Starting phenix.real_space_refine
on Wed Mar  4 06:58:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wc9_21603/03_2026/6wc9_21603.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wc9_21603/03_2026/6wc9_21603.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wc9_21603/03_2026/6wc9_21603.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wc9_21603/03_2026/6wc9_21603.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wc9_21603/03_2026/6wc9_21603.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wc9_21603/03_2026/6wc9_21603.cif"
  }
  resolution = 2.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.725
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: 6
    Type Number    sf(0)   Gaussians
     K       7      8.98       5
     S      38      5.16       5
     C    3754      2.51       5
     N     938      2.21       5
     O    1072      1.98       5
     H    5904      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 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: 11713
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 5800
          Classifications: {'peptide': 367}
          Link IDs: {'PTRANS': 16, 'TRANS': 350}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 5800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 5800
          Classifications: {'peptide': 367}
          Link IDs: {'PTRANS': 16, 'TRANS': 350}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {'  K': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {'  K': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 53
          Classifications: {'water': 53}
          Link IDs: {None: 52}
    Chain: "B"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 53
          Classifications: {'water': 53}
          Link IDs: {None: 52}
  Time building chain proxies: 2.10, per 1000 atoms: 0.18
  Number of scatterers: 11713
  At special positions: 0
  Unit cell: (104.992, 71.264, 76.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     K       7     19.00
     S      38     16.00
     O    1072      8.00
     N     938      7.00
     C    3754      6.00
     H    5904      1.00
    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: 0.84
  Conformation dependent library (CDL) restraints added in 343.1 milliseconds
  

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1404

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 0 sheets defined
      87.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 49
    Processing helix  chain 'A' and resid 52 through 57
    Processing helix  chain 'A' and resid 66 through 102
      removed outlier: 3.632A  pdb=" N   VAL A  70 " --> pdb=" O   PHE A  66 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   GLN A  71 " --> pdb=" O   ASP A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 121
    Processing helix  chain 'A' and resid 122 through 133
    Processing helix  chain 'A' and resid 137 through 164
    Processing helix  chain 'A' and resid 165 through 168
    Processing helix  chain 'A' and resid 169 through 173
    Processing helix  chain 'A' and resid 257 through 284
      removed outlier: 5.202A  pdb=" N   LEU A 276 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
      removed outlier: 5.293A  pdb=" N   ILE A 277 " --> pdb=" O   ALA A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 295
    Processing helix  chain 'A' and resid 298 through 306
      removed outlier: 3.690A  pdb=" N   ALA A 302 " --> pdb=" O   SER A 298 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 332
      removed outlier: 3.555A  pdb=" N   PHE A 310 " --> pdb=" O   THR A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 353
    Processing helix  chain 'A' and resid 354 through 364
    Processing helix  chain 'A' and resid 368 through 399
      removed outlier: 3.673A  pdb=" N   GLU A 372 " --> pdb=" O   GLN A 368 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   GLN A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 415 through 439
      removed outlier: 5.116A  pdb=" N   TYR A 426 " --> pdb=" O   LYS A 422 " (cutoff:3.500A)
      Proline residue:  A 427  - end of helix
    Processing helix  chain 'A' and resid 443 through 461
      Proline residue:  A 456  - end of helix
    Processing helix  chain 'A' and resid 461 through 508
    Processing helix  chain 'B' and resid 33 through 49
    Processing helix  chain 'B' and resid 52 through 57
    Processing helix  chain 'B' and resid 66 through 102
      removed outlier: 3.632A  pdb=" N   VAL B  70 " --> pdb=" O   PHE B  66 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   GLN B  71 " --> pdb=" O   ASP B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 121
    Processing helix  chain 'B' and resid 122 through 133
    Processing helix  chain 'B' and resid 137 through 164
    Processing helix  chain 'B' and resid 165 through 168
    Processing helix  chain 'B' and resid 169 through 173
    Processing helix  chain 'B' and resid 257 through 284
      removed outlier: 5.202A  pdb=" N   LEU B 276 " --> pdb=" O   VAL B 272 " (cutoff:3.500A)
      removed outlier: 5.293A  pdb=" N   ILE B 277 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 295
    Processing helix  chain 'B' and resid 298 through 306
      removed outlier: 3.690A  pdb=" N   ALA B 302 " --> pdb=" O   SER B 298 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR B 306 " --> pdb=" O   ALA B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 332
      removed outlier: 3.555A  pdb=" N   PHE B 310 " --> pdb=" O   THR B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 353
    Processing helix  chain 'B' and resid 354 through 364
    Processing helix  chain 'B' and resid 368 through 399
      removed outlier: 3.672A  pdb=" N   GLU B 372 " --> pdb=" O   GLN B 368 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   GLN B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 415 through 439
      removed outlier: 5.116A  pdb=" N   TYR B 426 " --> pdb=" O   LYS B 422 " (cutoff:3.500A)
      Proline residue:  B 427  - end of helix
    Processing helix  chain 'B' and resid 443 through 461
      Proline residue:  B 456  - end of helix
    Processing helix  chain 'B' and resid 461 through 476

    466 hydrogen bonds defined for protein.
