Starting phenix.real_space_refine
on Tue Mar  3 13:28:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ppj_13581/03_2026/7ppj_13581.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ppj_13581/03_2026/7ppj_13581.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.44
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ppj_13581/03_2026/7ppj_13581.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ppj_13581/03_2026/7ppj_13581.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ppj_13581/03_2026/7ppj_13581.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ppj_13581/03_2026/7ppj_13581.map"
  }
  resolution = 3.44
  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=  -0.001 sd=   0.081
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
     Zn      1      6.06       5
     S      37      5.16       5
     C    3304      2.51       5
     N     893      2.21       5
     O     940      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5175
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5174
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 643, 5157
          Classifications: {'peptide': 643}
          Link IDs: {'PTRANS': 27, 'TRANS': 615}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 643, 5157
          Classifications: {'peptide': 643}
          Link IDs: {'PTRANS': 27, 'TRANS': 615}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 5243
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1914  SG  CYS A 268      27.819  26.355  48.835  1.00 67.67           S
  ATOM   2198  SG  CYS A 303      26.980  29.739  48.695  1.00 50.58           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb="ZN    ZN A 901 " occ=0.83
  Time building chain proxies: 2.21, per 1000 atoms: 0.43
  Number of scatterers: 5175
  At special positions: 0
  Unit cell: (64.852, 91.002, 120.29, 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)
     Zn      1     29.99
     S      37     16.00
     O     940      8.00
     N     893      7.00
     C    3304      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.45
  Conformation dependent library (CDL) restraints added in 516.3 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" ND1 HIS A 266 "
        pdb="ZN    ZN A 901 " - pdb=" SG  CYS A 303 "
        pdb="ZN    ZN A 901 " - pdb=" SG  CYS A 268 "


  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1228

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 8 sheets defined
      37.3% alpha, 14.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 30
    Processing helix  chain 'A' and resid 32 through 54
      removed outlier: 3.765A  pdb=" N   ASN A  52 " --> pdb=" O   CYS A  48 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLY A  54 " --> pdb=" O   LEU A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 84
      removed outlier: 3.553A  pdb=" N   ARG A  83 " --> pdb=" O   PRO A  80 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   SER A  84 " --> pdb=" O   ILE A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 142
      removed outlier: 3.539A  pdb=" N   GLN A 142 " --> pdb=" O   LYS A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 178
    Processing helix  chain 'A' and resid 203 through 222
      Proline residue:  A 213  - end of helix
    Processing helix  chain 'A' and resid 247 through 261
    Processing helix  chain 'A' and resid 324 through 333
      removed outlier: 3.868A  pdb=" N   MET A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 378
    Processing helix  chain 'A' and resid 389 through 400
    Processing helix  chain 'A' and resid 402 through 411
    Processing helix  chain 'A' and resid 424 through 430
      removed outlier: 3.839A  pdb=" N   ASP A 428 " --> pdb=" O   SER A 424 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU A 429 " --> pdb=" O   TRP A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 480
    Processing helix  chain 'A' and resid 525 through 538
      removed outlier: 4.011A  pdb=" N   ILE A 535 " --> pdb=" O   GLN A 531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 566
    Processing helix  chain 'A' and resid 582 through 599
      removed outlier: 4.086A  pdb=" N   ARG A 590 " --> pdb=" O   ILE A 586 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   GLU A 593 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 604
      No H-bonds generated for 'chain 'A' and resid 602 through 604'
    Processing helix  chain 'A' and resid 612 through 621
    Processing helix  chain 'A' and resid 631 through 637
