Starting phenix.real_space_refine
on Wed Mar  4 01:59:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k8c_22726/03_2026/7k8c_22726.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k8c_22726/03_2026/7k8c_22726.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7k8c_22726/03_2026/7k8c_22726.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k8c_22726/03_2026/7k8c_22726.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k8c_22726/03_2026/7k8c_22726.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k8c_22726/03_2026/7k8c_22726.cif"
  }
  resolution = 4.27
  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
-------------------------------------------------------------------------------
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=   0.149
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5524 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    3579      2.51       5
     N     916      2.21       5
     O    1001      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 5524
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5524
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 723, 5516
          Classifications: {'peptide': 723}
          Link IDs: {'PTRANS': 36, 'TRANS': 686}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
      Conformer: "B"
        Number of residues, atoms: 723, 5516
          Classifications: {'peptide': 723}
          Link IDs: {'PTRANS': 36, 'TRANS': 686}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          bond proxies already assigned to first conformer: 5616
  Time building chain proxies: 2.03, per 1000 atoms: 0.37
  Number of scatterers: 5524
  At special positions: 0
  Unit cell: (75.92, 82.16, 109.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O    1001      8.00
     N     916      7.00
     C    3579      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: 0.64
  Conformation dependent library (CDL) restraints added in 420.3 milliseconds
  

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1324

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 2 sheets defined
      73.6% alpha, 3.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 13
      removed outlier: 3.524A  pdb=" N   TRP A   5 " --> pdb=" O   MET A   1 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ARG A  13 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 32
      removed outlier: 4.003A  pdb=" N   GLY A  18 " --> pdb=" O   TYR A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 62
      removed outlier: 3.583A  pdb=" N   ALA A  52 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 101
      removed outlier: 4.202A  pdb=" N   LYS A  89 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   VAL A  90 " --> pdb=" O   TRP A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 114
      removed outlier: 3.816A  pdb=" N   LYS A 113 " --> pdb=" O   GLY A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 124
    Processing helix  chain 'A' and resid 143 through 165
      removed outlier: 3.778A  pdb=" N   ILE A 147 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   VAL A 153 " --> pdb=" O   LYS A 149 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   VAL A 154 " --> pdb=" O   ASN A 150 " (cutoff:3.500A)
      Proline residue:  A 156  - end of helix
      removed outlier: 4.066A  pdb=" N   VAL A 161 " --> pdb=" O   GLU A 157 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   ASN A 162 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   GLY A 163 " --> pdb=" O   GLN A 159 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ASP A 165 " --> pdb=" O   VAL A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 205
      removed outlier: 3.569A  pdb=" N   LEU A 174 " --> pdb=" O   GLY A 170 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   GLU A 190 " --> pdb=" O   GLN A 186 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   VAL A 191 " --> pdb=" O   LYS A 187 " (cutoff:3.500A)
      Proline residue:  A 195  - end of helix
    Processing helix  chain 'A' and resid 207 through 234
      Proline residue:  A 214  - end of helix
    Processing helix  chain 'A' and resid 239 through 243
    Processing helix  chain 'A' and resid 245 through 272
      removed outlier: 3.564A  pdb=" N   ASP A 256 " --> pdb=" O   GLY A 252 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   ARG A 266 " --> pdb=" O   VAL A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 302
      removed outlier: 4.102A  pdb=" N   VAL A 279 " --> pdb=" O   THR A 275 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ARG A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 307
    Processing helix  chain 'A' and resid 309 through 342
    Processing helix  chain 'A' and resid 383 through 400
      removed outlier: 3.717A  pdb=" N   ARG A 400 " --> pdb=" O   VAL A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 420
      removed outlier: 3.551A  pdb=" N   ILE A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
      Proline residue:  A 418  - end of helix
    Processing helix  chain 'A' and resid 428 through 432
      removed outlier: 3.842A  pdb=" N   TYR A 431 " --> pdb=" O   SER A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 449
    Processing helix  chain 'A' and resid 470 through 483
    Processing helix  chain 'A' and resid 525 through 536
    Processing helix  chain 'A' and resid 548 through 583
      removed outlier: 3.548A  pdb=" N   GLU A 553 " --> pdb=" O   THR A 549 " (cutoff:3.500A)
      Proline residue:  A 565  - end of helix
    Processing helix  chain 'A' and resid 586 through 614
      removed outlier: 4.077A  pdb=" N   PHE A 611 " --> pdb=" O   LEU A 607 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   VAL A 612 " --> pdb=" O   THR A 608 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 621
      removed outlier: 3.891A  pdb=" N   MET A 620 " --> pdb=" O   GLY A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 661
      removed outlier: 3.749A  pdb=" N   ILE A 632 " --> pdb=" O   MET A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 695
      removed outlier: 3.569A  pdb=" N   THR A 675 " --> pdb=" O   GLY A 671 " (cutoff:3.500A)
      removed outlier: 5.411A  pdb=" N   ARG A 677 " --> pdb=" O   ALA A 673 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   LEU A 678 " --> pdb=" O   THR A 674 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU A 686 " --> pdb=" O   ALA A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 698 through 722
    Processing helix  chain 'A' and resid 722 through 728
    Processing helix  chain 'A' and resid 729 through 731
      No H-bonds generated for 'chain 'A' and resid 729 through 731'
    Processing helix  chain 'A' and resid 732 through 737
      removed outlier: 4.154A  pdb=" N   TRP A 736 " --> pdb=" O   GLY A 732 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   TRP A 737 " --> pdb=" O   ASP A 733 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 732 through 737'
    Processing helix  chain 'A' and resid 739 through 748
      removed outlier: 3.687A  pdb=" N   VAL A 745 " --> pdb=" O   TRP A 741 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   GLN A 746 " --> pdb=" O   MET A 742 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 136
    Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 500
      removed outlier: 3.646A  pdb=" N   ILE A 516 " --> pdb=" O   LEU A 459 " (cutoff:3.500A)

