix  chain 'B' and resid 403 through 420
      removed outlier: 3.757A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 470
      Proline residue:  B 455  - end of helix
    Processing helix  chain 'B' and resid 472 through 503
      removed outlier: 4.130A  pdb=" N   HIS B 476 " --> pdb=" O   ARG B 472 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   VAL B 478 " --> pdb=" O   PHE B 474 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   GLU B 501 " --> pdb=" O   SER B 497 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ARG B 502 " --> pdb=" O   THR B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 505 through 532
      removed outlier: 4.403A  pdb=" N   VAL B 509 " --> pdb=" O   SER B 505 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 571
      removed outlier: 4.104A  pdb=" N   TYR B 559 " --> pdb=" O   GLN B 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 571 through 583
      removed outlier: 3.820A  pdb=" N   ILE B 575 " --> pdb=" O   PHE B 571 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 618
      Proline residue:  B 598  - end of helix
      removed outlier: 3.835A  pdb=" N   PHE B 609 " --> pdb=" O   PHE B 605 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   PHE B 610 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)

    458 hydrogen bonds defined for protein.
    1374 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: 0.74

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 946
        1.31 -     1.43: 2116
        1.43 -     1.56: 3756
        1.56 -     1.68: 4
        1.68 -     1.81: 44
  Bond restraints: 6866
  Sorted by residual:
  bond pdb=" C11 6PL A1002 "
       pdb=" O3  6PL A1002 "
    ideal  model  delta    sigma   weight residual
    1.327  1.430 -0.103 2.00e-02 2.50e+03 2.66e+01
  bond pdb=" C11 6PL B1002 "
       pdb=" O3  6PL B1002 "
    ideal  model  delta    sigma   weight residual
    1.327  1.430 -0.103 2.00e-02 2.50e+03 2.66e+01
  bond pdb=" C31 6PL B1002 "
       pdb=" O2  6PL B1002 "
    ideal  model  delta    sigma   weight residual
    1.330  1.416 -0.086 2.00e-02 2.50e+03 1.85e+01
  bond pdb=" C31 6PL A1002 "
       pdb=" O2  6PL A1002 "
    ideal  model  delta    sigma   weight residual
    1.330  1.416 -0.086 2.00e-02 2.50e+03 1.85e+01
  bond pdb=" CA  TYR B 524 "
       pdb=" C   TYR B 524 "
    ideal  model  delta    sigma   weight residual
    1.524  1.471  0.053 1.29e-02 6.01e+03 1.69e+01
  ... (remaining 6861 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.78: 9252
        3.78 -     7.56: 58
        7.56 -    11.34: 4
       11.34 -    15.12: 0
       15.12 -    18.90: 4
  Bond angle restraints: 9318
  Sorted by residual:
  angle pdb=" O1P 6PL A1002 "
        pdb=" P   6PL A1002 "
        pdb=" O2P 6PL A1002 "
      ideal   model   delta    sigma   weight residual
     119.71  100.81   18.90 3.00e+00 1.11e-01 3.97e+01
  angle pdb=" O1P 6PL B1002 "
        pdb=" P   6PL B1002 "
        pdb=" O2P 6PL B1002 "
      ideal   model   delta    sigma   weight residual
     119.71  100.81   18.90 3.00e+00 1.11e-01 3.97e+01
  angle pdb=" O3P 6PL A1002 "
        pdb=" P   6PL A1002 "
        pdb=" O4P 6PL A1002 "
      ideal   model   delta    sigma   weight residual
      93.65  110.78  -17.13 3.00e+00 1.11e-01 3.26e+01
  angle pdb=" O3P 6PL B1002 "
        pdb=" P   6PL B1002 "
        pdb=" O4P 6PL B1002 "
      ideal   model   delta    sigma   weight residual
      93.65  110.78  -17.13 3.00e+00 1.11e-01 3.26e+01
  angle pdb=" CA  GLU B 549 "
        pdb=" CB  GLU B 549 "
        pdb=" CG  GLU B 549 "
      ideal   model   delta    sigma   weight residual
     114.10  121.53   -7.43 2.00e+00 2.50e-01 1.38e+01
  ... (remaining 9313 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.77: 3262
       14.77 -    29.53: 444
       29.53 -    44.30: 146
       44.30 -    59.07: 64
       59.07 -    73.83: 4
  Dihedral angle restraints: 3920
    sinusoidal: 1610
      harmonic: 2310
  Sorted by residual:
  dihedral pdb=" CA  PRO B 475 "
           pdb=" C   PRO B 475 "
           pdb=" N   HIS B 476 "
           pdb=" CA  HIS B 476 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.50  -16.50     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  PRO A 475 "
           pdb=" C   PRO A 475 "
           pdb=" N   HIS A 476 "
           pdb=" CA  HIS A 476 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.50  -16.50     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  GLY A 621 "
           pdb=" C   GLY A 621 "
           pdb=" N   GLU A 622 "
           pdb=" CA  GLU A 622 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.71  -16.29     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 3917 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 708
       0.037 -    0.074: 234
       0.074 -    0.112: 54
       0.112 -    0.149: 8