    Processing helix  chain 'A' and resid 651 through 654
    Processing helix  chain 'A' and resid 660 through 671
      removed outlier: 3.743A  pdb=" N   LYS A 664 " --> pdb=" O   ASP A 660 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 120
    Processing sheet with id=AA3, first strand: chain 'A' and resid 197 through 198
      removed outlier: 6.946A  pdb=" N   VAL A 283 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   TYR A 292 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   LEU A 281 " --> pdb=" O   TYR A 292 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   CYS A 294 " --> pdb=" O   ASN A 279 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   ASN A 279 " --> pdb=" O   CYS A 294 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   ILE A 296 " --> pdb=" O   VAL A 277 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   VAL A 277 " --> pdb=" O   ILE A 296 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 316
    Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 347
    Processing sheet with id=AA6, first strand: chain 'A' and resid 385 through 387
      removed outlier: 6.325A  pdb=" N   VAL A 386 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 7.850A  pdb=" N   PHE A 421 " --> pdb=" O   VAL A 386 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   CYS A 439 " --> pdb=" O   ILE A 455 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 539 through 541
    Processing sheet with id=AA8, first strand: chain 'A' and resid 573 through 575
      removed outlier: 6.299A  pdb=" N   LEU A 607 " --> pdb=" O   ILE A 647 " (cutoff:3.500A)
      removed outlier: 7.679A  pdb=" N   ASP A 649 " --> pdb=" O   LEU A 607 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   ILE A 609 " --> pdb=" O   ASP A 649 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLN A 628 " --> pdb=" O   ILE A 606 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   TYR A 608 " --> pdb=" O   GLN A 628 " (cutoff:3.500A)

    197 hydrogen bonds defined for protein.
    568 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: 0.78

  Time building geometry restraints manager: 0.57 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1618
        1.34 -     1.45: 679
        1.45 -     1.57: 2940
        1.57 -     1.69: 0
        1.69 -     1.81: 50
  Bond restraints: 5287
  Sorted by residual:
  bond pdb=" N   THR A 222 "
       pdb=" CA  THR A 222 "
    ideal  model  delta    sigma   weight residual
    1.454  1.491 -0.037 1.17e-02 7.31e+03 1.01e+01
  bond pdb=" N   VAL A 386 "
       pdb=" CA  VAL A 386 "
    ideal  model  delta    sigma   weight residual
    1.454  1.494 -0.040 1.28e-02 6.10e+03 9.91e+00
  bond pdb=" N   ILE A 451 "
       pdb=" CA  ILE A 451 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.17e-02 7.31e+03 9.91e+00
  bond pdb=" N   GLY A 225 "
       pdb=" CA  GLY A 225 "
    ideal  model  delta    sigma   weight residual
    1.446  1.474 -0.028 9.50e-03 1.11e+04 8.79e+00
  bond pdb=" N   ILE A   5 "
       pdb=" CA  ILE A   5 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.035 1.22e-02 6.72e+03 8.40e+00
  ... (remaining 5282 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 6755
        1.44 -     2.89: 323
        2.89 -     4.33: 58
        4.33 -     5.78: 11
        5.78 -     7.22: 2
  Bond angle restraints: 7149
  Sorted by residual:
  angle pdb=" N   VAL A   7 "
        pdb=" CA  VAL A   7 "
        pdb=" C   VAL A   7 "
      ideal   model   delta    sigma   weight residual
     112.83  107.38    5.45 9.90e-01 1.02e+00 3.03e+01
  angle pdb=" CA  GLN A 446 "
        pdb=" C   GLN A 446 "
        pdb=" O   GLN A 446 "
      ideal   model   delta    sigma   weight residual
     121.56  117.28    4.28 1.09e+00 8.42e-01 1.54e+01
  angle pdb=" CA  VAL A 386 "
        pdb=" C   VAL A 386 "
        pdb=" O   VAL A 386 "
      ideal   model   delta    sigma   weight residual
     121.72  118.20    3.52 9.60e-01 1.09e+00 1.34e+01
  angle pdb=" CA  HIS A 577 "
        pdb=" C   HIS A 577 "
        pdb=" O   HIS A 577 "
      ideal   model   delta    sigma   weight residual
     121.55  117.82    3.73 1.06e+00 8.90e-01 1.24e+01
  angle pdb=" CA  THR A   9 "
        pdb=" C   THR A   9 "
        pdb=" O   THR A   9 "
      ideal   model   delta    sigma   weight residual
     121.87  117.80    4.07 1.16e+00 7.43e-01 1.23e+01
  ... (remaining 7144 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.04: 2859
       17.04 -    34.07: 305
       34.07 -    51.11: 46
       51.11 -    68.14: 8
       68.14 -    85.18: 7