    384 hydrogen bonds defined for protein.
    1122 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: 0.84

  Time building geometry restraints manager: 0.81 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: 1106
        1.33 -     1.45: 1218
        1.45 -     1.57: 3258
        1.57 -     1.69: 0
        1.69 -     1.81: 54
  Bond restraints: 5636
  Sorted by residual:
  bond pdb=" N   VAL A 279 "
       pdb=" CA  VAL A 279 "
    ideal  model  delta    sigma   weight residual
    1.461  1.429  0.032 1.19e-02 7.06e+03 7.14e+00
  bond pdb=" C   ALA A 526 "
       pdb=" O   ALA A 526 "
    ideal  model  delta    sigma   weight residual
    1.237  1.209  0.028 1.17e-02 7.31e+03 5.71e+00
  bond pdb=" N   ASP A 274 "
       pdb=" CA  ASP A 274 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.29e-02 6.01e+03 5.26e+00
  bond pdb=" CA  ARG A 280 "
       pdb=" C   ARG A 280 "
    ideal  model  delta    sigma   weight residual
    1.524  1.491  0.033 1.44e-02 4.82e+03 5.23e+00
  bond pdb=" CA  TYR A 273 "
       pdb=" C   TYR A 273 "
    ideal  model  delta    sigma   weight residual
    1.523  1.551 -0.028 1.28e-02 6.10e+03 4.92e+00
  ... (remaining 5631 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 7277
        1.54 -     3.09: 280
        3.09 -     4.63: 57
        4.63 -     6.17: 45
        6.17 -     7.72: 10
  Bond angle restraints: 7669
  Sorted by residual:
  angle pdb=" N   ALA A 278 "
        pdb=" CA  ALA A 278 "
        pdb=" C   ALA A 278 "
      ideal   model   delta    sigma   weight residual
     111.28  105.35    5.93 1.09e+00 8.42e-01 2.96e+01
  angle pdb=" N   GLU A 276 "
        pdb=" CA  GLU A 276 "
        pdb=" C   GLU A 276 "
      ideal   model   delta    sigma   weight residual
     111.07  116.87   -5.80 1.07e+00 8.73e-01 2.94e+01
  angle pdb=" N   ALA A 270 "
        pdb=" CA  ALA A 270 "
        pdb=" C   ALA A 270 "
      ideal   model   delta    sigma   weight residual
     111.36  105.56    5.80 1.09e+00 8.42e-01 2.83e+01
  angle pdb=" N   THR A 121 "
        pdb=" CA  THR A 121 "
        pdb=" C   THR A 121 "
      ideal   model   delta    sigma   weight residual
     111.28  116.32   -5.04 1.09e+00 8.42e-01 2.14e+01
  angle pdb=" N   ALA A 527 "
        pdb=" CA  ALA A 527 "
        pdb=" C   ALA A 527 "
      ideal   model   delta    sigma   weight residual
     111.28  106.47    4.81 1.09e+00 8.42e-01 1.95e+01
  ... (remaining 7664 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.93: 3036
       16.93 -    33.86: 260
       33.86 -    50.79: 56
       50.79 -    67.72: 9
       67.72 -    84.66: 4
  Dihedral angle restraints: 3365
    sinusoidal: 1305
      harmonic: 2060
  Sorted by residual:
  dihedral pdb=" C   TYR A 273 "
           pdb=" N   TYR A 273 "
           pdb=" CA  TYR A 273 "
           pdb=" CB  TYR A 273 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.55   11.95     0      2.50e+00 1.60e-01 2.28e+01
  dihedral pdb=" CA  MET A 628 "
           pdb=" C   MET A 628 "
           pdb=" N   ALA A 629 "
           pdb=" CA  ALA A 629 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.55  -23.45     0      5.00e+00 4.00e-02 2.20e+01
  dihedral pdb=" N   TYR A 273 "
           pdb=" C   TYR A 273 "
           pdb=" CA  TYR A 273 "
           pdb=" CB  TYR A 273 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.08  -11.28     0      2.50e+00 1.60e-01 2.03e+01
  ... (remaining 3362 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 868
       0.093 -    0.187: 44
       0.187 -    0.280: 2
       0.280 -    0.373: 0
       0.373 -    0.467: 2
  Chirality restraints: 916
  Sorted by residual:
  chirality pdb=" CA  TYR A 273 "
            pdb=" N   TYR A 273 "
            pdb=" C   TYR A 273 "
            pdb=" CB  TYR A 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.44e+00
  chirality pdb=" CA  ASP A 274 "
            pdb=" N   ASP A 274 "
            pdb=" C   ASP A 274 "
            pdb=" CB  ASP A 274 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.26e+00
  chirality pdb=" CA  VAL A 279 "
            pdb=" N   VAL A 279 "
            pdb=" C   VAL A 279 "
            pdb=" CB  VAL A 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.71   -0.27 2.00e-01 2.50e+01 1.87e+00
  ... (remaining 913 not shown)