       0.149 -    0.186: 2
  Chirality restraints: 1006
  Sorted by residual:
  chirality pdb=" C2  6PL A1002 "
            pdb=" C1  6PL A1002 "
            pdb=" C3  6PL A1002 "
            pdb=" O2  6PL A1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.51    0.19 2.00e-01 2.50e+01 8.64e-01
  chirality pdb=" C2  6PL B1002 "
            pdb=" C1  6PL B1002 "
            pdb=" C3  6PL B1002 "
            pdb=" O2  6PL B1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.51    0.19 2.00e-01 2.50e+01 8.64e-01
  chirality pdb=" CA  GLU A 549 "
            pdb=" N   GLU A 549 "
            pdb=" C   GLU A 549 "
            pdb=" CB  GLU A 549 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.04e-01
  ... (remaining 1003 not shown)

  Planarity restraints: 1122
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B 523 "   -0.012 2.00e-02 2.50e+03   2.44e-02 5.96e+00
        pdb=" C   CYS B 523 "    0.042 2.00e-02 2.50e+03
        pdb=" O   CYS B 523 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   TYR B 524 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 523 "    0.012 2.00e-02 2.50e+03   2.43e-02 5.89e+00
        pdb=" C   CYS A 523 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   CYS A 523 "    0.016 2.00e-02 2.50e+03
        pdb=" N   TYR A 524 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 394 "   -0.010 2.00e-02 2.50e+03   2.03e-02 4.11e+00
        pdb=" C   PHE B 394 "    0.035 2.00e-02 2.50e+03
        pdb=" O   PHE B 394 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   TRP B 395 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1119 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 78
        2.61 -     3.18: 6004
        3.18 -     3.75: 10815
        3.75 -     4.33: 14931
        4.33 -     4.90: 24260
  Nonbonded interactions: 56088
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 366 "
            pdb=" NH1 ARG A 371 "
     model   vdw
     2.034 3.120
  nonbonded pdb=" O   PHE B 366 "
            pdb=" NH1 ARG B 371 "
     model   vdw
     2.034 3.120
  nonbonded pdb=" O   LYS A 482 "
            pdb=" OG1 THR A 485 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" O   LYS B 482 "
            pdb=" OG1 THR B 485 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" O   ILE B 579 "
            pdb=" OG1 THR B 583 "
     model   vdw
     2.206 3.040
  ... (remaining 56083 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             2.110
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.920
  Find NCS groups from input model:        0.050
  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:9.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
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      :  0.006   0.103   6868  Z= 0.286
  Angle     :  0.787  18.904   9322  Z= 0.363
  Chirality :  0.040   0.186   1006
  Planarity :  0.004   0.024   1122
  Dihedral  : 16.399  73.832   2426
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 14.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 25.36 %
    Favored  : 74.35 %
  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 aren not related in a simple way.
  whole:  0.55 (0.29), residues: 776
  helix:  1.12 (0.20), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.53 (0.45), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 472 
 TYR   0.014   0.001   TYR A 524 
 PHE   0.011   0.001   PHE A 610 
 TRP   0.010   0.001   TRP B 373 
 HIS   0.002   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 ( 6866)
  covalent geometry    : angle       0.78755 ( 9318)
  SS BOND              : bond        0.00029 (    2)
  SS BOND              : angle       0.02713 (    4)
  hydrogen bonds       : bond        0.12370 (  458)
  hydrogen bonds       : angle       5.48158 ( 1374)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.480 
Fit side-chains
REVERT: A  511 PHE cc_start: 0.9074 (t80) cc_final: 0.8849 (t80)
REVERT: B  511 PHE cc_start: 0.9073 (t80) cc_final: 0.8849 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 104
  average time/residue: 0.3814
  time to fit residues: 42.8500
Evaluate side-chains
  98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
A 452 GLN
B 248 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.181859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.146070 restraints weight = 8626.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 2.32
r_work: 0.3579 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.1038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6868  Z= 0.164
  Angle     :  0.570   5.754   9322  Z= 0.309
  Chirality :  0.041   0.126   1006
  Planarity :  0.004   0.027   1122
  Dihedral  : 10.677  84.356    960
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 22.48 %
    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 aren not related in a simple way.
