Starting phenix.real_space_refine
on Tue Feb  3 18:39:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kll_62408/02_2026/9kll_62408.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kll_62408/02_2026/9kll_62408.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kll_62408/02_2026/9kll_62408.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kll_62408/02_2026/9kll_62408.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kll_62408/02_2026/9kll_62408.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kll_62408/02_2026/9kll_62408.cif"
  }
  resolution = 2.7
  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=   0.001
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: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    3840      2.51       5
     N    1047      2.21       5
     O    1158      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6081
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 1237
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 158, 1237
          Classifications: {'peptide': 158}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 153}
    Chain: "C"
      Number of atoms: 4844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 621, 4844
          Classifications: {'peptide': 621}
          Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 588}
          Chain breaks: 1
  Time building chain proxies: 1.09, per 1000 atoms: 0.18
  Number of scatterers: 6081
  At special positions: 0
  Unit cell: (77.38, 84.68, 95.63, 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      36     16.00
     O    1158      8.00
     N    1047      7.00
     C    3840      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: 0.47
  Conformation dependent library (CDL) restraints added in 241.3 milliseconds
  

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1476

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 3 sheets defined
      44.4% alpha, 13.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'B' and resid 20 through 24
    Processing helix  chain 'B' and resid 26 through 33
    Processing helix  chain 'B' and resid 36 through 41
    Processing helix  chain 'B' and resid 48 through 71
    Processing helix  chain 'B' and resid 78 through 91
    Processing helix  chain 'B' and resid 94 through 109
    Processing helix  chain 'B' and resid 110 through 126
    Processing helix  chain 'B' and resid 129 through 138
    Processing helix  chain 'B' and resid 144 through 156
    Processing helix  chain 'C' and resid 36 through 40
    Processing helix  chain 'C' and resid 41 through 51
      removed outlier: 3.511A  pdb=" N   GLY C  51 " --> pdb=" O   ASN C  47 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 54 through 62
    Processing helix  chain 'C' and resid 65 through 76
    Processing helix  chain 'C' and resid 84 through 91
      removed outlier: 4.801A  pdb=" N   PHE C  89 " --> pdb=" O   ARG C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 120 through 132
      removed outlier: 3.782A  pdb=" N   ILE C 124 " --> pdb=" O   ASP C 120 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY C 125 " --> pdb=" O   SER C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 152
      removed outlier: 3.633A  pdb=" N   ILE C 148 " --> pdb=" O   ASP C 144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 153 through 155
      No H-bonds generated for 'chain 'C' and resid 153 through 155'
    Processing helix  chain 'C' and resid 176 through 186
    Processing helix  chain 'C' and resid 202 through 211
      removed outlier: 3.740A  pdb=" N   ALA C 206 " --> pdb=" O   ASP C 202 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   CYS C 211 " --> pdb=" O   ALA C 207 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 218
    Processing helix  chain 'C' and resid 233 through 244
    Processing helix  chain 'C' and resid 265 through 276
    Processing helix  chain 'C' and resid 288 through 291
    Processing helix  chain 'C' and resid 313 through 323
    Processing helix  chain 'C' and resid 341 through 352
      removed outlier: 3.732A  pdb=" N   LEU C 348 " --> pdb=" O   ALA C 344 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ASN C 349 " --> pdb=" O   LEU C 345 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   SER C 350 " --> pdb=" O   GLU C 346 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 375 through 380
    Processing helix  chain 'C' and resid 395 through 406
    Processing helix  chain 'C' and resid 421 through 432
    Processing helix  chain 'C' and resid 448 through 456
    Processing helix  chain 'C' and resid 547 through 553
      removed outlier: 4.585A  pdb=" N   ALA C 551 " --> pdb=" O   THR C 547 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 583 through 590
    Processing helix  chain 'C' and resid 616 through 626
    Processing helix  chain 'C' and resid 652 through 660
    Processing helix  chain 'C' and resid 675 through 683
      removed outlier: 3.572A  pdb=" N   PHE C 682 " --> pdb=" O   PHE C 678 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   LEU C 683 " --> pdb=" O   MET C 679 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 15 through 19
    Processing sheet with id=AA2, first strand: chain 'C' and resid 78 through 80
      removed outlier: 6.911A  pdb=" N   LEU C  79 " --> pdb=" O   ASP C 102 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   LEU C 138 " --> pdb=" O   LYS C 162 " (cutoff:3.500A)
      removed outlier: 7.865A  pdb=" N   VAL C 164 " --> pdb=" O   LEU C 138 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ILE C 140 " --> pdb=" O   VAL C 164 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   LEU C 161 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 5.620A  pdb=" N   LEU C 194 " --> pdb=" O   LEU C 161 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   LEU C 163 " --> pdb=" O   LEU C 194 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   SER C 196 " --> pdb=" O   LEU C 163 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   PHE C 250 " --> pdb=" O   HIS C 283 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   ALA C 285 " --> pdb=" O   PHE C 250 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   ALA C 252 " --> pdb=" O   ALA C 285 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   CYS C 335 " --> pdb=" O   ASP C 286 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   PHE C 363 " --> pdb=" O   LEU C 334 " (cutoff:3.500A)
      removed outlier: 10.210A  pdb=" N   ASN C 336 " --> pdb=" O   PHE C 363 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ASP C 469 " --> pdb=" O   ILE C 441 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   LEU C 466 " --> pdb=" O   SER C 537 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   TRP C 539 " --> pdb=" O   LEU C 466 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   ILE C 468 " --> pdb=" O   TRP C 539 " (cutoff:3.500A)
      removed outlier: 8.954A  pdb=" N   PHE C 541 " --> pdb=" O   ILE C 468 " (cutoff:3.500A)
      removed outlier: 4.756A  pdb=" N   GLY C 601 " --> pdb=" O   VAL C 567 " (cutoff:3.500A)
      removed outlier: 7.947A  pdb=" N   GLY C 569 " --> pdb=" O   GLY C 601 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   ILE C 603 " --> pdb=" O   GLY C 569 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 650 through 651