  Planarity restraints: 968
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 417 "   -0.056 5.00e-02 4.00e+02   8.52e-02 1.16e+01
        pdb=" N   PRO A 418 "    0.147 5.00e-02 4.00e+02
        pdb=" CA  PRO A 418 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 418 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 406 "    0.041 5.00e-02 4.00e+02   6.27e-02 6.28e+00
        pdb=" N   PRO A 407 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 407 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 407 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 520 "   -0.012 2.00e-02 2.50e+03   2.46e-02 6.07e+00
        pdb=" C   LEU A 520 "    0.043 2.00e-02 2.50e+03
        pdb=" O   LEU A 520 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   GLU A 521 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 965 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 437
        2.74 -     3.28: 6057
        3.28 -     3.82: 9256
        3.82 -     4.36: 9743
        4.36 -     4.90: 16756
  Nonbonded interactions: 42249
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 599 "
            pdb=" OD2 ASP A 715 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" NH1 ARG A  65 "
            pdb=" O   LEU A 139 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" OG1 THR A  74 "
            pdb=" ND1 HIS A 132 "
     model   vdw
     2.331 3.120
  nonbonded pdb=" O   LEU A 598 "
            pdb=" OG  SER A 602 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" O   GLY A 584 "
            pdb=" OG  SER A 585 "
     model   vdw
     2.349 3.040
  ... (remaining 42244 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=0.47 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             0.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.050
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5752
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   0.040   5636  Z= 0.225
  Angle     :  0.838   7.716   7669  Z= 0.465
  Chirality :  0.051   0.467    916
  Planarity :  0.007   0.085    968
  Dihedral  : 13.696  84.656   2041
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  0.68 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.30 %
  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 (0.31), residues: 720
  helix:  0.72 (0.25), residues: 458
  sheet:  0.05 (0.75), residues: 38
  loop : -1.08 (0.41), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 720 
 TYR   0.016   0.001   TYR A  10 
 PHE   0.036   0.002   PHE A 693 
 TRP   0.026   0.001   TRP A 498 
 HIS   0.002   0.000   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 5636)
  covalent geometry    : angle       0.83841 ( 7669)
  hydrogen bonds       : bond        0.14879 (  384)
  hydrogen bonds       : angle       6.18663 ( 1122)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 173
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 MET cc_start: 0.4955 (mmp) cc_final: 0.4507 (mmp)
REVERT: A  324 MET cc_start: 0.7751 (tpp) cc_final: 0.7458 (tpt)
REVERT: A  555 ASP cc_start: 0.7411 (m-30) cc_final: 0.7081 (m-30)
  outliers start: 4
  outliers final: 3
  residues processed: 177
  average time/residue: 0.0633
  time to fit residues: 14.9278
Evaluate side-chains
  156 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 153
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    0.0870
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    8.9990
   overall best weight:    3.0166

