Starting phenix.real_space_refine
on Sun Apr 27 07:14:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ef0_40857/04_2025/9ef0_40857.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ef0_40857/04_2025/9ef0_40857.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ef0_40857/04_2025/9ef0_40857.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ef0_40857/04_2025/9ef0_40857.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ef0_40857/04_2025/9ef0_40857.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ef0_40857/04_2025/9ef0_40857.cif"
  }
  resolution = 3.33
  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=   0.015
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       3      5.49       5
     S      23      5.16       5
     C    3147      2.51       5
     N     858      2.21       5
     O     962      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 4993
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 613, 4909
          Classifications: {'peptide': 613}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 586}
    Chain: "A"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 84
          Unusual residues: {'FAD': 1, 'FMN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.96, per 1000 atoms: 0.79
  Number of scatterers: 4993
  At special positions: 0
  Unit cell: (69.876, 76.346, 87.992, 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      23     16.00
     P       3     15.00
     O     962      8.00
     N     858      7.00
     C    3147      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: 1.56
  Conformation dependent library (CDL) restraints added in 615.5 milliseconds
  

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1140

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 6 sheets defined
      41.9% alpha, 16.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 69 through 77
    Processing helix  chain 'A' and resid 89 through 102
    Processing helix  chain 'A' and resid 103 through 106
    Processing helix  chain 'A' and resid 118 through 123
      removed outlier: 4.092A  pdb=" N   ASP A 121 " --> pdb=" O   ASP A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 128
    Processing helix  chain 'A' and resid 149 through 159
    Processing helix  chain 'A' and resid 182 through 196
    Processing helix  chain 'A' and resid 211 through 232
      removed outlier: 4.096A  pdb=" N   ASP A 215 " --> pdb=" O   ASN A 211 " (cutoff:3.500A)
      Proline residue:  A 225  - end of helix
    Processing helix  chain 'A' and resid 254 through 258
      removed outlier: 3.536A  pdb=" N   LYS A 257 " --> pdb=" O   ASP A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 339
    Processing helix  chain 'A' and resid 366 through 374
    Processing helix  chain 'A' and resid 382 through 391
      removed outlier: 4.574A  pdb=" N   GLN A 391 " --> pdb=" O   TYR A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 405
    Processing helix  chain 'A' and resid 410 through 420
      removed outlier: 3.587A  pdb=" N   GLU A 414 " --> pdb=" O   GLY A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 434
    Processing helix  chain 'A' and resid 440 through 448
    Processing helix  chain 'A' and resid 489 through 496
    Processing helix  chain 'A' and resid 533 through 535
      No H-bonds generated for 'chain 'A' and resid 533 through 535'
    Processing helix  chain 'A' and resid 536 through 553
      removed outlier: 4.107A  pdb=" N   PHE A 540 " --> pdb=" O   GLY A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 585
    Processing helix  chain 'A' and resid 604 through 612
      removed outlier: 3.590A  pdb=" N   LEU A 608 " --> pdb=" O   TYR A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 624
      removed outlier: 3.866A  pdb=" N   LYS A 618 " --> pdb=" O   GLU A 614 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLY A 624 " --> pdb=" O   ILE A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 651
    Processing helix  chain 'A' and resid 655 through 669
    Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 112
      removed outlier: 6.494A  pdb=" N   ILE A  80 " --> pdb=" O   MET A 110 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   ALA A 112 " --> pdb=" O   ILE A  80 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   VAL A  82 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   VAL A 133 " --> pdb=" O   ALA A 169 " (cutoff:3.500A)
      removed outlier: 8.175A  pdb=" N   PHE A 171 " --> pdb=" O   VAL A 133 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   PHE A 135 " --> pdb=" O   PHE A 171 " (cutoff:3.500A)
      removed outlier: 7.354A  pdb=" N   LEU A 173 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   MET A 137 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHE A 168 " --> pdb=" O   GLN A 198 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 112
      removed outlier: 6.494A  pdb=" N   ILE A  80 " --> pdb=" O   MET A 110 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   ALA A 112 " --> pdb=" O   ILE A  80 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   VAL A  82 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   VAL A 133 " --> pdb=" O   ALA A 169 " (cutoff:3.500A)
      removed outlier: 8.175A  pdb=" N   PHE A 171 " --> pdb=" O   VAL A 133 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   PHE A 135 " --> pdb=" O   PHE A 171 " (cutoff:3.500A)
      removed outlier: 7.354A  pdb=" N   LEU A 173 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   MET A 137 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 245 through 247
    Processing sheet with id=AA4, first strand: chain 'A' and resid 454 through 457
      removed outlier: 3.634A  pdb=" N   ALA A 285 " --> pdb=" O   ASP A 306 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   GLU A 304 " --> pdb=" O   THR A 287 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   ASN A 289 " --> pdb=" O   HIS A 302 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   HIS A 302 " --> pdb=" O   ASN A 289 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   LYS A 291 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   LEU A 300 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 477 through 479
    Processing sheet with id=AA6, first strand: chain 'A' and resid 590 through 595
      removed outlier: 6.838A  pdb=" N   THR A 560 " --> pdb=" O   GLN A 590 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   ASN A 592 " --> pdb=" O   THR A 560 " (cutoff:3.500A)
      removed outlier: 6.077A  pdb=" N   LEU A 562 " --> pdb=" O   ASN A 592 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   ALA A 594 " --> pdb=" O   LEU A 562 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   TYR A 564 " --> pdb=" O   ALA A 594 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   VAL A 528 " --> pdb=" O   LEU A 561 " (cutoff:3.500A)
      removed outlier: 8.003A  pdb=" N   TYR A 563 " --> pdb=" O   VAL A 528 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   MET A 530 " --> pdb=" O   TYR A 563 " (cutoff:3.500A)
      removed outlier: 8.272A  pdb=" N   GLY A 565 " --> pdb=" O   MET A 530 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ILE A 627 " --> pdb=" O   SER A 673 " (cutoff:3.500A)

    193 hydrogen bonds defined for protein.