  whole:  0.99 (0.30), residues: 776
  helix:  1.54 (0.20), residues: 564
  sheet:  None (None), residues: 0
  loop : -1.80 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 371 
 TYR   0.012   0.002   TYR B 352 
 PHE   0.017   0.002   PHE B 391 
 TRP   0.011   0.001   TRP A 232 
 HIS   0.002   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 6866)
  covalent geometry    : angle       0.57052 ( 9318)
  SS BOND              : bond        0.00094 (    2)
  SS BOND              : angle       0.31112 (    4)
  hydrogen bonds       : bond        0.05256 (  458)
  hydrogen bonds       : angle       4.47519 ( 1374)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A  511 PHE cc_start: 0.9079 (t80) cc_final: 0.8821 (t80)
REVERT: B  511 PHE cc_start: 0.9079 (t80) cc_final: 0.8823 (t80)
  outliers start: 18
  outliers final: 8
  residues processed: 119
  average time/residue: 0.3890
  time to fit residues: 49.9190
Evaluate side-chains
  117 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  408 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0570
   chunk 16 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 38 optimal weight:    0.2980
   chunk 26 optimal weight:    8.9990
   chunk 57 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
B 248 ASN
B 452 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.182580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.146654 restraints weight = 8470.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3739 rms_B_bonded: 2.38
r_work: 0.3591 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7269
moved from start:          0.1357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6868  Z= 0.135
  Angle     :  0.533   5.523   9322  Z= 0.290
  Chirality :  0.040   0.129   1006
  Planarity :  0.003   0.027   1122
  Dihedral  : 10.127  74.163    960
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 20.61 %
    Favored  : 75.65 %
  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 aren not related in a simple way.
  whole:  1.19 (0.30), residues: 776
  helix:  1.71 (0.20), residues: 566
  sheet:  None (None), residues: 0
  loop : -1.84 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 472 
 TYR   0.011   0.002   TYR B 352 
 PHE   0.015   0.001   PHE A 391 
 TRP   0.009   0.001   TRP A 327 
 HIS   0.001   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6866)
  covalent geometry    : angle       0.53333 ( 9318)
  SS BOND              : bond        0.00071 (    2)
  SS BOND              : angle       0.17528 (    4)
  hydrogen bonds       : bond        0.04759 (  458)
  hydrogen bonds       : angle       4.30558 ( 1374)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  511 PHE cc_start: 0.9085 (t80) cc_final: 0.8855 (t80)
REVERT: B  511 PHE cc_start: 0.9086 (t80) cc_final: 0.8858 (t80)
  outliers start: 26
  outliers final: 16
  residues processed: 128
  average time/residue: 0.3806
  time to fit residues: 52.5523
Evaluate side-chains
  120 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  393 ASP
Chi-restraints excluded: chain B residue  408 MET
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  447 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 12 optimal weight:    0.1980
   chunk 64 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0470
   chunk 48 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 72 optimal weight:    0.5980
   overall best weight:    0.4278

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
B 248 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.183210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.147540 restraints weight = 8623.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 2.35
r_work: 0.3603 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.1529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6868  Z= 0.134
  Angle     :  0.529   5.489   9322  Z= 0.288
  Chirality :  0.040   0.130   1006
  Planarity :  0.003   0.029   1122
  Dihedral  :  9.907  68.565    960
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 19.88 %
    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 aren not related in a simple way.