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

Flipped N/Q/H residues before XYZ refinement:
A 309 GLN
A 442 GLN
** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4646 r_free = 0.4646 target = 0.253305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.222797 restraints weight = 14164.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.227243 restraints weight = 9038.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.230333 restraints weight = 6118.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.232326 restraints weight = 4968.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.235734 restraints weight = 3596.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.4455
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4459
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4459 r_free = 0.4459    target_work(ls_wunit_k1) = 0.234         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4460 r_free = 0.4460    target_work(ls_wunit_k1) = 0.234         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4460
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6019
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5636  Z= 0.174
  Angle     :  0.737   7.076   7669  Z= 0.375
  Chirality :  0.045   0.200    916
  Planarity :  0.006   0.071    968
  Dihedral  :  4.792  24.295    770
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  2.88 %
    Favored  : 96.95 %
  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:  0.46 (0.31), residues: 720
  helix:  0.96 (0.24), residues: 467
  sheet:  1.06 (0.91), residues: 24
  loop : -1.07 (0.40), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 280 
 TYR   0.023   0.002   TYR A  10 
 PHE   0.027   0.002   PHE A 693 
 TRP   0.023   0.002   TRP A 640 
 HIS   0.003   0.001   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 5636)
  covalent geometry    : angle       0.73688 ( 7669)
  hydrogen bonds       : bond        0.04926 (  384)
  hydrogen bonds       : angle       4.86352 ( 1122)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 MET cc_start: 0.4917 (mmp) cc_final: 0.4396 (mmp)
REVERT: A   43 PHE cc_start: 0.5764 (p90) cc_final: 0.5427 (p90)
REVERT: A  188 ARG cc_start: 0.8521 (tpm170) cc_final: 0.8133 (tpp-160)
REVERT: A  281 ARG cc_start: 0.6793 (mtt180) cc_final: 0.6456 (mtt180)
REVERT: A  555 ASP cc_start: 0.7951 (m-30) cc_final: 0.7686 (m-30)
REVERT: A  560 LEU cc_start: 0.8133 (tt) cc_final: 0.7692 (tt)
REVERT: A  631 MET cc_start: 0.7296 (ptp) cc_final: 0.6479 (ptt)
REVERT: A  653 ARG cc_start: 0.6528 (tmt170) cc_final: 0.6220 (tmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.0675
  time to fit residues: 14.9206
Evaluate side-chains
  140 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 20 optimal weight:   20.0000
   chunk 57 optimal weight:    9.9990
   chunk 1 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 21 optimal weight:    9.9990
   chunk 6 optimal weight:    9.9990
   chunk 11 optimal weight:    0.8980
   chunk 47 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   overall best weight:    3.1786

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

Flipped N/Q/H residues before XYZ refinement:
A  49 GLN
A 243 GLN
A 309 GLN
** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.251411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.225176 restraints weight = 12107.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.229087 restraints weight = 8057.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.231930 restraints weight = 5690.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.233278 restraints weight = 4062.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.234120 restraints weight = 3346.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.4427
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4428
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4428 r_free = 0.4428    target_work(ls_wunit_k1) = 0.231         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4427 r_free = 0.4427    target_work(ls_wunit_k1) = 0.231         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4427
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6098
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5636  Z= 0.172
  Angle     :  0.732   7.128   7669  Z= 0.370
  Chirality :  0.044   0.182    916
  Planarity :  0.006   0.064    968
  Dihedral  :  4.909  25.708    770
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  4.07 %
    Favored  : 95.76 %
  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:  0.50 (0.31), residues: 720
  helix:  1.08 (0.24), residues: 458
  sheet:  0.17 (0.80), residues: 29
  loop : -1.09 (0.40), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 264 
 TYR   0.020   0.002   TYR A  10 
 PHE   0.029   0.002   PHE A 693 
 TRP   0.035   0.002   TRP A 640 
 HIS   0.006   0.001   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 5636)
  covalent geometry    : angle       0.73197 ( 7669)
  hydrogen bonds       : bond        0.04907 (  384)
  hydrogen bonds       : angle       4.79549 ( 1122)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A   20 MET cc_start: 0.5110 (mmp) cc_final: 0.4540 (mmp)
REVERT: A   43 PHE cc_start: 0.5702 (p90) cc_final: 0.5398 (p90)
REVERT: A  188 ARG cc_start: 0.8368 (tpm170) cc_final: 0.7978 (tpp-160)
REVERT: A  257 TYR cc_start: 0.8595 (m-80) cc_final: 0.8339 (m-80)
REVERT: A  281 ARG cc_start: 0.6758 (mtt180) cc_final: 0.6087 (mtt180)
REVERT: A  455 GLU cc_start: 0.7654 (mp0) cc_final: 0.7390 (mp0)
REVERT: A  560 LEU cc_start: 0.8412 (tt) cc_final: 0.8044 (tt)
REVERT: A  598 LEU cc_start: 0.8049 (tp) cc_final: 0.7752 (tp)
REVERT: A  662 MET cc_start: 0.5074 (mmt) cc_final: 0.4659 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.0649
  time to fit residues: 14.3747
Evaluate side-chains
  137 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 64 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 66 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 57 optimal weight:    7.9990
   chunk 26 optimal weight:    8.9990
   chunk 22 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0670
   chunk 20 optimal weight:    0.9990
   overall best weight:    3.2126