  Dihedral angle restraints: 3225
    sinusoidal: 1328
      harmonic: 1897
  Sorted by residual:
  dihedral pdb=" CA  PHE A 381 "
           pdb=" C   PHE A 381 "
           pdb=" N   SER A 382 "
           pdb=" CA  SER A 382 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.52  -17.48     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" C   ASN A 447 "
           pdb=" N   ASN A 447 "
           pdb=" CA  ASN A 447 "
           pdb=" CB  ASN A 447 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.75    8.15     0      2.50e+00 1.60e-01 1.06e+01
  dihedral pdb=" CA  GLN A  90 "
           pdb=" C   GLN A  90 "
           pdb=" N   LYS A  91 "
           pdb=" CA  LYS A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.72   16.28     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 3222 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 571
       0.045 -    0.090: 151
       0.090 -    0.134: 57
       0.134 -    0.179: 13
       0.179 -    0.224: 9
  Chirality restraints: 801
  Sorted by residual:
  chirality pdb=" CA  ASN A 447 "
            pdb=" N   ASN A 447 "
            pdb=" C   ASN A 447 "
            pdb=" CB  ASN A 447 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  VAL A 576 "
            pdb=" N   VAL A 576 "
            pdb=" C   VAL A 576 "
            pdb=" CB  VAL A 576 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  ILE A   5 "
            pdb=" N   ILE A   5 "
            pdb=" C   ILE A   5 "
            pdb=" CB  ILE A   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 798 not shown)

  Planarity restraints: 913
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 613 "   -0.028 5.00e-02 4.00e+02   4.24e-02 2.88e+00
        pdb=" N   PRO A 614 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 614 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 614 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 108 "   -0.026 5.00e-02 4.00e+02   3.95e-02 2.50e+00
        pdb=" N   PRO A 109 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 109 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 109 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 602 "   -0.025 5.00e-02 4.00e+02   3.86e-02 2.39e+00
        pdb=" N   PRO A 603 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 603 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 603 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 910 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 1037
        2.78 -     3.31: 5079
        3.31 -     3.84: 8303
        3.84 -     4.37: 9891
        4.37 -     4.90: 17121
  Nonbonded interactions: 41431
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A  52 "
            pdb=" O   TRP A 313 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" NZ  LYS A 481 "
            pdb=" O   GLY A 539 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" O   LYS A 616 "
            pdb=" OG  SER A 620 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   PRO A 310 "
            pdb=" NE2 GLN A 322 "
     model   vdw
     2.306 3.120
  nonbonded pdb=" O   SER A 353 "
            pdb=" OG  SER A 353 "
     model   vdw
     2.307 3.040
  ... (remaining 41426 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.99
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:             1.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.700
  Find NCS groups from input model:        0.030
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7289
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      :  0.007   0.250   5290  Z= 0.347
  Angle     :  0.719   7.221   7149  Z= 0.454
  Chirality :  0.054   0.224    801
  Planarity :  0.004   0.042    913
  Dihedral  : 14.044  85.176   1997
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.75 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  3.43 %
    Favored  : 95.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.05 (0.29), residues: 642
  helix: -1.57 (0.29), residues: 230
  sheet: -2.24 (0.50), residues: 89
  loop : -2.27 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 321 
 TYR   0.010   0.001   TYR A 608 
 PHE   0.013   0.001   PHE A 381 
 TRP   0.013   0.002   TRP A 313 
 HIS   0.003   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00544 ( 5287)
  covalent geometry    : angle       0.71889 ( 7149)
  hydrogen bonds       : bond        0.14377 (  197)
  hydrogen bonds       : angle       6.03842 (  568)
  metal coordination   : bond        0.15627 (    3)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  411 MET cc_start: 0.7701 (tpt) cc_final: 0.7485 (tpp)