    549 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: 1.69

  Time building geometry restraints manager: 1.63 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1033
        1.33 -     1.45: 1260
        1.45 -     1.57: 2780
        1.57 -     1.69: 5
        1.69 -     1.81: 39
  Bond restraints: 5117
  Sorted by residual:
  bond pdb=" C4  FMN A 701 "
       pdb=" C4A FMN A 701 "
    ideal  model  delta    sigma   weight residual
    1.485  1.386  0.099 2.00e-02 2.50e+03 2.43e+01
  bond pdb=" C4A FMN A 701 "
       pdb=" N5  FMN A 701 "
    ideal  model  delta    sigma   weight residual
    1.300  1.378 -0.078 2.00e-02 2.50e+03 1.51e+01
  bond pdb=" O5' FMN A 701 "
       pdb=" P   FMN A 701 "
    ideal  model  delta    sigma   weight residual
    1.676  1.609  0.067 2.00e-02 2.50e+03 1.13e+01
  bond pdb=" C10 FMN A 701 "
       pdb=" N1  FMN A 701 "
    ideal  model  delta    sigma   weight residual
    1.317  1.381 -0.064 2.00e-02 2.50e+03 1.02e+01
  bond pdb=" C10 FMN A 701 "
       pdb=" C4A FMN A 701 "
    ideal  model  delta    sigma   weight residual
    1.443  1.388  0.055 2.00e-02 2.50e+03 7.62e+00
  ... (remaining 5112 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 6830
        1.92 -     3.84: 90
        3.84 -     5.76: 16
        5.76 -     7.68: 4
        7.68 -     9.60: 2
  Bond angle restraints: 6942
  Sorted by residual:
  angle pdb=" N   MET A 346 "
        pdb=" CA  MET A 346 "
        pdb=" C   MET A 346 "
      ideal   model   delta    sigma   weight residual
     108.34  111.94   -3.60 1.31e+00 5.83e-01 7.56e+00
  angle pdb=" CA  LEU A 125 "
        pdb=" CB  LEU A 125 "
        pdb=" CG  LEU A 125 "
      ideal   model   delta    sigma   weight residual
     116.30  125.90   -9.60 3.50e+00 8.16e-02 7.52e+00
  angle pdb=" N   VAL A 464 "
        pdb=" CA  VAL A 464 "
        pdb=" C   VAL A 464 "
      ideal   model   delta    sigma   weight residual
     109.34  103.91    5.43 2.08e+00 2.31e-01 6.82e+00
  angle pdb=" CB  MET A 541 "
        pdb=" CG  MET A 541 "
        pdb=" SD  MET A 541 "
      ideal   model   delta    sigma   weight residual
     112.70  104.97    7.73 3.00e+00 1.11e-01 6.64e+00
  angle pdb=" O3P FMN A 701 "
        pdb=" P   FMN A 701 "
        pdb=" O5' FMN A 701 "
      ideal   model   delta    sigma   weight residual
     102.33  109.54   -7.21 3.00e+00 1.11e-01 5.77e+00
  ... (remaining 6937 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.50: 2927
       32.50 -    65.00: 124
       65.00 -    97.49: 9
       97.49 -   129.99: 0
      129.99 -   162.49: 1
  Dihedral angle restraints: 3061
    sinusoidal: 1278
      harmonic: 1783
  Sorted by residual:
  dihedral pdb=" O5' FAD A 702 "
           pdb=" O3P FAD A 702 "
           pdb=" P   FAD A 702 "
           pdb=" PA  FAD A 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -61.77  100.72 -162.49     1      3.00e+01 1.11e-03 2.08e+01
  dihedral pdb=" CA  PHE A 181 "
           pdb=" C   PHE A 181 "
           pdb=" N   ASN A 182 "
           pdb=" CA  ASN A 182 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.84  -16.16     0      5.00e+00 4.00e-02 1.04e+01
  dihedral pdb=" CB  GLU A 546 "
           pdb=" CG  GLU A 546 "
           pdb=" CD  GLU A 546 "
           pdb=" OE1 GLU A 546 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -84.24   84.24     1      3.00e+01 1.11e-03 9.60e+00
  ... (remaining 3058 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 442
       0.031 -    0.061: 198
       0.061 -    0.092: 54
       0.092 -    0.123: 33
       0.123 -    0.153: 1
  Chirality restraints: 728
  Sorted by residual:
  chirality pdb=" CA  VAL A 464 "
            pdb=" N   VAL A 464 "
            pdb=" C   VAL A 464 "
            pdb=" CB  VAL A 464 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.88e-01
  chirality pdb=" CG  LEU A 351 "
            pdb=" CB  LEU A 351 "
            pdb=" CD1 LEU A 351 "
            pdb=" CD2 LEU A 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.47   -0.12 2.00e-01 2.50e+01 3.74e-01
  chirality pdb=" CA  TRP A 224 "
            pdb=" N   TRP A 224 "
            pdb=" C   TRP A 224 "
            pdb=" CB  TRP A 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.70e-01
  ... (remaining 725 not shown)

  Planarity restraints: 899
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 652 "   -0.025 5.00e-02 4.00e+02   3.75e-02 2.24e+00
        pdb=" N   PRO A 653 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 653 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 653 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 465 "    0.022 5.00e-02 4.00e+02   3.32e-02 1.76e+00
        pdb=" N   PRO A 466 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 466 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 466 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 532 "   -0.021 5.00e-02 4.00e+02   3.21e-02 1.65e+00