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

Flipped N/Q/H residues before XYZ refinement:
A 309 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4611 r_free = 0.4611 target = 0.248431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.219935 restraints weight = 9461.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.224161 restraints weight = 6459.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.227324 restraints weight = 4788.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.229251 restraints weight = 3755.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.230969 restraints weight = 3132.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.4414
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4415
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4415 r_free = 0.4415    target_work(ls_wunit_k1) = 0.229         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4415 r_free = 0.4415    target_work(ls_wunit_k1) = 0.229         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4415
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6145
moved from start:          0.2900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5636  Z= 0.171
  Angle     :  0.749   7.345   7669  Z= 0.378
  Chirality :  0.045   0.148    916
  Planarity :  0.006   0.074    968
  Dihedral  :  4.957  26.141    770
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  1.86 %
    Favored  : 97.97 %
  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:  0.52 (0.31), residues: 720
  helix:  1.10 (0.24), residues: 460
  sheet:  0.12 (0.80), residues: 29
  loop : -1.10 (0.41), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 653 
 TYR   0.017   0.002   TYR A 622 
 PHE   0.029   0.002   PHE A 693 
 TRP   0.043   0.003   TRP A 640 
 HIS   0.003   0.001   HIS A 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 5636)
  covalent geometry    : angle       0.74941 ( 7669)
  hydrogen bonds       : bond        0.04730 (  384)
  hydrogen bonds       : angle       4.82751 ( 1122)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A   20 MET cc_start: 0.4897 (mmp) cc_final: 0.4314 (mmp)
REVERT: A  188 ARG cc_start: 0.8431 (tpm170) cc_final: 0.8055 (tpp-160)
REVERT: A  281 ARG cc_start: 0.6889 (mtt180) cc_final: 0.6196 (mtt180)
REVERT: A  595 MET cc_start: 0.6270 (tpt) cc_final: 0.6021 (tpt)
REVERT: A  662 MET cc_start: 0.4803 (mmt) cc_final: 0.4465 (ttm)
REVERT: A  723 LEU cc_start: 0.6445 (tt) cc_final: 0.5980 (tp)
REVERT: A  742 MET cc_start: 0.1727 (tpt) cc_final: 0.1475 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.0669
  time to fit residues: 15.2484
Evaluate side-chains
  140 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0770
   chunk 58 optimal weight:    0.0980
   chunk 65 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    2.4344