    1368 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: 2.35

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 5886
        1.03 -     1.22: 18
        1.22 -     1.42: 2380
        1.42 -     1.61: 3392
        1.61 -     1.81: 58
  Bond restraints: 11734
  Sorted by residual:
  bond pdb=" C   THR B 472 "
       pdb=" N   LEU B 473 "
    ideal  model  delta    sigma   weight residual
    1.335  1.544 -0.209 1.32e-02 5.74e+03 2.51e+02
  bond pdb=" C   THR A 472 "
       pdb=" N   LEU A 505 "
    ideal  model  delta    sigma   weight residual
    1.335  1.544 -0.209 1.32e-02 5.74e+03 2.51e+02
  bond pdb=" CB  GLN B  65 "
       pdb=" CG  GLN B  65 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.15e+00
  bond pdb=" CB  GLN A  65 "
       pdb=" CG  GLN A  65 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.15e+00
  bond pdb=" C   VAL B 409 "
       pdb=" O   VAL B 409 "
    ideal  model  delta    sigma   weight residual
    1.236  1.226  0.010 1.19e-02 7.06e+03 6.92e-01
  ... (remaining 11729 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.10: 19807
        1.10 -     2.21: 1381
        2.21 -     3.31: 54
        3.31 -     4.41: 23
        4.41 -     5.51: 3
  Bond angle restraints: 21268
  Sorted by residual:
  angle pdb=" N   PHE A  66 "
        pdb=" CA  PHE A  66 "
        pdb=" C   PHE A  66 "
      ideal   model   delta    sigma   weight residual
     112.72  109.17    3.55 1.36e+00 5.41e-01 6.80e+00
  angle pdb=" N   PHE B  66 "
        pdb=" CA  PHE B  66 "
        pdb=" C   PHE B  66 "
      ideal   model   delta    sigma   weight residual
     112.72  109.17    3.55 1.36e+00 5.41e-01 6.80e+00
  angle pdb=" CA  TRP A 394 "
        pdb=" CB  TRP A 394 "
        pdb=" CG  TRP A 394 "
      ideal   model   delta    sigma   weight residual
     113.60  117.90   -4.30 1.90e+00 2.77e-01 5.13e+00
  angle pdb=" CA  TRP B 394 "
        pdb=" CB  TRP B 394 "
        pdb=" CG  TRP B 394 "
      ideal   model   delta    sigma   weight residual
     113.60  117.87   -4.27 1.90e+00 2.77e-01 5.06e+00
  angle pdb=" CD  GLN A  65 "
        pdb=" CG  GLN A  65 "
        pdb=" HG3 GLN A  65 "
      ideal   model   delta    sigma   weight residual
     108.00  102.49    5.51 3.00e+00 1.11e-01 3.38e+00
  ... (remaining 21263 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.03: 4861
       16.03 -    32.06: 453
       32.06 -    48.10: 128
       48.10 -    64.13: 76
       64.13 -    80.16: 10
  Dihedral angle restraints: 5528
    sinusoidal: 2936
      harmonic: 2592
  Sorted by residual:
  dihedral pdb=" CA  PHE B  99 "
           pdb=" C   PHE B  99 "
           pdb=" N   GLN B 100 "
           pdb=" CA  GLN B 100 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.17   20.83     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" CA  PHE A  99 "
           pdb=" C   PHE A  99 "
           pdb=" N   GLN A 100 "
           pdb=" CA  GLN A 100 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.23   20.77     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" CA  GLN A  65 "
           pdb=" C   GLN A  65 "
           pdb=" N   PHE A  66 "
           pdb=" CA  PHE A  66 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.83   19.17     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 5525 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 552
       0.024 -    0.047: 237
       0.047 -    0.071: 127
       0.071 -    0.094: 30
       0.094 -    0.118: 32
  Chirality restraints: 978
  Sorted by residual:
  chirality pdb=" CA  VAL B 285 "
            pdb=" N   VAL B 285 "
            pdb=" C   VAL B 285 "
            pdb=" CB  VAL B 285 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.47e-01
  chirality pdb=" CA  VAL A 285 "
            pdb=" N   VAL A 285 "
            pdb=" C   VAL A 285 "
            pdb=" CB  VAL A 285 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.47e-01
  chirality pdb=" CA  PHE A  99 "
            pdb=" N   PHE A  99 "
            pdb=" C   PHE A  99 "
            pdb=" CB  PHE A  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.47e-01
  ... (remaining 975 not shown)

  Planarity restraints: 1672
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 472 "    0.007 2.00e-02 2.50e+03   1.42e-02 2.02e+00
        pdb=" N   LEU A 505 "   -0.024 2.00e-02 2.50e+03