        pdb=" N   PRO A 533 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A 533 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 533 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 896 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 393
        2.74 -     3.28: 5041
        3.28 -     3.82: 8498
        3.82 -     4.36: 9841
        4.36 -     4.90: 16898
  Nonbonded interactions: 40671
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A  88 "
            pdb=" O1P FMN A 701 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OH  TYR A 140 "
            pdb=" O2P FMN A 701 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OD2 ASP A 162 "
            pdb=" OG1 THR A 164 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OD1 ASN A  96 "
            pdb=" OG  SER A 111 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OH  TYR A 117 "
            pdb=" OD1 ASN A 356 "
     model   vdw
     2.273 3.040
  ... (remaining 40666 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=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:             1.360
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     17.630
  Find NCS groups from input model:        0.060
  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:             0.010
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.099   5117  Z= 0.173
  Angle     :  0.592   9.600   6942  Z= 0.287
  Chirality :  0.040   0.153    728
  Planarity :  0.004   0.037    899
  Dihedral  : 16.915 162.487   1921
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 22.75 %
    Favored  : 76.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    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: -0.60 (0.33), residues: 611
  helix:  0.64 (0.34), residues: 234
  sheet: -0.70 (0.48), residues: 124
  loop : -1.15 (0.36), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 617 
 HIS   0.002   0.000   HIS A 319 
 PHE   0.010   0.001   PHE A  94 
 TYR   0.010   0.001   TYR A 455 
 ARG   0.004   0.000   ARG A 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16760 (  189)
  hydrogen bonds       : angle       6.92328 (  549)
  covalent geometry    : bond        0.00362 ( 5117)
  covalent geometry    : angle       0.59153 ( 6942)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 0.576 
Fit side-chains
REVERT: A  257 LYS cc_start: 0.7716 (ptmt) cc_final: 0.7095 (tptp)
REVERT: A  271 ASN cc_start: 0.7566 (p0) cc_final: 0.6636 (p0)
REVERT: A  333 GLN cc_start: 0.7732 (mt0) cc_final: 0.7505 (tt0)
REVERT: A  564 TYR cc_start: 0.7881 (t80) cc_final: 0.7544 (t80)
REVERT: A  568 ARG cc_start: 0.6692 (mtp85) cc_final: 0.6353 (mtt-85)
REVERT: A  595 PHE cc_start: 0.7496 (m-10) cc_final: 0.7287 (m-10)
REVERT: A  632 ASP cc_start: 0.6951 (p0) cc_final: 0.6621 (m-30)
  outliers start: 5
  outliers final: 3
  residues processed: 97
  average time/residue: 0.1738
  time to fit residues: 21.5396
Evaluate side-chains
  82 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  605 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    9.9990
   chunk 46 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 24 optimal weight:    0.1980
   chunk 47 optimal weight:    0.9980
   chunk 18 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
A 182 ASN
A 486 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.149011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.118566 restraints weight = 6757.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 2.98
r_work: 0.3321 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.1163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5117  Z= 0.139
  Angle     :  0.563   7.327   6942  Z= 0.288
  Chirality :  0.042   0.150    728
  Planarity :  0.004   0.039    899
  Dihedral  :  9.213 171.574    738
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 19.89 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    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: -0.47 (0.34), residues: 611
  helix:  0.78 (0.34), residues: 236
  sheet: -0.58 (0.49), residues: 120
  loop : -1.15 (0.36), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 617 
 HIS   0.003   0.001   HIS A 319 
 PHE   0.012   0.002   PHE A 181 
 TYR   0.018   0.002   TYR A 478 
 ARG   0.005   0.000   ARG A 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03502 (  189)
  hydrogen bonds       : angle       5.09213 (  549)
  covalent geometry    : bond        0.00321 ( 5117)
  covalent geometry    : angle       0.56272 ( 6942)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
REVERT: A  164 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.7919 (p)
REVERT: A  244 GLN cc_start: 0.8435 (tp40) cc_final: 0.8151 (mm-40)