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

Flipped N/Q/H residues before XYZ refinement:
A  49 GLN
A 309 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.248887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.218643 restraints weight = 19227.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.224098 restraints weight = 12215.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.228387 restraints weight = 7250.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.231481 restraints weight = 4715.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.232241 restraints weight = 3767.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.4434
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4434
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4434 r_free = 0.4434    target_work(ls_wunit_k1) = 0.231         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4435 r_free = 0.4435    target_work(ls_wunit_k1) = 0.231         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4435
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6129
moved from start:          0.3072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5636  Z= 0.154
  Angle     :  0.750   7.560   7669  Z= 0.370
  Chirality :  0.044   0.145    916
  Planarity :  0.006   0.062    968
  Dihedral  :  4.911  26.231    770
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.68 %
    Favored  : 99.15 %
  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:  0.58 (0.31), residues: 720
  helix:  1.14 (0.24), residues: 460
  sheet:  0.39 (0.82), residues: 29
  loop : -1.09 (0.41), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 534 
 TYR   0.012   0.001   TYR A 622 
 PHE   0.035   0.003   PHE A 693 
 TRP   0.022   0.002   TRP A 640 
 HIS   0.002   0.001   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 5636)
  covalent geometry    : angle       0.75028 ( 7669)
  hydrogen bonds       : bond        0.04553 (  384)
  hydrogen bonds       : angle       4.75959 ( 1122)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 MET cc_start: 0.4568 (mmp) cc_final: 0.3941 (mmp)
REVERT: A   43 PHE cc_start: 0.5544 (p90) cc_final: 0.5334 (p90)
REVERT: A  281 ARG cc_start: 0.6703 (mtt180) cc_final: 0.6109 (mtt180)
REVERT: A  455 GLU cc_start: 0.7590 (mp0) cc_final: 0.7353 (mp0)
REVERT: A  487 PHE cc_start: 0.6847 (m-10) cc_final: 0.6596 (m-80)
REVERT: A  504 ASN cc_start: 0.8109 (t0) cc_final: 0.7847 (t0)
REVERT: A  595 MET cc_start: 0.6405 (tpt) cc_final: 0.6085 (tpt)
REVERT: A  662 MET cc_start: 0.5078 (mmt) cc_final: 0.4583 (ttp)
REVERT: A  723 LEU cc_start: 0.6622 (tt) cc_final: 0.6111 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.0640
  time to fit residues: 14.4861
Evaluate side-chains
  141 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 23 optimal weight:   30.0000
   chunk 35 optimal weight:    0.8980
   chunk 12 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 47 optimal weight:   20.0000
   chunk 48 optimal weight:    8.9990
   chunk 66 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 32 optimal weight:   20.0000
   chunk 17 optimal weight:    7.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 309 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4578 r_free = 0.4578 target = 0.245673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.219192 restraints weight = 11363.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.222349 restraints weight = 7226.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.225921 restraints weight = 4959.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.227730 restraints weight = 3286.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.228963 restraints weight = 2691.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.4404
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4404
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4404 r_free = 0.4404    target_work(ls_wunit_k1) = 0.228         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4404 r_free = 0.4404    target_work(ls_wunit_k1) = 0.228         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4404
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6206
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   5636  Z= 0.173
  Angle     :  0.760   7.653   7669  Z= 0.381
  Chirality :  0.044   0.145    916
  Planarity :  0.006   0.066    968
  Dihedral  :  4.990  27.130    770
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  2.03 %
    Favored  : 97.80 %
  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:  0.26 (0.31), residues: 720
  helix:  0.93 (0.24), residues: 465
  sheet:  0.38 (0.86), residues: 31
  loop : -1.41 (0.41), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 264 
 TYR   0.019   0.002   TYR A  10 
 PHE   0.030   0.002   PHE A 693 
 TRP   0.024   0.002   TRP A 498 
 HIS   0.003   0.001   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 5636)
  covalent geometry    : angle       0.76042 ( 7669)
  hydrogen bonds       : bond        0.04741 (  384)
  hydrogen bonds       : angle       4.86999 ( 1122)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 MET cc_start: 0.4774 (mmp) cc_final: 0.4047 (mmp)
REVERT: A   43 PHE cc_start: 0.5843 (p90) cc_final: 0.5610 (p90)
REVERT: A  167 ARG cc_start: 0.8282 (mmm-85) cc_final: 0.6812 (mmm-85)
REVERT: A  281 ARG cc_start: 0.7030 (mtt180) cc_final: 0.6365 (mtt180)
REVERT: A  455 GLU cc_start: 0.7590 (mp0) cc_final: 0.7328 (mp0)
REVERT: A  464 GLU cc_start: 0.6762 (tt0) cc_final: 0.6547 (tt0)
REVERT: A  504 ASN cc_start: 0.8297 (t0) cc_final: 0.8094 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.0730
  time to fit residues: 15.8680
Evaluate side-chains
  145 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 3 optimal weight:    8.9990
   chunk 22 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 60 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 64 optimal weight:    8.9990
   chunk 70 optimal weight:    0.2980
   overall best weight:    3.0588