        pdb=" CA  LEU A 505 "    0.006 2.00e-02 2.50e+03
        pdb=" H   LEU A 505 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 307 "    0.020 5.00e-02 4.00e+02   3.03e-02 1.47e+00
        pdb=" N   PRO A 308 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 308 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 308 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 307 "   -0.020 5.00e-02 4.00e+02   3.03e-02 1.47e+00
        pdb=" N   PRO B 308 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO B 308 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 308 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1669 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.31: 2625
        2.31 -     3.02: 32108
        3.02 -     3.72: 44488
        3.72 -     4.43: 66574
        4.43 -     5.14: 103031
  Nonbonded interactions: 248826
  Sorted by model distance:
  nonbonded pdb=" HE2 HIS A  95 "
            pdb=" OD1 ASN A 113 "
     model   vdw
     1.601 2.450
  nonbonded pdb=" HE2 HIS B  95 "
            pdb=" OD1 ASN B 113 "
     model   vdw
     1.602 2.450
  nonbonded pdb=" OD1 ASP A 266 "
            pdb=" HE1 TRP A 324 "
     model   vdw
     1.614 2.450
  nonbonded pdb=" OD1 ASP B 266 "
            pdb=" HE1 TRP B 324 "
     model   vdw
     1.614 2.450
  nonbonded pdb=" OE2 GLU A 282 "
            pdb=" HD1 HIS B  57 "
     model   vdw
     1.664 2.450
  ... (remaining 248821 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 30 through 703)
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.430
  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:             0.050
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.130
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.209   5830  Z= 0.346
  Angle     :  0.537   4.603   7946  Z= 0.304
  Chirality :  0.037   0.118    978
  Planarity :  0.003   0.030    974
  Dihedral  : 15.749  80.161   2034
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 15.37 %
    Favored  : 82.52 %
  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: -0.42 (0.30), residues: 726
  helix:  0.31 (0.20), residues: 595
  sheet:  None (None), residues: 0
  loop : -2.68 (0.52), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 367 
 TYR   0.006   0.001   TYR B 359 
 PHE   0.013   0.001   PHE A  99 
 TRP   0.015   0.002   TRP B 394 
 HIS   0.008   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00592 ( 5830)
  covalent geometry    : angle       0.53684 ( 7946)
  hydrogen bonds       : bond        0.12139 (  466)
  hydrogen bonds       : angle       4.86041 ( 1368)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.192 
Fit side-chains
REVERT: A   34 GLN cc_start: 0.7379 (tt0) cc_final: 0.6849 (tm-30)
REVERT: A  106 ASP cc_start: 0.8089 (p0) cc_final: 0.7549 (p0)
REVERT: A  415 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7060 (mm-30)
REVERT: A  444 SER cc_start: 0.6049 (OUTLIER) cc_final: 0.5758 (p)
REVERT: B   34 GLN cc_start: 0.7379 (tt0) cc_final: 0.6851 (tm-30)
REVERT: B  106 ASP cc_start: 0.8093 (p0) cc_final: 0.7540 (p0)
REVERT: B  415 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7061 (mm-30)
REVERT: B  434 PHE cc_start: 0.7190 (t80) cc_final: 0.6963 (t80)
REVERT: B  444 SER cc_start: 0.6032 (OUTLIER) cc_final: 0.5755 (p)
  outliers start: 13
  outliers final: 4
  residues processed: 106
  average time/residue: 1.0262
  time to fit residues: 114.3588
Evaluate side-chains
  87 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  444 SER
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  408 SER
Chi-restraints excluded: chain B residue  444 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
A  64 GLN
A 360 GLN
B  34 GLN
B  64 GLN
B 360 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.168123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.146972 restraints weight = 13941.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 0.87
r_work: 0.3162 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   5830  Z= 0.171
  Angle     :  0.545   4.965   7946  Z= 0.294
  Chirality :  0.038   0.148    978
  Planarity :  0.004   0.038    974
  Dihedral  :  5.059  30.279    786
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 1.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.64 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.31), residues: 726