REVERT: A  247 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7400 (mt)
REVERT: A  257 LYS cc_start: 0.7792 (ptmt) cc_final: 0.7120 (tptp)
REVERT: A  271 ASN cc_start: 0.7487 (p0) cc_final: 0.6756 (p0)
REVERT: A  376 ASP cc_start: 0.8566 (t0) cc_final: 0.8230 (t0)
REVERT: A  506 ARG cc_start: 0.5829 (mtm-85) cc_final: 0.5071 (mmm160)
REVERT: A  564 TYR cc_start: 0.8032 (t80) cc_final: 0.7699 (t80)
REVERT: A  632 ASP cc_start: 0.6949 (p0) cc_final: 0.6613 (m-30)
REVERT: A  664 LYS cc_start: 0.8929 (mmtp) cc_final: 0.8662 (mmtt)
  outliers start: 21
  outliers final: 9
  residues processed: 95
  average time/residue: 0.2287
  time to fit residues: 28.3284
Evaluate side-chains
  85 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  486 ASN
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  630 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 12 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
A 432 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.144983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.112784 restraints weight = 6955.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 3.08
r_work: 0.3248 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.1493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5117  Z= 0.179
  Angle     :  0.571   7.374   6942  Z= 0.293
  Chirality :  0.043   0.183    728
  Planarity :  0.004   0.037    899
  Dihedral  :  9.577 178.044    737
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 20.84 %
    Favored  : 75.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    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: -0.57 (0.34), residues: 611
  helix:  0.71 (0.34), residues: 236
  sheet: -0.75 (0.49), residues: 120
  loop : -1.16 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 219 
 HIS   0.005   0.001   HIS A 319 
 PHE   0.015   0.002   PHE A 518 
 TYR   0.013   0.002   TYR A 575 
 ARG   0.005   0.000   ARG A 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03542 (  189)
  hydrogen bonds       : angle       4.83222 (  549)
  covalent geometry    : bond        0.00417 ( 5117)
  covalent geometry    : angle       0.57138 ( 6942)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
REVERT: A  214 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7826 (mm-30)
REVERT: A  244 GLN cc_start: 0.8479 (tp40) cc_final: 0.8200 (mm-40)
REVERT: A  247 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7398 (mt)
REVERT: A  257 LYS cc_start: 0.7920 (ptmt) cc_final: 0.7278 (tptp)
REVERT: A  271 ASN cc_start: 0.7518 (p0) cc_final: 0.6815 (p0)
REVERT: A  376 ASP cc_start: 0.8585 (t0) cc_final: 0.8209 (t0)
REVERT: A  422 GLU cc_start: 0.8233 (tp30) cc_final: 0.7995 (tp30)
REVERT: A  506 ARG cc_start: 0.5894 (mtm-85) cc_final: 0.5136 (mmm160)
REVERT: A  564 TYR cc_start: 0.8121 (t80) cc_final: 0.7750 (t80)
REVERT: A  595 PHE cc_start: 0.7340 (m-10) cc_final: 0.7129 (m-10)
REVERT: A  632 ASP cc_start: 0.6989 (p0) cc_final: 0.6634 (m-30)
  outliers start: 20
  outliers final: 12
  residues processed: 98
  average time/residue: 0.1697
  time to fit residues: 21.8500
Evaluate side-chains
  91 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  182 ASN
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  630 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 6 optimal weight:    0.0770
   chunk 28 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 24 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.6342

-------------------------------------------------------------------------------
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 = 0.3870 r_free = 0.3870 target = 0.146235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.115191 restraints weight = 6990.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 3.04
r_work: 0.3351 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5117  Z= 0.104
  Angle     :  0.520   6.642   6942  Z= 0.266
  Chirality :  0.041   0.166    728
  Planarity :  0.004   0.038    899
  Dihedral  :  9.362 176.014    737
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 20.65 %
    Favored  : 75.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    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: -0.42 (0.34), residues: 611
  helix:  0.85 (0.34), residues: 237
  sheet: -0.56 (0.51), residues: 113
  loop : -1.16 (0.36), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 419 
 HIS   0.003   0.000   HIS A 319 
 PHE   0.022   0.002   PHE A 201 
 TYR   0.015   0.001   TYR A 187 
 ARG   0.004   0.000   ARG A 514 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02946 (  189)
  hydrogen bonds       : angle       4.65351 (  549)
  covalent geometry    : bond        0.00236 ( 5117)
  covalent geometry    : angle       0.51957 ( 6942)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