    268 hydrogen bonds defined for protein.
    756 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: 0.93

  Time building geometry restraints manager: 0.63 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2040
        1.34 -     1.46: 1257
        1.46 -     1.58: 2852
        1.58 -     1.70: 0
        1.70 -     1.81: 49
  Bond restraints: 6198
  Sorted by residual:
  bond pdb=" N   VAL B  73 "
       pdb=" CA  VAL B  73 "
    ideal  model  delta    sigma   weight residual
    1.459  1.500 -0.041 1.25e-02 6.40e+03 1.08e+01
  bond pdb=" N   ALA B  72 "
       pdb=" CA  ALA B  72 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.29e-02 6.01e+03 7.59e+00
  bond pdb=" N   ALA B  76 "
       pdb=" CA  ALA B  76 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.029 1.10e-02 8.26e+03 7.13e+00
  bond pdb=" N   GLU B  74 "
       pdb=" CA  GLU B  74 "
    ideal  model  delta    sigma   weight residual
    1.455  1.485 -0.030 1.18e-02 7.18e+03 6.33e+00
  bond pdb=" CA  SER B  68 "
       pdb=" CB  SER B  68 "
    ideal  model  delta    sigma   weight residual
    1.529  1.493  0.037 1.58e-02 4.01e+03 5.39e+00
  ... (remaining 6193 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 8185
        1.70 -     3.39: 184
        3.39 -     5.09: 27
        5.09 -     6.79: 8
        6.79 -     8.49: 4
  Bond angle restraints: 8408
  Sorted by residual:
  angle pdb=" N   ALA B  70 "
        pdb=" CA  ALA B  70 "
        pdb=" C   ALA B  70 "
      ideal   model   delta    sigma   weight residual
     113.01  106.63    6.38 1.20e+00 6.94e-01 2.83e+01
  angle pdb=" N   GLU B  71 "
        pdb=" CA  GLU B  71 "
        pdb=" CB  GLU B  71 "
      ideal   model   delta    sigma   weight residual
     110.49  102.00    8.49 1.69e+00 3.50e-01 2.52e+01
  angle pdb=" N   GLU B  64 "
        pdb=" CA  GLU B  64 "
        pdb=" C   GLU B  64 "
      ideal   model   delta    sigma   weight residual
     111.03  105.53    5.50 1.11e+00 8.12e-01 2.46e+01
  angle pdb=" N   LEU B  83 "
        pdb=" CA  LEU B  83 "
        pdb=" C   LEU B  83 "
      ideal   model   delta    sigma   weight residual
     111.37  104.05    7.32 1.64e+00 3.72e-01 1.99e+01
  angle pdb=" N   LYS B  69 "
        pdb=" CA  LYS B  69 "
        pdb=" C   LYS B  69 "
      ideal   model   delta    sigma   weight residual
     112.89  107.83    5.06 1.24e+00 6.50e-01 1.67e+01
  ... (remaining 8403 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.26: 3326
       17.26 -    34.52: 338
       34.52 -    51.78: 89
       51.78 -    69.04: 19
       69.04 -    86.30: 7
  Dihedral angle restraints: 3779
    sinusoidal: 1512
      harmonic: 2267
  Sorted by residual:
  dihedral pdb=" CA  ASP B 142 "
           pdb=" CB  ASP B 142 "
           pdb=" CG  ASP B 142 "
           pdb=" OD1 ASP B 142 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.78   59.78     1      2.00e+01 2.50e-03 1.19e+01
  dihedral pdb=" N   GLU B  71 "
           pdb=" C   GLU B  71 "
           pdb=" CA  GLU B  71 "
           pdb=" CB  GLU B  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  114.18    8.62     0      2.50e+00 1.60e-01 1.19e+01