  helix:  1.46 (0.21), residues: 597
  sheet:  None (None), residues: 0
  loop : -1.95 (0.58), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 474 
 TYR   0.013   0.003   TYR B 359 
 PHE   0.019   0.002   PHE A 389 
 TRP   0.017   0.004   TRP A 324 
 HIS   0.005   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 5830)
  covalent geometry    : angle       0.54455 ( 7946)
  hydrogen bonds       : bond        0.05642 (  466)
  hydrogen bonds       : angle       3.89285 ( 1368)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A   34 GLN cc_start: 0.8325 (tt0) cc_final: 0.7651 (tm-30)
REVERT: A  306 THR cc_start: 0.7766 (p) cc_final: 0.7406 (m)
REVERT: A  408 SER cc_start: 0.8161 (OUTLIER) cc_final: 0.7864 (p)
REVERT: A  415 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7431 (mm-30)
REVERT: B   34 GLN cc_start: 0.8318 (tt0) cc_final: 0.7656 (tm-30)
REVERT: B  306 THR cc_start: 0.7749 (p) cc_final: 0.7392 (m)
REVERT: B  408 SER cc_start: 0.8160 (OUTLIER) cc_final: 0.7859 (p)
REVERT: B  415 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7425 (mm-30)
  outliers start: 14
  outliers final: 4
  residues processed: 98
  average time/residue: 1.0501
  time to fit residues: 108.1499
Evaluate side-chains
  83 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  408 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 360 GLN
B 360 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.166790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.143645 restraints weight = 13919.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 0.88
r_work: 0.3133 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5830  Z= 0.179
  Angle     :  0.538   4.842   7946  Z= 0.290
  Chirality :  0.039   0.153    978
  Planarity :  0.004   0.040    974
  Dihedral  :  4.960  33.545    784
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 15.21 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.31), residues: 726
  helix:  1.75 (0.21), residues: 597
  sheet:  None (None), residues: 0
  loop : -1.89 (0.56), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 375 
 TYR   0.014   0.003   TYR A 359 
 PHE   0.021   0.002   PHE B  99 
 TRP   0.018   0.004   TRP B 324 
 HIS   0.006   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 5830)
  covalent geometry    : angle       0.53823 ( 7946)
  hydrogen bonds       : bond        0.05701 (  466)
  hydrogen bonds       : angle       3.84362 ( 1368)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 75
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A   34 GLN cc_start: 0.8396 (tt0) cc_final: 0.7657 (tm-30)
REVERT: A  152 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.7987 (t)
REVERT: A  408 SER cc_start: 0.8206 (OUTLIER) cc_final: 0.7919 (p)
REVERT: A  415 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7519 (mm-30)
REVERT: A  444 SER cc_start: 0.6413 (OUTLIER) cc_final: 0.6207 (p)
REVERT: A  460 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8131 (tt)
REVERT: B   34 GLN cc_start: 0.8388 (tt0) cc_final: 0.7655 (tm-30)
REVERT: B  152 VAL cc_start: 0.8291 (OUTLIER) cc_final: 0.7981 (t)
REVERT: B  306 THR cc_start: 0.7806 (p) cc_final: 0.7432 (m)
REVERT: B  408 SER cc_start: 0.8200 (OUTLIER) cc_final: 0.7905 (p)
REVERT: B  415 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7463 (mm-30)
REVERT: B  460 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8152 (tt)
  outliers start: 27
  outliers final: 9
  residues processed: 94
  average time/residue: 1.1344
  time to fit residues: 111.7815
Evaluate side-chains
  88 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  444 SER
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  408 SER
Chi-restraints excluded: chain B residue  426 TYR
Chi-restraints excluded: chain B residue  460 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 4 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9980
   chunk 1 optimal weight:    0.4980
   chunk 17 optimal weight:    0.2980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 360 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.169110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.148855 restraints weight = 13762.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 0.82
r_work: 0.3209 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5830  Z= 0.131