  outliers start: 5
  outliers final: 1
  residues processed: 107
  average time/residue: 0.0952
  time to fit residues: 12.5794
Evaluate side-chains
  72 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0020
   chunk 45 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.6188

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

Flipped N/Q/H residues before XYZ refinement:
A  10 ASN
A  40 ASN
A  94 HIS
A 182 GLN
A 221 ASN
A 416 GLN
A 446 GLN
A 476 GLN
A 512 GLN
A 605 ASN
A 670 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.158550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.121910 restraints weight = 22723.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 8.47
r_work: 0.3169 rms_B_bonded: 7.29 restraints_weight: 2.0000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3170
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       48 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       48 |
|-----------------------------------------------------------------------------|
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.1646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5290  Z= 0.149
  Angle     :  0.673  12.037   7149  Z= 0.338
  Chirality :  0.047   0.185    801
  Planarity :  0.004   0.053    913
  Dihedral  :  4.395  27.016    704
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 12.35 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.69 (0.32), residues: 642
  helix: -0.28 (0.34), residues: 236
  sheet: -1.83 (0.52), residues: 85
  loop : -1.52 (0.33), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 290 
 TYR   0.017   0.002   TYR A 183 
 PHE   0.017   0.002   PHE A 575 
 TRP   0.032   0.002   TRP A 661 
 HIS   0.004   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 5287)
  covalent geometry    : angle       0.67321 ( 7149)
  hydrogen bonds       : bond        0.03843 (  197)
  hydrogen bonds       : angle       4.90536 (  568)
  metal coordination   : bond        0.00468 (    3)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  458 LYS cc_start: 0.7987 (tptp) cc_final: 0.7775 (tptp)
REVERT: A  661 TRP cc_start: 0.7399 (p90) cc_final: 0.7188 (p90)
  outliers start: 6
  outliers final: 2
  residues processed: 85
  average time/residue: 0.0843
  time to fit residues: 9.1065
Evaluate side-chains
  71 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 69
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 TYR
Chi-restraints excluded: chain A residue  393 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 53 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 31 optimal weight:    0.3980
   chunk 4 optimal weight:    1.9990
   chunk 63 optimal weight:    0.4980
   chunk 6 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 416 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.157307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.121881 restraints weight = 32458.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 11.32
r_work: 0.3074 rms_B_bonded: 8.78 restraints_weight: 2.0000
r_work: 0.3244 rms_B_bonded: 5.70 restraints_weight: 4.0000
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3241
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       48 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       48 |
|-----------------------------------------------------------------------------|
r_final: 0.3241
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5290  Z= 0.163
  Angle     :  0.670  13.509   7149  Z= 0.331
  Chirality :  0.048   0.339    801
  Planarity :  0.004   0.050    913
  Dihedral  :  4.430  27.008    704
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 13.38 %
    Favored  : 85.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.32), residues: 642
  helix:  0.11 (0.35), residues: 236
  sheet: -1.62 (0.49), residues: 97
  loop : -1.29 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 120 
 TYR   0.032   0.002   TYR A 183 
 PHE   0.019   0.002   PHE A 654 
 TRP   0.016   0.002   TRP A 661 
 HIS   0.004   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 5287)
  covalent geometry    : angle       0.67026 ( 7149)
  hydrogen bonds       : bond        0.03830 (  197)
  hydrogen bonds       : angle       4.76835 (  568)
  metal coordination   : bond        0.00343 (    3)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: A  458 LYS cc_start: 0.7933 (tptp) cc_final: 0.7730 (tptp)
REVERT: A  661 TRP cc_start: 0.7393 (p90) cc_final: 0.7060 (p90)