  whole:  1.31 (0.29), residues: 776
  helix:  1.79 (0.20), residues: 566
  sheet:  None (None), residues: 0
  loop : -1.79 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 448 
 TYR   0.012   0.001   TYR B 352 
 PHE   0.016   0.001   PHE A 257 
 TRP   0.008   0.001   TRP A 327 
 HIS   0.002   0.000   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6866)
  covalent geometry    : angle       0.52955 ( 9318)
  SS BOND              : bond        0.00092 (    2)
  SS BOND              : angle       0.14842 (    4)
  hydrogen bonds       : bond        0.04613 (  458)
  hydrogen bonds       : angle       4.23062 ( 1374)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 113
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A  477 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8163 (mm)
REVERT: A  499 HIS cc_start: 0.8256 (OUTLIER) cc_final: 0.7935 (m-70)
REVERT: A  511 PHE cc_start: 0.9077 (t80) cc_final: 0.8840 (t80)
REVERT: A  549 GLU cc_start: 0.7715 (pp20) cc_final: 0.7499 (pp20)
REVERT: B  477 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8170 (mm)
REVERT: B  499 HIS cc_start: 0.8251 (OUTLIER) cc_final: 0.7931 (m-70)
REVERT: B  511 PHE cc_start: 0.9078 (t80) cc_final: 0.8842 (t80)
REVERT: B  549 GLU cc_start: 0.7739 (pp20) cc_final: 0.7517 (pp20)
  outliers start: 36
  outliers final: 15
  residues processed: 135
  average time/residue: 0.3883
  time to fit residues: 56.3426
Evaluate side-chains
  117 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  499 HIS
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  393 ASP
Chi-restraints excluded: chain B residue  408 MET
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  499 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 65 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 56 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
A 294 GLN
B 248 ASN
B 294 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.180156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.144115 restraints weight = 8666.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3721 rms_B_bonded: 2.36
r_work: 0.3579 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   6868  Z= 0.166
  Angle     :  0.574   6.981   9322  Z= 0.309
  Chirality :  0.041   0.128   1006
  Planarity :  0.004   0.033   1122
  Dihedral  : 10.008  67.708    960
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 19.45 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.22 (0.30), residues: 776
  helix:  1.71 (0.20), residues: 566
  sheet:  None (None), residues: 0
  loop : -1.75 (0.45), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 448 
 TYR   0.012   0.002   TYR A 352 
 PHE   0.015   0.002   PHE B 610 
 TRP   0.007   0.001   TRP A 327 
 HIS   0.002   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 6866)
  covalent geometry    : angle       0.57389 ( 9318)
  SS BOND              : bond        0.00114 (    2)
  SS BOND              : angle       0.33886 (    4)
  hydrogen bonds       : bond        0.04806 (  458)
  hydrogen bonds       : angle       4.34603 ( 1374)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A  261 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.7926 (t)
REVERT: A  377 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6439 (tp)
REVERT: A  511 PHE cc_start: 0.9075 (t80) cc_final: 0.8829 (t80)
REVERT: A  549 GLU cc_start: 0.7698 (pp20) cc_final: 0.7432 (pp20)
REVERT: B  261 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.7928 (t)
REVERT: B  377 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6430 (tp)
REVERT: B  511 PHE cc_start: 0.9074 (t80) cc_final: 0.8832 (t80)
REVERT: B  549 GLU cc_start: 0.7721 (pp20) cc_final: 0.7452 (pp20)
  outliers start: 24
  outliers final: 12
  residues processed: 122
  average time/residue: 0.3899
  time to fit residues: 51.2546
Evaluate side-chains
  116 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain B residue  261 THR
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  393 ASP
Chi-restraints excluded: chain B residue  408 MET
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  447 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 69 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
B 248 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.179410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.142676 restraints weight = 8678.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3698 rms_B_bonded: 2.43
r_work: 0.3547 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   6868  Z= 0.169
  Angle     :  0.575   6.501   9322  Z= 0.311
  Chirality :  0.041   0.129   1006
  Planarity :  0.004   0.033   1122
  Dihedral  :  9.566  63.405    960
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 18.73 %
    Favored  : 76.22 %
  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 aren not related in a simple way.
