Starting phenix.real_space_refine
on Thu Jun  5 23:05:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ijz_60646/06_2025/9ijz_60646_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ijz_60646/06_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_60646/06_2025/9ijz_60646.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ijz_60646/06_2025/9ijz_60646.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ijz_60646/06_2025/9ijz_60646_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ijz_60646/06_2025/9ijz_60646_trim.cif"
  }
  resolution = 2.91
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.058
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.27, per 1000 atoms: 0.94
  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: 1.74
  Conformation dependent library (CDL) restraints added in 926.3 milliseconds
  

  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: 0.65
  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: 1.94

  Time building geometry restraints manager: 2.07 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: 0.04
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:             2.040
  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:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     21.430
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  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:14.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.990
-------------------------------------------------------------------------------
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 : 14.61
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (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
 TRP   0.010   0.001   TRP B 373 
 HIS   0.002   0.001   HIS A 476 
 PHE   0.011   0.001   PHE A 610 
 TYR   0.014   0.001   TYR A 524 
 ARG   0.003   0.000   ARG A 472 

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

*********************** 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  : 0.675 
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: 0.7488
  time to fit residues: 84.4890
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  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0770
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0770
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.4496

-------------------------------------------------------------------------------
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
B 452 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.183661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.148337 restraints weight = 8482.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 2.30
r_work: 0.3606 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.1060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6868  Z= 0.143
  Angle     :  0.553   5.618   9322  Z= 0.300
  Chirality :  0.040   0.126   1006
  Planarity :  0.004   0.027   1122
  Dihedral  : 10.475  80.278    960
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 9.29
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.30), residues: 776
  helix:  1.63 (0.20), residues: 564
  sheet:  None (None), residues: 0
  loop : -1.78 (0.44), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 232 
 HIS   0.001   0.001   HIS A 476 
 PHE   0.018   0.002   PHE A 257 
 TYR   0.013   0.002   TYR B 352 
 ARG   0.005   0.000   ARG B 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05019 (  458)
  hydrogen bonds       : angle       4.38419 ( 1374)
  SS BOND              : bond        0.00075 (    2)
  SS BOND              : angle       0.26316 (    4)
  covalent geometry    : bond        0.00308 ( 6866)
  covalent geometry    : angle       0.55265 ( 9318)

*********************** 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
  124 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.644 
Fit side-chains
REVERT: A  477 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8181 (mm)
REVERT: A  511 PHE cc_start: 0.9077 (t80) cc_final: 0.8810 (t80)
REVERT: B  477 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8191 (mm)
REVERT: B  511 PHE cc_start: 0.9076 (t80) cc_final: 0.8812 (t80)
  outliers start: 18
  outliers final: 8
  residues processed: 116
  average time/residue: 0.7550
  time to fit residues: 94.7780
Evaluate side-chains
  110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
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 A residue  477 LEU
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
Chi-restraints excluded: chain B residue  477 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4122 r_free = 0.4122 target = 0.179613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.142915 restraints weight = 8630.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 2.39
r_work: 0.3542 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.1344

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= 0.176
  Angle     :  0.563   5.637   9322  Z= 0.304
  Chirality :  0.041   0.136   1006
  Planarity :  0.004   0.058   1122
  Dihedral  : 10.383  77.855    960
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 19.88 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.30), residues: 776
  helix:  1.65 (0.20), residues: 564
  sheet:  None (None), residues: 0
  loop : -1.78 (0.45), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 232 
 HIS   0.002   0.001   HIS A 313 
 PHE   0.018   0.002   PHE A 391 
 TYR   0.012   0.002   TYR B 467 
 ARG   0.002   0.000   ARG B 380 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05098 (  458)
  hydrogen bonds       : angle       4.48145 ( 1374)
  SS BOND              : bond        0.00120 (    2)
  SS BOND              : angle       0.37331 (    4)
  covalent geometry    : bond        0.00399 ( 6866)
  covalent geometry    : angle       0.56318 ( 9318)