  Angle     :  0.485   4.396   7946  Z= 0.258
  Chirality :  0.036   0.133    978
  Planarity :  0.004   0.039    974
  Dihedral  :  4.694  34.959    784
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 1.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.99 %
    Favored  : 80.42 %
  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:  2.30 (0.32), residues: 726
  helix:  2.16 (0.21), residues: 598
  sheet:  None (None), residues: 0
  loop : -1.68 (0.56), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 506 
 TYR   0.013   0.002   TYR A 359 
 PHE   0.017   0.001   PHE A  99 
 TRP   0.014   0.003   TRP A 324 
 HIS   0.005   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 5830)
  covalent geometry    : angle       0.48542 ( 7946)
  hydrogen bonds       : bond        0.04884 (  466)
  hydrogen bonds       : angle       3.70042 ( 1368)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.8277 (tt0) cc_final: 0.7668 (tm-30)
REVERT: A  152 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.7996 (t)
REVERT: A  306 THR cc_start: 0.7856 (p) cc_final: 0.7445 (m)
REVERT: A  460 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8101 (tt)
REVERT: B   34 GLN cc_start: 0.8261 (tt0) cc_final: 0.7670 (tm-30)
REVERT: B  152 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.7980 (t)
REVERT: B  306 THR cc_start: 0.7852 (p) cc_final: 0.7453 (m)
REVERT: B  460 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8092 (tt)
  outliers start: 16
  outliers final: 7
  residues processed: 89
  average time/residue: 1.0895
  time to fit residues: 101.6772
Evaluate side-chains
  89 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  426 TYR
Chi-restraints excluded: chain B residue  460 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 30 optimal weight:    0.4980
   chunk 41 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3726 r_free = 0.3726 target = 0.166913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.142001 restraints weight = 13800.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 0.96
r_work: 0.3119 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.2706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5830  Z= 0.169
  Angle     :  0.525   4.774   7946  Z= 0.282
  Chirality :  0.038   0.149    978
  Planarity :  0.004   0.039    974
  Dihedral  :  4.717  36.614    782
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 2.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 17.31 %
    Favored  : 79.29 %
  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:  2.16 (0.31), residues: 726
  helix:  2.05 (0.21), residues: 599
  sheet:  None (None), residues: 0
  loop : -1.64 (0.55), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 260 
 TYR   0.014   0.002   TYR B 359 
 PHE   0.023   0.002   PHE B  99 
 TRP   0.017   0.003   TRP A 324 
 HIS   0.006   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 5830)
  covalent geometry    : angle       0.52456 ( 7946)
  hydrogen bonds       : bond        0.05472 (  466)
  hydrogen bonds       : angle       3.76396 ( 1368)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.8375 (tt0) cc_final: 0.7715 (tm-30)
REVERT: A  152 VAL cc_start: 0.8336 (OUTLIER) cc_final: 0.8013 (t)
REVERT: A  306 THR cc_start: 0.7805 (p) cc_final: 0.7396 (m)
REVERT: A  444 SER cc_start: 0.6371 (OUTLIER) cc_final: 0.6155 (p)
REVERT: B   34 GLN cc_start: 0.8366 (tt0) cc_final: 0.7678 (tm-30)
REVERT: B  152 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.8005 (t)
REVERT: B  306 THR cc_start: 0.7806 (p) cc_final: 0.7398 (m)
  outliers start: 21
  outliers final: 10
  residues processed: 94
  average time/residue: 1.0054
  time to fit residues: 99.4826
Evaluate side-chains
  93 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  444 SER
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  426 TYR
Chi-restraints excluded: chain B residue  444 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 68 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 2 optimal weight:    0.3980
   chunk 61 optimal weight:    0.5980
   chunk 69 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3741 r_free = 0.3741 target = 0.168386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.144432 restraints weight = 13882.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 0.97