REVERT: A  164 THR cc_start: 0.8243 (m) cc_final: 0.7762 (p)
REVERT: A  244 GLN cc_start: 0.8472 (tp40) cc_final: 0.8149 (mm-40)
REVERT: A  247 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7382 (mt)
REVERT: A  257 LYS cc_start: 0.7833 (ptmt) cc_final: 0.7148 (tptp)
REVERT: A  271 ASN cc_start: 0.7487 (p0) cc_final: 0.6824 (p0)
REVERT: A  376 ASP cc_start: 0.8547 (t0) cc_final: 0.8180 (t0)
REVERT: A  422 GLU cc_start: 0.8225 (tp30) cc_final: 0.8011 (tp30)
REVERT: A  446 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7650 (tp30)
REVERT: A  506 ARG cc_start: 0.5772 (mtm-85) cc_final: 0.5097 (mmm160)
REVERT: A  564 TYR cc_start: 0.8063 (t80) cc_final: 0.7660 (t80)
REVERT: A  632 ASP cc_start: 0.6873 (p0) cc_final: 0.6592 (m-30)
  outliers start: 22
  outliers final: 13
  residues processed: 99
  average time/residue: 0.1744
  time to fit residues: 22.7961
Evaluate side-chains
  94 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  182 ASN
Chi-restraints excluded: chain A residue  193 GLU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  630 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 24 optimal weight:    0.0030
   chunk 39 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 53 optimal weight:    8.9990
   chunk 1 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0770
   chunk 27 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.6950

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 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 = 0.3877 r_free = 0.3877 target = 0.146499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.114984 restraints weight = 7081.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 3.11
r_work: 0.3333 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5117  Z= 0.104
  Angle     :  0.518   8.506   6942  Z= 0.261
  Chirality :  0.040   0.161    728
  Planarity :  0.004   0.039    899
  Dihedral  :  9.211 173.619    737
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 20.84 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    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: -0.39 (0.34), residues: 611
  helix:  0.91 (0.34), residues: 236
  sheet: -0.53 (0.51), residues: 113
  loop : -1.18 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 617 
 HIS   0.002   0.000   HIS A 319 
 PHE   0.026   0.002   PHE A 201 
 TYR   0.015   0.001   TYR A 367 
 ARG   0.004   0.000   ARG A 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02853 (  189)
  hydrogen bonds       : angle       4.55601 (  549)
  covalent geometry    : bond        0.00239 ( 5117)
  covalent geometry    : angle       0.51807 ( 6942)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 86
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 THR cc_start: 0.8196 (m) cc_final: 0.7715 (p)
REVERT: A  244 GLN cc_start: 0.8540 (tp40) cc_final: 0.8267 (mm-40)
REVERT: A  247 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7359 (mt)
REVERT: A  257 LYS cc_start: 0.7834 (ptmt) cc_final: 0.7164 (tptp)
REVERT: A  271 ASN cc_start: 0.7485 (p0) cc_final: 0.6807 (p0)
REVERT: A  376 ASP cc_start: 0.8540 (t0) cc_final: 0.8181 (t0)
REVERT: A  391 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.6295 (pm20)
REVERT: A  422 GLU cc_start: 0.8263 (tp30) cc_final: 0.8058 (tp30)
REVERT: A  446 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7625 (tp30)
REVERT: A  506 ARG cc_start: 0.5743 (mtm-85) cc_final: 0.5058 (mmm160)
REVERT: A  564 TYR cc_start: 0.8033 (t80) cc_final: 0.7568 (t80)
REVERT: A  632 ASP cc_start: 0.6850 (p0) cc_final: 0.6607 (m-30)
  outliers start: 23
  outliers final: 14
  residues processed: 103
  average time/residue: 0.1820
  time to fit residues: 25.0638
Evaluate side-chains
  94 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  182 ASN
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  391 GLN
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  630 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 10 optimal weight:    0.2980
   chunk 53 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 54 optimal weight:    7.9990
   chunk 16 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 59 optimal weight:   10.0000
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 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 = 0.3822 r_free = 0.3822 target = 0.142387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.110219 restraints weight = 7013.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 3.06
r_work: 0.3208 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   5117  Z= 0.206
  Angle     :  0.618   9.891   6942  Z= 0.311
  Chirality :  0.044   0.167    728
  Planarity :  0.004   0.044    899
  Dihedral  :  9.651 168.499    737
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 21.61 %