REVERT: A  680 TRP cc_start: 0.8593 (m100) cc_final: 0.8335 (m100)
  outliers start: 6
  outliers final: 5
  residues processed: 72
  average time/residue: 0.0834
  time to fit residues: 7.6738
Evaluate side-chains
  64 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  226 TYR
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  678 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0980
   chunk 12 optimal weight:    3.9990
   chunk 31 optimal weight:    0.3980
   chunk 45 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.159294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.121941 restraints weight = 20489.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 8.92
r_work: 0.3179 rms_B_bonded: 7.16 restraints_weight: 2.0000
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       48 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
r_final: 0.3178
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   5290  Z= 0.130
  Angle     :  0.673  16.314   7149  Z= 0.321
  Chirality :  0.048   0.299    801
  Planarity :  0.004   0.050    913
  Dihedral  :  4.323  27.385    704
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 14.92 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.33), residues: 642
  helix:  0.36 (0.35), residues: 236
  sheet: -1.39 (0.50), residues: 98
  loop : -1.08 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 384 
 TYR   0.009   0.001   TYR A 393 
 PHE   0.011   0.001   PHE A 575 
 TRP   0.013   0.002   TRP A 661 
 HIS   0.003   0.001   HIS A 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 5287)
  covalent geometry    : angle       0.67325 ( 7149)
  hydrogen bonds       : bond        0.03371 (  197)
  hydrogen bonds       : angle       4.79506 (  568)
  metal coordination   : bond        0.00197 (    3)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
REVERT: A  458 LYS cc_start: 0.7994 (tptp) cc_final: 0.7781 (tptp)
REVERT: A  625 ASN cc_start: 0.6701 (t0) cc_final: 0.6230 (p0)
REVERT: A  644 GLN cc_start: 0.7554 (mt0) cc_final: 0.7209 (mp10)
REVERT: A  661 TRP cc_start: 0.7304 (p90) cc_final: 0.7056 (p90)
  outliers start: 7
  outliers final: 4
  residues processed: 68
  average time/residue: 0.0784
  time to fit residues: 6.9913
Evaluate side-chains
  61 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  585 THR
Chi-restraints excluded: chain A residue  634 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 28 optimal weight:    0.0980
   chunk 22 optimal weight:    0.2980
   chunk 50 optimal weight:    7.9990
   chunk 46 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.157732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.121072 restraints weight = 23593.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 8.74
r_work: 0.3146 rms_B_bonded: 7.45 restraints_weight: 2.0000
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3152
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
r_final: 0.3152
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   5290  Z= 0.155
  Angle     :  0.661  14.330   7149  Z= 0.318
  Chirality :  0.046   0.210    801
  Planarity :  0.004   0.049    913
  Dihedral  :  4.157  17.526    702
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.09 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.33), residues: 642
  helix:  0.36 (0.35), residues: 237
  sheet: -1.19 (0.51), residues: 98
  loop : -0.99 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A 632 
 TYR   0.009   0.001   TYR A 226 
 PHE   0.024   0.002   PHE A 136 
 TRP   0.023   0.002   TRP A 328 
 HIS   0.003   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 5287)
  covalent geometry    : angle       0.66054 ( 7149)
  hydrogen bonds       : bond        0.03380 (  197)
  hydrogen bonds       : angle       4.76946 (  568)
  metal coordination   : bond        0.00296 (    3)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A  333 MET cc_start: 0.8492 (mtp) cc_final: 0.8273 (mpp)
REVERT: A  458 LYS cc_start: 0.7991 (tptp) cc_final: 0.7756 (tptp)
REVERT: A  526 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.7123 (ptp)
REVERT: A  625 ASN cc_start: 0.6722 (t0) cc_final: 0.6251 (p0)
REVERT: A  644 GLN cc_start: 0.7560 (mt0) cc_final: 0.7241 (mp10)
REVERT: A  661 TRP cc_start: 0.7368 (p90) cc_final: 0.7134 (p90)
  outliers start: 9
  outliers final: 6
  residues processed: 74
  average time/residue: 0.0850
  time to fit residues: 8.0796
Evaluate side-chains
  65 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  585 THR