*********************** 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
  146 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 116
  time to evaluate  : 0.665 
Fit side-chains
REVERT: A  261 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.7919 (t)
REVERT: A  511 PHE cc_start: 0.9082 (t80) cc_final: 0.8852 (t80)
REVERT: A  549 GLU cc_start: 0.7767 (pp20) cc_final: 0.7549 (pp20)
REVERT: B  261 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7921 (t)
REVERT: B  511 PHE cc_start: 0.9083 (t80) cc_final: 0.8854 (t80)
REVERT: B  549 GLU cc_start: 0.7777 (pp20) cc_final: 0.7553 (pp20)
  outliers start: 30
  outliers final: 16
  residues processed: 138
  average time/residue: 0.8100
  time to fit residues: 120.2229
Evaluate side-chains
  118 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
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  439 ILE
Chi-restraints excluded: chain A residue  447 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  447 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 4 optimal weight:    0.4980
   chunk 8 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 46 optimal weight:    0.2980
   chunk 39 optimal weight:    0.6980
   chunk 26 optimal weight:    9.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4138 r_free = 0.4138 target = 0.181142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.144704 restraints weight = 8612.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3725 rms_B_bonded: 2.40
r_work: 0.3571 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6868  Z= 0.148
  Angle     :  0.554   5.541   9322  Z= 0.303
  Chirality :  0.040   0.133   1006
  Planarity :  0.004   0.043   1122
  Dihedral  : 10.131  73.464    960
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 20.75 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.30), residues: 776
  helix:  1.66 (0.20), residues: 566
  sheet:  None (None), residues: 0
  loop : -1.82 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 327 
 HIS   0.002   0.001   HIS B 313 
 PHE   0.018   0.002   PHE A 391 
 TYR   0.012   0.002   TYR A 352 
 ARG   0.003   0.000   ARG B 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04820 (  458)
  hydrogen bonds       : angle       4.36553 ( 1374)
  SS BOND              : bond        0.00107 (    2)
  SS BOND              : angle       0.26578 (    4)
  covalent geometry    : bond        0.00325 ( 6866)
  covalent geometry    : angle       0.55423 ( 9318)

*********************** 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
  136 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  377 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6440 (tp)
REVERT: A  511 PHE cc_start: 0.9074 (t80) cc_final: 0.8839 (t80)
REVERT: A  549 GLU cc_start: 0.7779 (pp20) cc_final: 0.7526 (pp20)
REVERT: B  377 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6432 (tp)
REVERT: B  511 PHE cc_start: 0.9075 (t80) cc_final: 0.8841 (t80)
REVERT: B  549 GLU cc_start: 0.7773 (pp20) cc_final: 0.7521 (pp20)
  outliers start: 28
  outliers final: 16
  residues processed: 126
  average time/residue: 0.8471
  time to fit residues: 114.4684
Evaluate side-chains
  122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
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 A residue  448 ARG
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  448 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 5 optimal weight:    0.5980
   chunk 30 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 58 optimal weight:    0.4980
   chunk 23 optimal weight:    0.5980
   chunk 55 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.4129 r_free = 0.4129 target = 0.180244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.143967 restraints weight = 8623.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 2.41
r_work: 0.3560 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.1640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6868  Z= 0.155
  Angle     :  0.557   5.534   9322  Z= 0.303
  Chirality :  0.041   0.141   1006
  Planarity :  0.004   0.035   1122
  Dihedral  :  9.919  71.386    960
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 20.75 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.30), residues: 776
  helix:  1.66 (0.20), residues: 566
  sheet:  None (None), residues: 0
  loop : -1.76 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 327 
 HIS   0.002   0.001   HIS A 313 
 PHE   0.019   0.002   PHE A 391 
 TYR   0.013   0.002   TYR A 352 
 ARG   0.004   0.000   ARG A 380 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04782 (  458)
  hydrogen bonds       : angle       4.38939 ( 1374)
  SS BOND              : bond        0.00115 (    2)
  SS BOND              : angle       0.31813 (    4)
  covalent geometry    : bond        0.00349 ( 6866)
  covalent geometry    : angle       0.55739 ( 9318)