    Favored  : 73.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    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: -0.64 (0.33), residues: 611
  helix:  0.68 (0.34), residues: 236
  sheet: -0.87 (0.48), residues: 120
  loop : -1.18 (0.36), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 617 
 HIS   0.006   0.001   HIS A 319 
 PHE   0.033   0.002   PHE A 201 
 TYR   0.015   0.002   TYR A 373 
 ARG   0.005   0.001   ARG A 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03593 (  189)
  hydrogen bonds       : angle       4.77829 (  549)
  covalent geometry    : bond        0.00482 ( 5117)
  covalent geometry    : angle       0.61815 ( 6942)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 79
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
REVERT: A  202 GLU cc_start: 0.8248 (pm20) cc_final: 0.7973 (pm20)
REVERT: A  247 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7368 (mt)
REVERT: A  257 LYS cc_start: 0.7950 (ptmt) cc_final: 0.7566 (tptp)
REVERT: A  271 ASN cc_start: 0.7533 (p0) cc_final: 0.6866 (p0)
REVERT: A  376 ASP cc_start: 0.8527 (t0) cc_final: 0.8153 (t0)
REVERT: A  391 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.6464 (pm20)
REVERT: A  398 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6368 (mt-10)
REVERT: A  422 GLU cc_start: 0.8318 (tp30) cc_final: 0.8109 (tp30)
REVERT: A  446 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7721 (tp30)
REVERT: A  506 ARG cc_start: 0.5891 (mtm-85) cc_final: 0.5170 (mmm160)
REVERT: A  564 TYR cc_start: 0.8125 (t80) cc_final: 0.7714 (t80)
REVERT: A  632 ASP cc_start: 0.6928 (p0) cc_final: 0.6583 (m-30)
  outliers start: 24
  outliers final: 12
  residues processed: 97
  average time/residue: 0.2053
  time to fit residues: 27.2891
Evaluate side-chains
  89 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  182 ASN
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  391 GLN
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  630 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 41 optimal weight:    8.9990
   chunk 27 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0970
   chunk 48 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 615 HIS
A 642 ASN
A 658 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.143941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.111930 restraints weight = 6941.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 3.04
r_work: 0.3242 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5117  Z= 0.139
  Angle     :  0.588   9.636   6942  Z= 0.292
  Chirality :  0.042   0.165    728
  Planarity :  0.004   0.045    899
  Dihedral  :  9.649 171.187    737
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 22.75 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    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: -0.61 (0.33), residues: 611
  helix:  0.69 (0.34), residues: 237
  sheet: -0.90 (0.49), residues: 120
  loop : -1.11 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 617 
 HIS   0.005   0.001   HIS A 319 
 PHE   0.028   0.002   PHE A 201 
 TYR   0.014   0.001   TYR A 478 
 ARG   0.005   0.000   ARG A 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03163 (  189)
  hydrogen bonds       : angle       4.69801 (  549)
  covalent geometry    : bond        0.00328 ( 5117)
  covalent geometry    : angle       0.58754 ( 6942)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 MET cc_start: 0.7286 (tpp) cc_final: 0.7047 (tpp)
REVERT: A  202 GLU cc_start: 0.8256 (pm20) cc_final: 0.8001 (pm20)
REVERT: A  244 GLN cc_start: 0.8651 (tp40) cc_final: 0.8329 (mm-40)
REVERT: A  247 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7388 (mt)
REVERT: A  257 LYS cc_start: 0.7915 (ptmt) cc_final: 0.7525 (tptp)
REVERT: A  271 ASN cc_start: 0.7492 (p0) cc_final: 0.6826 (p0)
REVERT: A  374 TYR cc_start: 0.8919 (m-80) cc_final: 0.8708 (m-10)
REVERT: A  376 ASP cc_start: 0.8537 (t0) cc_final: 0.8142 (t0)
REVERT: A  391 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.6425 (pm20)
REVERT: A  398 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6274 (mt-10)
REVERT: A  506 ARG cc_start: 0.5842 (mtm-85) cc_final: 0.5174 (mmm160)
REVERT: A  564 TYR cc_start: 0.8055 (t80) cc_final: 0.7682 (t80)
REVERT: A  595 PHE cc_start: 0.7463 (m-10) cc_final: 0.7201 (m-10)
REVERT: A  632 ASP cc_start: 0.6911 (p0) cc_final: 0.6610 (m-30)
  outliers start: 21
  outliers final: 16
  residues processed: 96
  average time/residue: 0.1662
  time to fit residues: 20.5218
Evaluate side-chains
  95 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  182 ASN
Chi-restraints excluded: chain A residue  193 GLU
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  391 GLN