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  678 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 42 optimal weight:    0.3980
   chunk 50 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 43 optimal weight:    0.5980
   chunk 6 optimal weight:    0.3980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.156930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.119698 restraints weight = 23997.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 9.55
r_work: 0.3104 rms_B_bonded: 7.28 restraints_weight: 2.0000
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3105
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
r_final: 0.3105
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5290  Z= 0.131
  Angle     :  0.615  13.651   7149  Z= 0.302
  Chirality :  0.045   0.161    801
  Planarity :  0.004   0.048    913
  Dihedral  :  4.101  17.596    702
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.27 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.33), residues: 642
  helix:  0.51 (0.35), residues: 237
  sheet: -0.95 (0.56), residues: 84
  loop : -0.87 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 290 
 TYR   0.008   0.001   TYR A 226 
 PHE   0.014   0.002   PHE A 136 
 TRP   0.048   0.003   TRP A 328 
 HIS   0.006   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 5287)
  covalent geometry    : angle       0.61494 ( 7149)
  hydrogen bonds       : bond        0.03223 (  197)
  hydrogen bonds       : angle       4.69217 (  568)
  metal coordination   : bond        0.00226 (    3)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A  333 MET cc_start: 0.8468 (mtp) cc_final: 0.8058 (mpp)
REVERT: A  458 LYS cc_start: 0.8034 (tptp) cc_final: 0.7718 (tptp)
REVERT: A  526 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.7000 (ptp)
REVERT: A  541 LYS cc_start: 0.7994 (mptt) cc_final: 0.6914 (mtmt)
REVERT: A  574 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8021 (tt)
REVERT: A  625 ASN cc_start: 0.6714 (t0) cc_final: 0.6247 (p0)
REVERT: A  644 GLN cc_start: 0.7484 (mt0) cc_final: 0.7093 (mp10)
REVERT: A  661 TRP cc_start: 0.7279 (p90) cc_final: 0.7014 (p90)
  outliers start: 9
  outliers final: 6
  residues processed: 73
  average time/residue: 0.0745
  time to fit residues: 7.2430
Evaluate side-chains
  66 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ASP
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  585 THR
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  678 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0770
   chunk 53 optimal weight:    6.9990
   chunk 17 optimal weight:    0.0270
   chunk 41 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 60 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.2000

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

Flipped N/Q/H residues before XYZ refinement:
** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.154058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.116966 restraints weight = 20387.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 8.54
r_work: 0.3089 rms_B_bonded: 6.77 restraints_weight: 2.0000
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3089
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3089 r_free = 0.3089    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3089 r_free = 0.3089    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
r_final: 0.3089
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   5290  Z= 0.191
  Angle     :  0.646  13.520   7149  Z= 0.318
  Chirality :  0.046   0.149    801
  Planarity :  0.004   0.048    913
  Dihedral  :  4.296  17.254    702
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 15.09 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.33), residues: 642
  helix:  0.39 (0.35), residues: 237
  sheet: -0.97 (0.53), residues: 94
  loop : -0.87 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 290 
 TYR   0.011   0.001   TYR A 472 
 PHE   0.015   0.002   PHE A 306 
 TRP   0.042   0.003   TRP A 328 
 HIS   0.004   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 5287)
  covalent geometry    : angle       0.64586 ( 7149)
  hydrogen bonds       : bond        0.03504 (  197)
  hydrogen bonds       : angle       4.76280 (  568)
  metal coordination   : bond        0.00426 (    3)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A  458 LYS cc_start: 0.8038 (tptp) cc_final: 0.7765 (tptp)
REVERT: A  526 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.7072 (ptp)
REVERT: A  574 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8071 (tt)