r_work: 0.3137 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5830  Z= 0.135
  Angle     :  0.487   4.419   7946  Z= 0.259
  Chirality :  0.037   0.137    978
  Planarity :  0.004   0.039    974
  Dihedral  :  4.583  37.580    782
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 16.99 %
    Favored  : 79.45 %
  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:  2.53 (0.31), residues: 726
  helix:  2.33 (0.21), residues: 598
  sheet:  None (None), residues: 0
  loop : -1.63 (0.54), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 506 
 TYR   0.013   0.002   TYR B 359 
 PHE   0.018   0.001   PHE B  99 
 TRP   0.014   0.003   TRP A 324 
 HIS   0.005   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 5830)
  covalent geometry    : angle       0.48736 ( 7946)
  hydrogen bonds       : bond        0.04936 (  466)
  hydrogen bonds       : angle       3.70217 ( 1368)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.8369 (tt0) cc_final: 0.7686 (tm-30)
REVERT: A  152 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.8004 (t)
REVERT: A  306 THR cc_start: 0.7826 (p) cc_final: 0.7419 (m)
REVERT: A  444 SER cc_start: 0.6392 (OUTLIER) cc_final: 0.6162 (p)
REVERT: B   34 GLN cc_start: 0.8364 (tt0) cc_final: 0.7691 (tm-30)
REVERT: B  152 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8000 (t)
REVERT: B  306 THR cc_start: 0.7833 (p) cc_final: 0.7431 (m)
  outliers start: 22
  outliers final: 11
  residues processed: 95
  average time/residue: 1.0628
  time to fit residues: 106.3193
Evaluate side-chains
  92 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  444 SER
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  426 TYR
Chi-restraints excluded: chain B residue  444 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.3724 r_free = 0.3724 target = 0.166767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.146293 restraints weight = 13875.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 0.88
r_work: 0.3180 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5830  Z= 0.171
  Angle     :  0.529   4.921   7946  Z= 0.285
  Chirality :  0.038   0.151    978
  Planarity :  0.004   0.039    974
  Dihedral  :  4.765  39.063    782
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 17.15 %
    Favored  : 79.29 %
  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:  2.26 (0.31), residues: 726
  helix:  2.11 (0.21), residues: 599
  sheet:  None (None), residues: 0
  loop : -1.55 (0.54), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 474 
 TYR   0.015   0.003   TYR B 359 
 PHE   0.024   0.002   PHE B  99 
 TRP   0.017   0.004   TRP A 324 
 HIS   0.006   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 5830)
  covalent geometry    : angle       0.52920 ( 7946)
  hydrogen bonds       : bond        0.05528 (  466)
  hydrogen bonds       : angle       3.77885 ( 1368)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.8610 (tt0) cc_final: 0.7752 (tm-30)
REVERT: A  129 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8465 (mt)
REVERT: A  152 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.8020 (t)
REVERT: A  306 THR cc_start: 0.7803 (p) cc_final: 0.7419 (m)
REVERT: A  444 SER cc_start: 0.6455 (OUTLIER) cc_final: 0.6194 (p)
REVERT: B   34 GLN cc_start: 0.8608 (tt0) cc_final: 0.7757 (tm-30)
REVERT: B  152 VAL cc_start: 0.8348 (OUTLIER) cc_final: 0.8019 (t)
REVERT: B  306 THR cc_start: 0.7808 (p) cc_final: 0.7429 (m)
REVERT: B  363 SER cc_start: 0.7807 (OUTLIER) cc_final: 0.7533 (m)
  outliers start: 22
  outliers final: 10
  residues processed: 95
  average time/residue: 1.0540
  time to fit residues: 105.5566
Evaluate side-chains
  94 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  444 SER
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  426 TYR
Chi-restraints excluded: chain B residue  444 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0370
   chunk 50 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.7858

-------------------------------------------------------------------------------
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 = 0.3725 r_free = 0.3725 target = 0.167032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.142080 restraints weight = 13932.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 1.01
r_work: 0.3112 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5830  Z= 0.152