  whole:  1.19 (0.30), residues: 776
  helix:  1.69 (0.20), residues: 564
  sheet:  None (None), residues: 0
  loop : -1.72 (0.45), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 448 
 TYR   0.013   0.002   TYR B 352 
 PHE   0.016   0.002   PHE B 257 
 TRP   0.008   0.001   TRP A 327 
 HIS   0.002   0.001   HIS B 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 6866)
  covalent geometry    : angle       0.57518 ( 9318)
  SS BOND              : bond        0.00115 (    2)
  SS BOND              : angle       0.29560 (    4)
  hydrogen bonds       : bond        0.04891 (  458)
  hydrogen bonds       : angle       4.40857 ( 1374)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 112
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A  261 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.7928 (t)
REVERT: A  448 ARG cc_start: 0.7638 (ttp-110) cc_final: 0.7307 (ttm110)
REVERT: A  499 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.7909 (m-70)
REVERT: A  511 PHE cc_start: 0.9036 (t80) cc_final: 0.8827 (t80)
REVERT: A  549 GLU cc_start: 0.7723 (pp20) cc_final: 0.7490 (pp20)
REVERT: B  261 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.7936 (t)
REVERT: B  448 ARG cc_start: 0.7634 (ttp-110) cc_final: 0.7322 (ttm110)
REVERT: B  499 HIS cc_start: 0.8310 (OUTLIER) cc_final: 0.7921 (m-70)
REVERT: B  511 PHE cc_start: 0.9037 (t80) cc_final: 0.8830 (t80)
REVERT: B  549 GLU cc_start: 0.7713 (pp20) cc_final: 0.7482 (pp20)
  outliers start: 35
  outliers final: 17
  residues processed: 135
  average time/residue: 0.4005
  time to fit residues: 58.0655
Evaluate side-chains
  121 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  498 THR
Chi-restraints excluded: chain A residue  499 HIS
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain B residue  261 THR
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  393 ASP
Chi-restraints excluded: chain B residue  408 MET
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  552 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 71 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 68 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 65 optimal weight:    9.9990
   chunk 18 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
B 248 ASN
B 294 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.179653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.143066 restraints weight = 8579.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 2.42
r_work: 0.3546 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   6868  Z= 0.170
  Angle     :  0.583   6.495   9322  Z= 0.315
  Chirality :  0.041   0.133   1006
  Planarity :  0.004   0.034   1122
  Dihedral  :  9.353  58.462    960
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 19.88 %
    Favored  : 75.50 %
  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 aren not related in a simple way.
  whole:  1.08 (0.30), residues: 776
  helix:  1.59 (0.20), residues: 564
  sheet:  None (None), residues: 0
  loop : -1.71 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 380 
 TYR   0.014   0.002   TYR A 352 
 PHE   0.016   0.002   PHE A 610 
 TRP   0.009   0.001   TRP A 327 
 HIS   0.003   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 6866)
  covalent geometry    : angle       0.58349 ( 9318)
  SS BOND              : bond        0.00092 (    2)
  SS BOND              : angle       0.31709 (    4)
  hydrogen bonds       : bond        0.04881 (  458)
  hydrogen bonds       : angle       4.44172 ( 1374)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 103
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A  261 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.7911 (t)
REVERT: A  377 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6513 (tp)
REVERT: A  448 ARG cc_start: 0.7499 (ttp-110) cc_final: 0.7177 (ttm110)
REVERT: A  499 HIS cc_start: 0.8319 (OUTLIER) cc_final: 0.7941 (m-70)
REVERT: A  511 PHE cc_start: 0.9030 (t80) cc_final: 0.8815 (t80)
REVERT: B  261 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.7913 (t)
REVERT: B  377 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6503 (tp)
REVERT: B  448 ARG cc_start: 0.7489 (ttp-110) cc_final: 0.7170 (ttm110)
REVERT: B  499 HIS cc_start: 0.8325 (OUTLIER) cc_final: 0.7949 (m-70)
REVERT: B  511 PHE cc_start: 0.9031 (t80) cc_final: 0.8816 (t80)
  outliers start: 32
  outliers final: 15
  residues processed: 127
  average time/residue: 0.3596
  time to fit residues: 49.5089
Evaluate side-chains
  121 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  498 THR
Chi-restraints excluded: chain A residue  499 HIS
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain B residue  261 THR
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  393 ASP
Chi-restraints excluded: chain B residue  408 MET
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  552 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 54 optimal weight:    0.4980
   chunk 7 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 73 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
A 294 GLN
B 248 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.179917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.143339 restraints weight = 8623.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 2.42
r_work: 0.3560 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   6868  Z= 0.156
  Angle     :  0.579   6.250   9322  Z= 0.313
  Chirality :  0.041   0.136   1006
  Planarity :  0.004   0.034   1122
  Dihedral  :  8.867  54.816    960
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 20.61 %
    Favored  : 75.36 %
  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 aren not related in a simple way.