*********************** 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
  144 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 114
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  377 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6471 (tp)
REVERT: A  499 HIS cc_start: 0.8258 (OUTLIER) cc_final: 0.7903 (m-70)
REVERT: A  511 PHE cc_start: 0.9076 (t80) cc_final: 0.8826 (t80)
REVERT: A  549 GLU cc_start: 0.7781 (pp20) cc_final: 0.7516 (pp20)
REVERT: A  615 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.6895 (mt-10)
REVERT: B  377 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.6464 (tp)
REVERT: B  499 HIS cc_start: 0.8261 (OUTLIER) cc_final: 0.7904 (m-70)
REVERT: B  511 PHE cc_start: 0.9076 (t80) cc_final: 0.8827 (t80)
REVERT: B  549 GLU cc_start: 0.7785 (pp20) cc_final: 0.7521 (pp20)
REVERT: B  615 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.6907 (mt-10)
  outliers start: 30
  outliers final: 12
  residues processed: 134
  average time/residue: 0.7997
  time to fit residues: 116.1788
Evaluate side-chains
  124 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
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  408 MET
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  448 ARG
Chi-restraints excluded: chain A residue  499 HIS
Chi-restraints excluded: chain A residue  615 GLU
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  408 MET
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 ARG
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  615 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 55 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 66 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4126 r_free = 0.4126 target = 0.179917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.143515 restraints weight = 8465.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 2.41
r_work: 0.3562 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6868  Z= 0.164
  Angle     :  0.572   5.557   9322  Z= 0.313
  Chirality :  0.041   0.141   1006
  Planarity :  0.004   0.033   1122
  Dihedral  :  9.506  68.876    960
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 20.75 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.30), residues: 776
  helix:  1.64 (0.20), residues: 566
  sheet:  None (None), residues: 0
  loop : -1.71 (0.45), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 327 
 HIS   0.002   0.001   HIS B 313 
 PHE   0.040   0.002   PHE A 391 
 TYR   0.013   0.002   TYR A 352 
 ARG   0.002   0.000   ARG A 380 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04845 (  458)
  hydrogen bonds       : angle       4.40867 ( 1374)
  SS BOND              : bond        0.00132 (    2)
  SS BOND              : angle       0.41943 (    4)
  covalent geometry    : bond        0.00371 ( 6866)
  covalent geometry    : angle       0.57188 ( 9318)

*********************** 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
  132 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  261 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.7919 (t)
REVERT: A  377 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6459 (tp)
REVERT: A  511 PHE cc_start: 0.9044 (t80) cc_final: 0.8828 (t80)
REVERT: A  549 GLU cc_start: 0.7802 (pp20) cc_final: 0.7536 (pp20)
REVERT: B  261 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.7920 (t)
REVERT: B  377 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6440 (tp)
REVERT: B  511 PHE cc_start: 0.9045 (t80) cc_final: 0.8829 (t80)
REVERT: B  549 GLU cc_start: 0.7805 (pp20) cc_final: 0.7542 (pp20)
  outliers start: 30
  outliers final: 14
  residues processed: 122
  average time/residue: 0.8499
  time to fit residues: 112.5662
Evaluate side-chains
  116 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
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  439 ILE
Chi-restraints excluded: chain A residue  448 ARG
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  448 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0010
   chunk 2 optimal weight:    0.5980
   chunk 33 optimal weight:    0.3980
   chunk 1 optimal weight:    0.7980
   chunk 35 optimal weight:    8.9990
   chunk 52 optimal weight:    0.7980
   chunk 3 optimal weight:    0.1980
   chunk 64 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.3786

-------------------------------------------------------------------------------
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 = 0.4159 r_free = 0.4159 target = 0.183313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.147498 restraints weight = 8580.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 2.37
r_work: 0.3608 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6868  Z= 0.131
  Angle     :  0.541   5.417   9322  Z= 0.295
  Chirality :  0.040   0.136   1006
  Planarity :  0.004   0.032   1122
  Dihedral  :  8.964  62.140    960
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 21.61 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.30), residues: 776
  helix:  1.76 (0.20), residues: 566
  sheet:  None (None), residues: 0
  loop : -1.65 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 327 
 HIS   0.001   0.000   HIS B 313 
 PHE   0.037   0.002   PHE A 391 
 TYR   0.014   0.001   TYR B 352 
 ARG   0.003   0.000   ARG B 380 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04526 (  458)
  hydrogen bonds       : angle       4.29397 ( 1374)
  SS BOND              : bond        0.00110 (    2)
  SS BOND              : angle       0.28488 (    4)
  covalent geometry    : bond        0.00286 ( 6866)
  covalent geometry    : angle       0.54095 ( 9318)