  Angle     :  0.507   4.472   7946  Z= 0.271
  Chirality :  0.037   0.146    978
  Planarity :  0.004   0.039    974
  Dihedral  :  4.694  40.011    782
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 17.80 %
    Favored  : 78.80 %
  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:  2.42 (0.31), residues: 726
  helix:  2.21 (0.21), residues: 599
  sheet:  None (None), residues: 0
  loop : -1.48 (0.55), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 474 
 TYR   0.014   0.002   TYR B 359 
 PHE   0.020   0.002   PHE A  99 
 TRP   0.016   0.003   TRP A 324 
 HIS   0.005   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 5830)
  covalent geometry    : angle       0.50723 ( 7946)
  hydrogen bonds       : bond        0.05214 (  466)
  hydrogen bonds       : angle       3.75600 ( 1368)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.8424 (tt0) cc_final: 0.7700 (tm-30)
REVERT: A  129 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8434 (mt)
REVERT: A  152 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.8022 (t)
REVERT: A  306 THR cc_start: 0.7831 (p) cc_final: 0.7419 (m)
REVERT: A  363 SER cc_start: 0.7753 (OUTLIER) cc_final: 0.7428 (m)
REVERT: A  408 SER cc_start: 0.8220 (OUTLIER) cc_final: 0.7899 (p)
REVERT: A  444 SER cc_start: 0.6411 (OUTLIER) cc_final: 0.6169 (p)
REVERT: B   34 GLN cc_start: 0.8403 (tt0) cc_final: 0.7704 (tm-30)
REVERT: B  152 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8016 (t)
REVERT: B  306 THR cc_start: 0.7837 (p) cc_final: 0.7425 (m)
REVERT: B  363 SER cc_start: 0.7738 (OUTLIER) cc_final: 0.7432 (m)
REVERT: B  408 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7894 (p)
  outliers start: 21
  outliers final: 9
  residues processed: 95
  average time/residue: 0.9823
  time to fit residues: 98.3774
Evaluate side-chains
  96 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  444 SER
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  408 SER
Chi-restraints excluded: chain B residue  426 TYR
Chi-restraints excluded: chain B residue  444 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 53 optimal weight:    0.4980
   chunk 60 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3728 r_free = 0.3728 target = 0.167330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.143753 restraints weight = 13889.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 0.98
r_work: 0.3127 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5830  Z= 0.148
  Angle     :  0.504   4.522   7946  Z= 0.270
  Chirality :  0.037   0.144    978
  Planarity :  0.004   0.039    974
  Dihedral  :  4.681  40.960    782
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 17.64 %
    Favored  : 78.96 %
  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:  2.49 (0.31), residues: 726
  helix:  2.26 (0.21), residues: 599
  sheet:  None (None), residues: 0
  loop : -1.41 (0.56), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 463 
 TYR   0.014   0.002   TYR B 359 
 PHE   0.020   0.002   PHE B  99 
 TRP   0.016   0.003   TRP A 324 
 HIS   0.005   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 5830)
  covalent geometry    : angle       0.50422 ( 7946)
  hydrogen bonds       : bond        0.05152 (  466)
  hydrogen bonds       : angle       3.73294 ( 1368)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.8402 (tt0) cc_final: 0.7695 (tm-30)
REVERT: A  129 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8436 (mt)
REVERT: A  152 VAL cc_start: 0.8348 (OUTLIER) cc_final: 0.8011 (t)
REVERT: A  306 THR cc_start: 0.7840 (p) cc_final: 0.7425 (m)
REVERT: A  363 SER cc_start: 0.7753 (OUTLIER) cc_final: 0.7435 (m)
REVERT: A  408 SER cc_start: 0.8227 (OUTLIER) cc_final: 0.7908 (p)
REVERT: A  444 SER cc_start: 0.6402 (OUTLIER) cc_final: 0.6163 (p)
REVERT: B   34 GLN cc_start: 0.8372 (tt0) cc_final: 0.7690 (tm-30)
REVERT: B  152 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8004 (t)
REVERT: B  306 THR cc_start: 0.7840 (p) cc_final: 0.7420 (m)
REVERT: B  363 SER cc_start: 0.7728 (OUTLIER) cc_final: 0.7434 (m)
REVERT: B  408 SER cc_start: 0.8218 (OUTLIER) cc_final: 0.7898 (p)
  outliers start: 21
  outliers final: 9
  residues processed: 96
  average time/residue: 0.9987
  time to fit residues: 101.2580
Evaluate side-chains