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  630 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 54 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 642 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.144553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.112365 restraints weight = 7007.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 3.08
r_work: 0.3241 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5117  Z= 0.142
  Angle     :  0.587   9.413   6942  Z= 0.291
  Chirality :  0.042   0.161    728
  Planarity :  0.004   0.044    899
  Dihedral  :  9.666 170.712    737
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 22.37 %
    Favored  : 74.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    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: -0.63 (0.34), residues: 611
  helix:  0.67 (0.34), residues: 237
  sheet: -0.95 (0.49), residues: 120
  loop : -1.11 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 617 
 HIS   0.004   0.001   HIS A 319 
 PHE   0.028   0.002   PHE A 201 
 TYR   0.015   0.001   TYR A 367 
 ARG   0.006   0.000   ARG A 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03092 (  189)
  hydrogen bonds       : angle       4.68303 (  549)
  covalent geometry    : bond        0.00336 ( 5117)
  covalent geometry    : angle       0.58694 ( 6942)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 MET cc_start: 0.7255 (tpp) cc_final: 0.6983 (tpp)
REVERT: A  202 GLU cc_start: 0.8286 (pm20) cc_final: 0.7985 (pm20)
REVERT: A  247 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7397 (mt)
REVERT: A  257 LYS cc_start: 0.7893 (ptmt) cc_final: 0.7536 (tptp)
REVERT: A  271 ASN cc_start: 0.7449 (p0) cc_final: 0.6797 (p0)
REVERT: A  376 ASP cc_start: 0.8528 (t0) cc_final: 0.8131 (t0)
REVERT: A  391 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.6469 (pm20)
REVERT: A  398 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6314 (mt-10)
REVERT: A  506 ARG cc_start: 0.5834 (mtm-85) cc_final: 0.5246 (mmm160)
REVERT: A  564 TYR cc_start: 0.8107 (t80) cc_final: 0.7745 (t80)
REVERT: A  568 ARG cc_start: 0.6612 (mtp85) cc_final: 0.6199 (mtt-85)
REVERT: A  595 PHE cc_start: 0.7409 (m-10) cc_final: 0.7149 (m-10)
REVERT: A  632 ASP cc_start: 0.6924 (p0) cc_final: 0.6638 (m-30)
  outliers start: 19
  outliers final: 16
  residues processed: 93
  average time/residue: 0.1887
  time to fit residues: 22.5290
Evaluate side-chains
  93 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  182 ASN
Chi-restraints excluded: chain A residue  193 GLU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  391 GLN
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  630 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 49 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 29 optimal weight:    0.2980
   chunk 18 optimal weight:    8.9990
   chunk 25 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   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  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 349 ASN
** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 642 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.147316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.115693 restraints weight = 6854.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 3.05
r_work: 0.3298 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5117  Z= 0.107
  Angle     :  0.556   9.427   6942  Z= 0.275
  Chirality :  0.041   0.157    728
  Planarity :  0.004   0.044    899
  Dihedral  :  9.581 178.017    737
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 22.94 %
    Favored  : 73.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    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: -0.49 (0.34), residues: 611
  helix:  0.82 (0.34), residues: 236
  sheet: -0.86 (0.49), residues: 118
  loop : -1.07 (0.37), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 617 
 HIS   0.003   0.000   HIS A 319 
 PHE   0.013   0.001   PHE A 201 
 TYR   0.013   0.001   TYR A 478 
 ARG   0.011   0.000   ARG A 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02764 (  189)
  hydrogen bonds       : angle       4.59652 (  549)
  covalent geometry    : bond        0.00252 ( 5117)
  covalent geometry    : angle       0.55607 ( 6942)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 MET cc_start: 0.6993 (tpp) cc_final: 0.6427 (tpp)
REVERT: A  202 GLU cc_start: 0.8206 (pm20) cc_final: 0.7966 (pm20)
REVERT: A  242 ILE cc_start: 0.8996 (tp) cc_final: 0.8778 (tp)
REVERT: A  244 GLN cc_start: 0.8643 (tp40) cc_final: 0.8365 (mm-40)
REVERT: A  247 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7325 (mt)
REVERT: A  257 LYS cc_start: 0.7840 (ptmt) cc_final: 0.7509 (tptp)
REVERT: A  271 ASN cc_start: 0.7466 (p0) cc_final: 0.6789 (p0)
REVERT: A  376 ASP cc_start: 0.8568 (t0) cc_final: 0.8167 (t0)