REVERT: A  644 GLN cc_start: 0.7425 (mt0) cc_final: 0.7044 (mp10)
REVERT: A  661 TRP cc_start: 0.7334 (p90) cc_final: 0.7114 (p90)
  outliers start: 10
  outliers final: 7
  residues processed: 71
  average time/residue: 0.0678
  time to fit residues: 6.4837
Evaluate side-chains
  67 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ASP
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  585 THR
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  647 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   chunk 45 optimal weight:    0.2980
   chunk 9 optimal weight:    2.9990
   chunk 1 optimal weight:    0.3980
   chunk 20 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   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 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.156597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.120116 restraints weight = 28283.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 10.11
r_work: 0.3077 rms_B_bonded: 7.64 restraints_weight: 2.0000
r_work: 0.3230 rms_B_bonded: 5.05 restraints_weight: 4.0000
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3230
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
r_final: 0.3230
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5290  Z= 0.125
  Angle     :  0.617  14.060   7149  Z= 0.300
  Chirality :  0.045   0.153    801
  Planarity :  0.004   0.048    913
  Dihedral  :  4.087  17.902    702
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.95 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.33), residues: 642
  helix:  0.61 (0.35), residues: 236
  sheet: -0.91 (0.52), residues: 98
  loop : -0.70 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 290 
 TYR   0.008   0.001   TYR A 226 
 PHE   0.011   0.001   PHE A 306 
 TRP   0.039   0.002   TRP A 328 
 HIS   0.004   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 5287)
  covalent geometry    : angle       0.61711 ( 7149)
  hydrogen bonds       : bond        0.03121 (  197)
  hydrogen bonds       : angle       4.65128 (  568)
  metal coordination   : bond        0.00215 (    3)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A  411 MET cc_start: 0.6822 (tpp) cc_final: 0.6520 (tpt)
REVERT: A  458 LYS cc_start: 0.8009 (tptp) cc_final: 0.7660 (tptp)
REVERT: A  541 LYS cc_start: 0.7940 (mptt) cc_final: 0.6820 (mtmt)
REVERT: A  574 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7930 (tt)
REVERT: A  644 GLN cc_start: 0.7304 (mt0) cc_final: 0.6919 (mp10)
  outliers start: 8
  outliers final: 5
  residues processed: 69
  average time/residue: 0.0713
  time to fit residues: 6.5542
Evaluate side-chains
  65 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  585 THR
Chi-restraints excluded: chain A residue  634 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 41 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.154635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.117535 restraints weight = 24219.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 9.36
r_work: 0.3068 rms_B_bonded: 7.32 restraints_weight: 2.0000
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3067
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3067 r_free = 0.3067    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3067 r_free = 0.3067    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
r_final: 0.3067
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5290  Z= 0.183
  Angle     :  0.650  14.100   7149  Z= 0.320
  Chirality :  0.046   0.150    801
  Planarity :  0.004   0.047    913
  Dihedral  :  4.244  17.317    702
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.95 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.33), residues: 642
  helix:  0.51 (0.35), residues: 236
  sheet: -0.92 (0.52), residues: 97
  loop : -0.72 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 290 
 TYR   0.010   0.001   TYR A 472 
 PHE   0.016   0.002   PHE A 200 
 TRP   0.070   0.005   TRP A 661 
 HIS   0.003   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 5287)
  covalent geometry    : angle       0.64972 ( 7149)
  hydrogen bonds       : bond        0.03405 (  197)
  hydrogen bonds       : angle       4.73087 (  568)
  metal coordination   : bond        0.00416 (    3)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A  411 MET cc_start: 0.7037 (tpp) cc_final: 0.6669 (tpt)
REVERT: A  458 LYS cc_start: 0.8107 (tptp) cc_final: 0.7809 (tptp)
REVERT: A  526 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.7094 (ptp)
REVERT: A  574 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8064 (tt)