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

Flipped N/Q/H residues before XYZ refinement:
A  49 GLN
A 309 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.246618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.217738 restraints weight = 17207.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.224328 restraints weight = 11290.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.226777 restraints weight = 6394.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.229013 restraints weight = 4716.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.230878 restraints weight = 3484.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.4418
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4418
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4418 r_free = 0.4418    target_work(ls_wunit_k1) = 0.230         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4419 r_free = 0.4419    target_work(ls_wunit_k1) = 0.230         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4419
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6178
moved from start:          0.3728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5636  Z= 0.164
  Angle     :  0.774  11.424   7669  Z= 0.379
  Chirality :  0.044   0.144    916
  Planarity :  0.006   0.061    968
  Dihedral  :  5.047  27.193    770
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  1.19 %
    Favored  : 98.64 %
  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:  0.40 (0.31), residues: 720
  helix:  0.94 (0.24), residues: 466
  sheet:  0.41 (0.87), residues: 31
  loop : -1.11 (0.42), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 653 
 TYR   0.020   0.002   TYR A  10 
 PHE   0.033   0.002   PHE A 693 
 TRP   0.038   0.003   TRP A 640 
 HIS   0.003   0.001   HIS A 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 5636)
  covalent geometry    : angle       0.77391 ( 7669)
  hydrogen bonds       : bond        0.04645 (  384)
  hydrogen bonds       : angle       4.88548 ( 1122)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 MET cc_start: 0.4787 (mmp) cc_final: 0.4010 (mmp)
REVERT: A  167 ARG cc_start: 0.8267 (mmm-85) cc_final: 0.6885 (mmm-85)
REVERT: A  281 ARG cc_start: 0.6926 (mtt180) cc_final: 0.6671 (mtt180)
REVERT: A  464 GLU cc_start: 0.6824 (tt0) cc_final: 0.6618 (tt0)
REVERT: A  560 LEU cc_start: 0.8298 (tt) cc_final: 0.7920 (tt)
REVERT: A  598 LEU cc_start: 0.8181 (tp) cc_final: 0.7813 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.0687
  time to fit residues: 15.1478
Evaluate side-chains
  145 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 33 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 24 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 32 optimal weight:    8.9990
   chunk 23 optimal weight:    8.9990
   chunk 44 optimal weight:    9.9990
   chunk 45 optimal weight:    9.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
A  49 GLN
A 309 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4584 r_free = 0.4584 target = 0.246645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.214351 restraints weight = 17070.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.219989 restraints weight = 10594.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.224815 restraints weight = 6158.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.227387 restraints weight = 4022.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.228837 restraints weight = 3308.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.4385
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4385
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4385 r_free = 0.4385    target_work(ls_wunit_k1) = 0.227         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4385 r_free = 0.4385    target_work(ls_wunit_k1) = 0.227         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4385
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6211
moved from start:          0.3925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5636  Z= 0.163
  Angle     :  0.756   7.230   7669  Z= 0.377
  Chirality :  0.044   0.146    916
  Planarity :  0.006   0.056    968
  Dihedral  :  4.969  27.811    770
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  1.02 %
    Favored  : 98.81 %
  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:  0.20 (0.31), residues: 720
  helix:  0.89 (0.24), residues: 465
  sheet:  0.26 (0.89), residues: 31
  loop : -1.43 (0.41), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 264 
 TYR   0.020   0.002   TYR A  10 
 PHE   0.033   0.002   PHE A 693 
 TRP   0.024   0.002   TRP A 498 
 HIS   0.002   0.001   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 5636)
  covalent geometry    : angle       0.75568 ( 7669)
  hydrogen bonds       : bond        0.04654 (  384)
  hydrogen bonds       : angle       4.89248 ( 1122)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 MET cc_start: 0.4855 (mmp) cc_final: 0.4016 (mmp)
REVERT: A   43 PHE cc_start: 0.5894 (p90) cc_final: 0.5640 (p90)
REVERT: A  281 ARG cc_start: 0.7071 (mtt180) cc_final: 0.6784 (mtt180)
REVERT: A  560 LEU cc_start: 0.8238 (tt) cc_final: 0.7862 (tt)
REVERT: A  723 LEU cc_start: 0.6779 (tt) cc_final: 0.6269 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.0667
  time to fit residues: 15.4768
Evaluate side-chains
  147 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 70 optimal weight:    9.9990
   chunk 23 optimal weight:    6.9990
   chunk 19 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 16 optimal weight:   20.0000
   chunk 39 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  49 GLN
A 309 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.242970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.216399 restraints weight = 11628.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.220409 restraints weight = 7763.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.223259 restraints weight = 5077.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.224625 restraints weight = 3644.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.225102 restraints weight = 3010.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.4364
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4364
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4364 r_free = 0.4364    target_work(ls_wunit_k1) = 0.224         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4364 r_free = 0.4364    target_work(ls_wunit_k1) = 0.224         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4364
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6299
moved from start:          0.4238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076   5636  Z= 0.206
  Angle     :  0.822  14.094   7669  Z= 0.409
  Chirality :  0.046   0.197    916
  Planarity :  0.006   0.056    968
  Dihedral  :  5.247  29.241    770
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 13.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.68 %
    Favored  : 99.15 %
  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: -0.00 (0.31), residues: 720
  helix:  0.70 (0.24), residues: 472
  sheet: -0.09 (0.89), residues: 31
  loop : -1.45 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 653 
 TYR   0.023   0.002   TYR A  10 
 PHE   0.034   0.003   PHE A 134 
 TRP   0.064   0.004   TRP A 640 
 HIS   0.004   0.001   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 5636)
  covalent geometry    : angle       0.82216 ( 7669)
  hydrogen bonds       : bond        0.04995 (  384)
  hydrogen bonds       : angle       5.06225 ( 1122)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 MET cc_start: 0.5145 (mmp) cc_final: 0.4252 (mmp)
REVERT: A  281 ARG cc_start: 0.7076 (mtt180) cc_final: 0.6449 (mtt180)
REVERT: A  464 GLU cc_start: 0.7018 (tt0) cc_final: 0.6815 (tt0)
REVERT: A  560 LEU cc_start: 0.8356 (tt) cc_final: 0.8007 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.0682
  time to fit residues: 15.0270
Evaluate side-chains
  140 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 56 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0870
   chunk 23 optimal weight:    0.4980
   chunk 47 optimal weight:    1.9990
   chunk 42 optimal weight:    7.9990
   chunk 71 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 69 optimal weight:    7.9990
   chunk 32 optimal weight:    6.9990
   overall best weight:    2.5164