REVERT: A  391 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6513 (pm20)
REVERT: A  411 GLU cc_start: 0.8219 (pm20) cc_final: 0.7683 (mm-30)
REVERT: A  506 ARG cc_start: 0.5880 (mtm-85) cc_final: 0.5224 (mmm160)
REVERT: A  564 TYR cc_start: 0.8053 (t80) cc_final: 0.7612 (t80)
REVERT: A  568 ARG cc_start: 0.6585 (mtp85) cc_final: 0.6169 (mtt-85)
  outliers start: 19
  outliers final: 14
  residues processed: 101
  average time/residue: 0.2241
  time to fit residues: 29.1087
Evaluate side-chains
  95 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  182 ASN
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  391 GLN
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  630 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 3 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 36 optimal weight:    0.4980
   chunk 4 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 51 optimal weight:    7.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 642 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.145393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.113481 restraints weight = 7001.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 3.09
r_work: 0.3293 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5117  Z= 0.126
  Angle     :  0.583   9.172   6942  Z= 0.289
  Chirality :  0.042   0.156    728
  Planarity :  0.004   0.046    899
  Dihedral  :  9.522 177.907    737
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 23.52 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    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: -0.51 (0.34), residues: 611
  helix:  0.77 (0.34), residues: 236
  sheet: -0.79 (0.51), residues: 113
  loop : -1.10 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 617 
 HIS   0.003   0.001   HIS A 319 
 PHE   0.022   0.002   PHE A 201 
 TYR   0.023   0.001   TYR A 367 
 ARG   0.007   0.000   ARG A 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02893 (  189)
  hydrogen bonds       : angle       4.65497 (  549)
  covalent geometry    : bond        0.00295 ( 5117)
  covalent geometry    : angle       0.58290 ( 6942)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 MET cc_start: 0.6987 (tpp) cc_final: 0.6413 (tpp)
REVERT: A  242 ILE cc_start: 0.8993 (tp) cc_final: 0.8775 (tp)
REVERT: A  247 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7440 (tt)
REVERT: A  257 LYS cc_start: 0.7809 (ptmt) cc_final: 0.7484 (tptp)
REVERT: A  271 ASN cc_start: 0.7446 (p0) cc_final: 0.6806 (p0)
REVERT: A  376 ASP cc_start: 0.8581 (t0) cc_final: 0.8159 (t0)
REVERT: A  391 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6553 (pm20)
REVERT: A  411 GLU cc_start: 0.8223 (pm20) cc_final: 0.7686 (mm-30)
REVERT: A  422 GLU cc_start: 0.8222 (tp30) cc_final: 0.7998 (tp30)
REVERT: A  506 ARG cc_start: 0.5884 (mtm-85) cc_final: 0.5181 (mmm160)
REVERT: A  564 TYR cc_start: 0.8079 (t80) cc_final: 0.7625 (t80)
REVERT: A  595 PHE cc_start: 0.7262 (m-10) cc_final: 0.6989 (m-10)
  outliers start: 17
  outliers final: 14
  residues processed: 96
  average time/residue: 0.2524
  time to fit residues: 32.9534
Evaluate side-chains
  92 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  182 ASN
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  391 GLN
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  630 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 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 = 0.3854 r_free = 0.3854 target = 0.144685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.113112 restraints weight = 6990.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 3.04
r_work: 0.3308 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.2639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5117  Z= 0.151
  Angle     :  0.638   9.557   6942  Z= 0.320
  Chirality :  0.043   0.158    728
  Planarity :  0.004   0.047    899
  Dihedral  :  9.478 174.009    737
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 22.94 %
    Favored  : 73.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    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: -0.65 (0.33), residues: 611
  helix:  0.69 (0.34), residues: 236
  sheet: -1.03 (0.48), residues: 118
  loop : -1.10 (0.37), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 617 
 HIS   0.004   0.001   HIS A 319 
 PHE   0.025   0.002   PHE A 201 
 TYR   0.027   0.002   TYR A 367 
 ARG   0.010   0.000   ARG A 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03161 (  189)
  hydrogen bonds       : angle       4.68419 (  549)
  covalent geometry    : bond        0.00357 ( 5117)
  covalent geometry    : angle       0.63822 ( 6942)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3886.05 seconds
wall clock time: 70 minutes 24.02 seconds (4224.02 seconds total)