  whole:  1.12 (0.30), residues: 776
  helix:  1.62 (0.20), residues: 564
  sheet:  None (None), residues: 0
  loop : -1.70 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 380 
 TYR   0.014   0.002   TYR A 352 
 PHE   0.016   0.002   PHE A 610 
 TRP   0.009   0.001   TRP A 327 
 HIS   0.002   0.001   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 6866)
  covalent geometry    : angle       0.57948 ( 9318)
  SS BOND              : bond        0.00080 (    2)
  SS BOND              : angle       0.26603 (    4)
  hydrogen bonds       : bond        0.04784 (  458)
  hydrogen bonds       : angle       4.42852 ( 1374)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A  261 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.7906 (t)
REVERT: A  377 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6448 (tp)
REVERT: A  448 ARG cc_start: 0.7477 (ttp-110) cc_final: 0.7166 (ttm110)
REVERT: A  499 HIS cc_start: 0.8320 (OUTLIER) cc_final: 0.7940 (m-70)
REVERT: A  533 ASP cc_start: 0.7540 (m-30) cc_final: 0.7260 (t0)
REVERT: A  615 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7654 (mp0)
REVERT: B  261 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.7908 (t)
REVERT: B  377 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6437 (tp)
REVERT: B  448 ARG cc_start: 0.7478 (ttp-110) cc_final: 0.7175 (ttm110)
REVERT: B  499 HIS cc_start: 0.8333 (OUTLIER) cc_final: 0.7958 (m-70)
REVERT: B  533 ASP cc_start: 0.7535 (m-30) cc_final: 0.7265 (t0)
REVERT: B  615 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7670 (mp0)
  outliers start: 28
  outliers final: 13
  residues processed: 127
  average time/residue: 0.3575
  time to fit residues: 49.2098
Evaluate side-chains
  123 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  498 THR
Chi-restraints excluded: chain A residue  499 HIS
Chi-restraints excluded: chain A residue  615 GLU
Chi-restraints excluded: chain B residue  261 THR
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  393 ASP
Chi-restraints excluded: chain B residue  408 MET
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  615 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 13 optimal weight:    0.0980
   chunk 61 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0010
   chunk 11 optimal weight:    0.9980
   chunk 70 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 5 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
B 248 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.183057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.147086 restraints weight = 8622.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 2.36
r_work: 0.3595 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6868  Z= 0.135
  Angle     :  0.564   6.007   9322  Z= 0.306
  Chirality :  0.041   0.137   1006
  Planarity :  0.004   0.033   1122
  Dihedral  :  8.355  51.159    960
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 21.47 %
    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 aren not related in a simple way.
  whole:  1.17 (0.29), residues: 776
  helix:  1.66 (0.20), residues: 564
  sheet:  None (None), residues: 0
  loop : -1.71 (0.43), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 380 
 TYR   0.015   0.001   TYR A 290 
 PHE   0.015   0.001   PHE B 610 
 TRP   0.011   0.001   TRP A 327 
 HIS   0.001   0.000   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6866)
  covalent geometry    : angle       0.56419 ( 9318)
  SS BOND              : bond        0.00079 (    2)
  SS BOND              : angle       0.19949 (    4)
  hydrogen bonds       : bond        0.04582 (  458)
  hydrogen bonds       : angle       4.36607 ( 1374)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  261 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.7912 (t)
REVERT: A  448 ARG cc_start: 0.7419 (ttp-110) cc_final: 0.7157 (ttm110)
REVERT: A  499 HIS cc_start: 0.8281 (OUTLIER) cc_final: 0.7864 (m-70)
REVERT: A  532 MET cc_start: 0.7614 (mmp) cc_final: 0.7305 (mmm)
REVERT: A  590 ASP cc_start: 0.7805 (m-30) cc_final: 0.7597 (m-30)
REVERT: A  615 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7669 (mp0)
REVERT: B  261 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.7914 (t)
REVERT: B  448 ARG cc_start: 0.7428 (ttp-110) cc_final: 0.7181 (ttm110)
REVERT: B  499 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7878 (m-70)
REVERT: B  532 MET cc_start: 0.7621 (mmp) cc_final: 0.7308 (mmm)
REVERT: B  590 ASP cc_start: 0.7807 (m-30) cc_final: 0.7595 (m-30)
REVERT: B  615 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7695 (mp0)
  outliers start: 25
  outliers final: 16
  residues processed: 119