*********************** 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
  132 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A  261 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.7921 (t)
REVERT: A  377 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6364 (tp)
REVERT: A  448 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7293 (ttm110)
REVERT: A  622 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7542 (mt-10)
REVERT: B  261 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.7923 (t)
REVERT: B  377 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6369 (tp)
REVERT: B  448 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7302 (ttm110)
REVERT: B  622 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7547 (mt-10)
  outliers start: 22
  outliers final: 10
  residues processed: 122
  average time/residue: 0.7525
  time to fit residues: 100.1555
Evaluate side-chains
  116 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
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  448 ARG
Chi-restraints excluded: chain A residue  622 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  448 ARG
Chi-restraints excluded: chain B residue  622 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0980
   chunk 1 optimal weight:    0.6980
   chunk 19 optimal weight:    8.9990
   chunk 71 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.4155 r_free = 0.4155 target = 0.182972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.147397 restraints weight = 8720.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 2.34
r_work: 0.3594 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
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   0.058   6868  Z= 0.143
  Angle     :  0.566   7.414   9322  Z= 0.305
  Chirality :  0.041   0.134   1006
  Planarity :  0.004   0.031   1122
  Dihedral  :  8.891  59.002    960
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 22.19 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.29), residues: 776
  helix:  1.73 (0.20), residues: 566
  sheet:  None (None), residues: 0
  loop : -1.59 (0.44), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 327 
 HIS   0.002   0.001   HIS B 313 
 PHE   0.035   0.002   PHE A 391 
 TYR   0.013   0.001   TYR B 352 
 ARG   0.002   0.000   ARG B 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04628 (  458)
  hydrogen bonds       : angle       4.35453 ( 1374)
  SS BOND              : bond        0.00131 (    2)
  SS BOND              : angle       0.32513 (    4)
  covalent geometry    : bond        0.00320 ( 6866)
  covalent geometry    : angle       0.56658 ( 9318)

*********************** 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
  116 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.913 
Fit side-chains
REVERT: A  261 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.7910 (t)
REVERT: A  377 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6418 (tp)
REVERT: A  448 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7347 (ttm110)
REVERT: B  261 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.7912 (t)
REVERT: B  377 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6415 (tp)
REVERT: B  448 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7368 (ttm110)
  outliers start: 20
  outliers final: 12
  residues processed: 108
  average time/residue: 0.9494
  time to fit residues: 110.6186
Evaluate side-chains
  114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
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  370 SER
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  448 ARG
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  370 SER
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  448 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    0.1980
   chunk 18 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   chunk 33 optimal weight:    0.5980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4146 r_free = 0.4146 target = 0.182355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.146343 restraints weight = 8654.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 2.37
r_work: 0.3590 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   6868  Z= 0.147
  Angle     :  0.579   6.948   9322  Z= 0.312
  Chirality :  0.041   0.134   1006
  Planarity :  0.004   0.032   1122
  Dihedral  :  8.908  59.799    960
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 21.61 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.29), residues: 776
  helix:  1.72 (0.20), residues: 564
  sheet:  None (None), residues: 0
  loop : -1.59 (0.43), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 327 
 HIS   0.002   0.001   HIS A 313 
 PHE   0.034   0.002   PHE A 391 
 TYR   0.013   0.001   TYR A 352 
 ARG   0.002   0.000   ARG A 380 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04643 (  458)
  hydrogen bonds       : angle       4.35394 ( 1374)
  SS BOND              : bond        0.00107 (    2)
  SS BOND              : angle       0.37336 (    4)
  covalent geometry    : bond        0.00333 ( 6866)
  covalent geometry    : angle       0.57883 ( 9318)