REVERT: A  644 GLN cc_start: 0.7425 (mt0) cc_final: 0.7069 (mp10)
  outliers start: 8
  outliers final: 6
  residues processed: 67
  average time/residue: 0.0704
  time to fit residues: 6.3282
Evaluate side-chains
  66 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  585 THR
Chi-restraints excluded: chain A residue  634 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 32 optimal weight:    0.4980
   chunk 47 optimal weight:    0.0570
   chunk 17 optimal weight:    0.0770
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0270
   chunk 36 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.2714

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

Flipped N/Q/H residues before XYZ refinement:
A 446 GLN
A 613 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.158724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.121040 restraints weight = 23571.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 9.09
r_work: 0.3128 rms_B_bonded: 7.32 restraints_weight: 2.0000
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3127
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
r_final: 0.3127
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5290  Z= 0.111
  Angle     :  0.617  14.810   7149  Z= 0.299
  Chirality :  0.044   0.151    801
  Planarity :  0.004   0.049    913
  Dihedral  :  4.010  18.220    702
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 16.47 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.34), residues: 642
  helix:  0.72 (0.36), residues: 236
  sheet: -0.74 (0.53), residues: 97
  loop : -0.57 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 290 
 TYR   0.008   0.001   TYR A 226 
 PHE   0.008   0.001   PHE A 306 
 TRP   0.068   0.004   TRP A 328 
 HIS   0.003   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 5287)
  covalent geometry    : angle       0.61659 ( 7149)
  hydrogen bonds       : bond        0.03087 (  197)
  hydrogen bonds       : angle       4.60341 (  568)
  metal coordination   : bond        0.00134 (    3)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A  200 PHE cc_start: 0.7483 (m-10) cc_final: 0.7270 (m-10)
REVERT: A  458 LYS cc_start: 0.8020 (tptp) cc_final: 0.7696 (tptp)
REVERT: A  541 LYS cc_start: 0.7946 (mptt) cc_final: 0.6878 (mtmt)
REVERT: A  574 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7955 (tt)
REVERT: A  625 ASN cc_start: 0.6760 (t0) cc_final: 0.6359 (p0)
REVERT: A  644 GLN cc_start: 0.7403 (mt0) cc_final: 0.7027 (mp10)
  outliers start: 5
  outliers final: 4
  residues processed: 72
  average time/residue: 0.0694
  time to fit residues: 6.7855
Evaluate side-chains
  65 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  585 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0270
   chunk 22 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 58 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9980
   chunk 13 optimal weight:    0.4980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
A 670 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.157695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.119734 restraints weight = 22121.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 8.33
r_work: 0.3126 rms_B_bonded: 7.12 restraints_weight: 2.0000
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3125
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
r_final: 0.3125
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.3073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5290  Z= 0.122
  Angle     :  0.613  14.544   7149  Z= 0.297
  Chirality :  0.044   0.152    801
  Planarity :  0.004   0.048    913
  Dihedral  :  3.961  17.171    702
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 16.64 %
    Favored  : 81.65 %
  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 are not related in a simple way.
  whole: -0.14 (0.34), residues: 642
  helix:  0.75 (0.36), residues: 236
  sheet: -0.56 (0.58), residues: 86
  loop : -0.51 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 290 
 TYR   0.008   0.001   TYR A 183 
 PHE   0.012   0.001   PHE A 267 
 TRP   0.061   0.004   TRP A 328 
 HIS   0.002   0.000   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5287)
  covalent geometry    : angle       0.61287 ( 7149)
  hydrogen bonds       : bond        0.03093 (  197)
  hydrogen bonds       : angle       4.57278 (  568)
  metal coordination   : bond        0.00181 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1551.82 seconds
wall clock time: 27 minutes 12.05 seconds (1632.05 seconds total)