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

Flipped N/Q/H residues before XYZ refinement:
A  49 GLN
A 309 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.245544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.214202 restraints weight = 17820.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.220125 restraints weight = 11807.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.224298 restraints weight = 6569.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.226573 restraints weight = 4408.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.228251 restraints weight = 3422.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.4380
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4381
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4381 r_free = 0.4381    target_work(ls_wunit_k1) = 0.226         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4381 r_free = 0.4381    target_work(ls_wunit_k1) = 0.226         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4381
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6236
moved from start:          0.4258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5636  Z= 0.163
  Angle     :  0.794   8.308   7669  Z= 0.394
  Chirality :  0.046   0.186    916
  Planarity :  0.006   0.063    968
  Dihedral  :  5.096  28.680    770
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.51 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.31), residues: 720
  helix:  0.78 (0.24), residues: 467
  sheet:  0.04 (0.90), residues: 31
  loop : -1.48 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 439 
 TYR   0.019   0.002   TYR A  10 
 PHE   0.035   0.002   PHE A 693 
 TRP   0.026   0.003   TRP A 498 
 HIS   0.003   0.001   HIS A 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 5636)
  covalent geometry    : angle       0.79374 ( 7669)
  hydrogen bonds       : bond        0.04828 (  384)
  hydrogen bonds       : angle       4.97467 ( 1122)

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

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

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1440 Ramachandran restraints generated.
    720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 MET cc_start: 0.5012 (mmp) cc_final: 0.4123 (mmp)
REVERT: A   43 PHE cc_start: 0.6066 (p90) cc_final: 0.5808 (p90)
REVERT: A  461 MET cc_start: 0.7430 (mpp) cc_final: 0.7154 (mpp)
REVERT: A  477 MET cc_start: 0.7731 (mmm) cc_final: 0.7344 (ttm)
REVERT: A  504 ASN cc_start: 0.8256 (t0) cc_final: 0.8047 (t0)
REVERT: A  560 LEU cc_start: 0.8177 (tt) cc_final: 0.7802 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.0650
  time to fit residues: 14.4244
Evaluate side-chains
  143 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 35 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    0.4980
   chunk 59 optimal weight:    9.9990
   chunk 63 optimal weight:   10.0000
   chunk 9 optimal weight:    7.9990
   chunk 45 optimal weight:    4.9990
   chunk 12 optimal weight:    7.9990
   chunk 16 optimal weight:    0.0040
   overall best weight:    3.8998

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

Flipped N/Q/H residues before XYZ refinement:
A  49 GLN
A 309 GLN
A 442 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.242696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.216912 restraints weight = 11793.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.219911 restraints weight = 8305.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.222832 restraints weight = 5530.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.225183 restraints weight = 3902.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.225359 restraints weight = 3188.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.4364
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4364
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4364 r_free = 0.4364    target_work(ls_wunit_k1) = 0.224         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4364 r_free = 0.4364    target_work(ls_wunit_k1) = 0.224         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4364
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6294
moved from start:          0.4468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   5636  Z= 0.187
  Angle     :  0.824   8.034   7669  Z= 0.410
  Chirality :  0.046   0.162    916
  Planarity :  0.007   0.080    968
  Dihedral  :  5.222  29.511    770
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  0.34 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.32), residues: 720
  helix:  0.71 (0.24), residues: 469
  sheet: -0.21 (0.90), residues: 31
  loop : -1.58 (0.42), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 439 
 TYR   0.021   0.002   TYR A  10 
 PHE   0.035   0.002   PHE A 693 
 TRP   0.025   0.003   TRP A 498 
 HIS   0.003   0.001   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 5636)
  covalent geometry    : angle       0.82394 ( 7669)
  hydrogen bonds       : bond        0.04875 (  384)
  hydrogen bonds       : angle       5.01262 ( 1122)

===============================================================================
Job complete
usr+sys time: 1043.53 seconds
wall clock time: 18 minutes 34.99 seconds (1114.99 seconds total)