  average time/residue: 0.3512
  time to fit residues: 45.4615
Evaluate side-chains
  119 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  498 THR
Chi-restraints excluded: chain A residue  499 HIS
Chi-restraints excluded: chain A residue  615 GLU
Chi-restraints excluded: chain B residue  261 THR
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  393 ASP
Chi-restraints excluded: chain B residue  408 MET
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  552 VAL
Chi-restraints excluded: chain B residue  615 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0040
   chunk 23 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 44 optimal weight:    0.5980
   chunk 70 optimal weight:    0.3980
   chunk 36 optimal weight:    0.2980
   chunk 62 optimal weight:    0.3980
   chunk 54 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.3392

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
B 248 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.183797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.148125 restraints weight = 8668.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3759 rms_B_bonded: 2.37
r_work: 0.3616 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   6868  Z= 0.134
  Angle     :  0.570   6.465   9322  Z= 0.309
  Chirality :  0.041   0.136   1006
  Planarity :  0.004   0.031   1122
  Dihedral  :  8.133  46.130    960
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 21.61 %
    Favored  : 74.78 %
  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 aren not related in a simple way.
  whole:  1.27 (0.29), residues: 776
  helix:  1.73 (0.20), residues: 564
  sheet:  None (None), residues: 0
  loop : -1.66 (0.43), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 380 
 TYR   0.013   0.001   TYR B 352 
 PHE   0.016   0.001   PHE A 610 
 TRP   0.009   0.001   TRP A 327 
 HIS   0.001   0.000   HIS B 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6866)
  covalent geometry    : angle       0.56974 ( 9318)
  SS BOND              : bond        0.00081 (    2)
  SS BOND              : angle       0.15592 (    4)
  hydrogen bonds       : bond        0.04560 (  458)
  hydrogen bonds       : angle       4.31367 ( 1374)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 100
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A  448 ARG cc_start: 0.7418 (ttp-110) cc_final: 0.7166 (ttm110)
REVERT: A  499 HIS cc_start: 0.8231 (OUTLIER) cc_final: 0.7814 (m-70)
REVERT: A  590 ASP cc_start: 0.7792 (m-30) cc_final: 0.7580 (m-30)
REVERT: B  448 ARG cc_start: 0.7456 (ttp-110) cc_final: 0.7223 (ttm110)
REVERT: B  499 HIS cc_start: 0.8260 (OUTLIER) cc_final: 0.7820 (m-70)
REVERT: B  590 ASP cc_start: 0.7798 (m-30) cc_final: 0.7587 (m-30)
REVERT: B  622 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7470 (mt-10)
  outliers start: 25
  outliers final: 14
  residues processed: 117
  average time/residue: 0.3329
  time to fit residues: 42.1473
Evaluate side-chains
  111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  499 HIS
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  393 ASP
Chi-restraints excluded: chain B residue  408 MET
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  622 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
B 248 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.180336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.143938 restraints weight = 8625.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3710 rms_B_bonded: 2.42
r_work: 0.3562 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   6868  Z= 0.170
  Angle     :  0.610   6.561   9322  Z= 0.330
  Chirality :  0.042   0.154   1006
  Planarity :  0.004   0.033   1122
  Dihedral  :  8.198  45.951    960
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 22.48 %
    Favored  : 75.07 %
  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 aren not related in a simple way.
  whole:  1.15 (0.29), residues: 776
  helix:  1.65 (0.20), residues: 564
  sheet:  None (None), residues: 0
  loop : -1.72 (0.43), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 380 
 TYR   0.013   0.002   TYR B 352 
 PHE   0.013   0.002   PHE B 283 
 TRP   0.015   0.001   TRP B 607 
 HIS   0.002   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 6866)
  covalent geometry    : angle       0.60967 ( 9318)
  SS BOND              : bond        0.00097 (    2)
  SS BOND              : angle       0.31731 (    4)
  hydrogen bonds       : bond        0.04802 (  458)
  hydrogen bonds       : angle       4.41278 ( 1374)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2101.32 seconds
wall clock time: 36 minutes 44.45 seconds (2204.45 seconds total)