*********************** 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
  126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.754 
Fit side-chains
REVERT: A  261 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.7902 (t)
REVERT: A  377 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6408 (tp)
REVERT: A  448 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7359 (ttm110)
REVERT: A  477 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8104 (mm)
REVERT: A  499 HIS cc_start: 0.8178 (OUTLIER) cc_final: 0.7752 (m-70)
REVERT: B  261 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.7903 (t)
REVERT: B  377 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6404 (tp)
REVERT: B  448 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7370 (ttm110)
REVERT: B  477 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8110 (mm)
REVERT: B  499 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7758 (m-70)
  outliers start: 24
  outliers final: 12
  residues processed: 116
  average time/residue: 0.7346
  time to fit residues: 92.3490
Evaluate side-chains
  120 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
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  370 SER
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  448 ARG
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  499 HIS
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  370 SER
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  448 ARG
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  499 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 49 optimal weight:    0.3980
   chunk 8 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4140 r_free = 0.4140 target = 0.181557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.144955 restraints weight = 8770.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 2.44
r_work: 0.3570 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6868  Z= 0.153
  Angle     :  0.581   7.035   9322  Z= 0.314
  Chirality :  0.041   0.145   1006
  Planarity :  0.004   0.032   1122
  Dihedral  :  8.548  50.017    960
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 22.33 %
    Favored  : 74.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.29), residues: 776
  helix:  1.68 (0.20), residues: 564
  sheet:  None (None), residues: 0
  loop : -1.54 (0.43), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 327 
 HIS   0.002   0.001   HIS B 313 
 PHE   0.034   0.002   PHE A 391 
 TYR   0.014   0.002   TYR B 352 
 ARG   0.002   0.000   ARG B 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04703 (  458)
  hydrogen bonds       : angle       4.37472 ( 1374)
  SS BOND              : bond        0.00135 (    2)
  SS BOND              : angle       0.41265 (    4)
  covalent geometry    : bond        0.00347 ( 6866)
  covalent geometry    : angle       0.58083 ( 9318)

********************** 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
  126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  261 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.7900 (t)
REVERT: A  377 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6398 (tp)
REVERT: A  477 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8131 (mm)
REVERT: A  499 HIS cc_start: 0.8274 (OUTLIER) cc_final: 0.7817 (m-70)
REVERT: A  533 ASP cc_start: 0.7458 (m-30) cc_final: 0.7230 (m-30)
REVERT: B  261 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.7901 (t)
REVERT: B  377 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6392 (tp)
REVERT: B  477 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8139 (mm)
REVERT: B  499 HIS cc_start: 0.8282 (OUTLIER) cc_final: 0.7826 (m-70)
REVERT: B  533 ASP cc_start: 0.7453 (m-30) cc_final: 0.7228 (m-30)
  outliers start: 22
  outliers final: 14
  residues processed: 116
  average time/residue: 0.6793
  time to fit residues: 86.8923
Evaluate side-chains
  122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
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  370 SER
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  448 ARG
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  499 HIS
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  370 SER
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  448 ARG
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  499 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:   10.0000
   chunk 23 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 52 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.4139 r_free = 0.4139 target = 0.181308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.144868 restraints weight = 8677.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 2.43
r_work: 0.3564 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   6868  Z= 0.168
  Angle     :  0.596   6.981   9322  Z= 0.322
  Chirality :  0.042   0.148   1006
  Planarity :  0.004   0.033   1122
  Dihedral  :  8.361  46.540    960
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 21.61 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.29), residues: 776
  helix:  1.56 (0.20), residues: 564
  sheet:  None (None), residues: 0
  loop : -1.61 (0.43), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 327 
 HIS   0.003   0.001   HIS B 616 
 PHE   0.048   0.002   PHE A 391 
 TYR   0.014   0.002   TYR B 352 
 ARG   0.002   0.000   ARG B 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04756 (  458)
  hydrogen bonds       : angle       4.40675 ( 1374)
  SS BOND              : bond        0.00139 (    2)
  SS BOND              : angle       0.47043 (    4)
  covalent geometry    : bond        0.00389 ( 6866)
  covalent geometry    : angle       0.59617 ( 9318)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4311.68 seconds
wall clock time: 76 minutes 9.66 seconds (4569.66 seconds total)