  96 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  444 SER
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  408 SER
Chi-restraints excluded: chain B residue  426 TYR
Chi-restraints excluded: chain B residue  444 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0980
   chunk 10 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 7 optimal weight:    0.3980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 360 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.167583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.141905 restraints weight = 13877.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 0.85
r_work: 0.3115 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5830  Z= 0.133
  Angle     :  0.490   4.604   7946  Z= 0.261
  Chirality :  0.036   0.136    978
  Planarity :  0.004   0.040    974
  Dihedral  :  4.615  41.227    782
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 18.77 %
    Favored  : 78.48 %
  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:  2.66 (0.31), residues: 726
  helix:  2.35 (0.21), residues: 601
  sheet:  None (None), residues: 0
  loop : -1.33 (0.57), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 474 
 TYR   0.013   0.002   TYR B 359 
 PHE   0.018   0.001   PHE B  99 
 TRP   0.014   0.003   TRP A 324 
 HIS   0.004   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 5830)
  covalent geometry    : angle       0.48954 ( 7946)
  hydrogen bonds       : bond        0.04894 (  466)
  hydrogen bonds       : angle       3.69778 ( 1368)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 GLN cc_start: 0.8418 (tt0) cc_final: 0.7683 (tm-30)
REVERT: A  152 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.8007 (t)
REVERT: A  306 THR cc_start: 0.7834 (p) cc_final: 0.7420 (m)
REVERT: A  363 SER cc_start: 0.7730 (OUTLIER) cc_final: 0.7428 (m)
REVERT: A  408 SER cc_start: 0.8210 (OUTLIER) cc_final: 0.7903 (p)
REVERT: A  444 SER cc_start: 0.6375 (OUTLIER) cc_final: 0.6128 (p)
REVERT: B   34 GLN cc_start: 0.8404 (tt0) cc_final: 0.7676 (tm-30)
REVERT: B  152 VAL cc_start: 0.8335 (OUTLIER) cc_final: 0.7999 (t)
REVERT: B  306 THR cc_start: 0.7841 (p) cc_final: 0.7431 (m)
REVERT: B  363 SER cc_start: 0.7729 (OUTLIER) cc_final: 0.7440 (m)
REVERT: B  408 SER cc_start: 0.8188 (OUTLIER) cc_final: 0.7878 (p)
  outliers start: 17
  outliers final: 9
  residues processed: 92
  average time/residue: 1.0674
  time to fit residues: 103.4494
Evaluate side-chains
  94 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  444 SER
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  371 ASP
Chi-restraints excluded: chain B residue  408 SER
Chi-restraints excluded: chain B residue  426 TYR
Chi-restraints excluded: chain B residue  444 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0870
   chunk 7 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0970
   chunk 38 optimal weight:    0.9990
   chunk 30 optimal weight:    0.2980
   chunk 29 optimal weight:    0.3980
   overall best weight:    0.3356

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

Flipped N/Q/H residues before XYZ refinement:
A 360 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.169541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.148836 restraints weight = 13839.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 0.87
r_work: 0.3202 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5830  Z= 0.107
  Angle     :  0.458   4.740   7946  Z= 0.242
  Chirality :  0.035   0.126    978
  Planarity :  0.004   0.040    974
  Dihedral  :  4.423  40.923    782
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.26 %
    Favored  : 78.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.12 (0.32), residues: 726
  helix:  2.70 (0.21), residues: 599
  sheet:  None (None), residues: 0
  loop : -1.30 (0.56), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 474 
 TYR   0.012   0.002   TYR B 359 
 PHE   0.016   0.001   PHE B  99 
 TRP   0.011   0.002   TRP B 394 
 HIS   0.002   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 5830)
  covalent geometry    : angle       0.45824 ( 7946)
  hydrogen bonds       : bond        0.04298 (  466)
  hydrogen bonds       : angle       3.58869 ( 1368)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3761.74 seconds
wall clock time: 64 minutes 22.78 seconds (3862.78 seconds total)