  dihedral pdb=" CG  ARG C 294 "
           pdb=" CD  ARG C 294 "
           pdb=" NE  ARG C 294 "
           pdb=" CZ  ARG C 294 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.35   43.65     2      1.50e+01 4.44e-03 1.02e+01
  ... (remaining 3776 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 695
       0.041 -    0.082: 197
       0.082 -    0.124: 66
       0.124 -    0.165: 6
       0.165 -    0.206: 3
  Chirality restraints: 967
  Sorted by residual:
  chirality pdb=" CA  LEU B  83 "
            pdb=" N   LEU B  83 "
            pdb=" C   LEU B  83 "
            pdb=" CB  LEU B  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  GLU B  71 "
            pdb=" N   GLU B  71 "
            pdb=" C   GLU B  71 "
            pdb=" CB  GLU B  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.30e-01
  chirality pdb=" CA  LYS B  84 "
            pdb=" N   LYS B  84 "
            pdb=" C   LYS B  84 "
            pdb=" CB  LYS B  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.20e-01
  ... (remaining 964 not shown)

  Planarity restraints: 1087
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C 342 "   -0.023 5.00e-02 4.00e+02   3.49e-02 1.95e+00
        pdb=" N   PRO C 343 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO C 343 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO C 343 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 610 "    0.020 5.00e-02 4.00e+02   2.99e-02 1.43e+00
        pdb=" N   PRO C 611 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO C 611 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 611 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS C 244 "    0.019 5.00e-02 4.00e+02   2.91e-02 1.36e+00
        pdb=" N   PRO C 245 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO C 245 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 245 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1084 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1565
        2.80 -     3.33: 5641
        3.33 -     3.85: 10202
        3.85 -     4.38: 12499
        4.38 -     4.90: 20773
  Nonbonded interactions: 50680
  Sorted by model distance:
  nonbonded pdb=" O   LEU C 181 "
            pdb=" OG  SER C 184 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   ASN C 647 "
            pdb=" ND2 ASN C 647 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" O   GLU C 267 "
            pdb=" OG  SER C 271 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" O   SER C 115 "
            pdb=" OG  SER C 121 "
     model   vdw
     2.359 3.040
  nonbonded pdb=" OD2 ASP B 142 "
            pdb=" ND1 HIS C  66 "
     model   vdw
     2.388 3.120
  ... (remaining 50675 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
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     5.880
  Find NCS groups from input model:        0.020
  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:6.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8832
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   0.041   6198  Z= 0.201
  Angle     :  0.643   8.486   8408  Z= 0.381
  Chirality :  0.043   0.206    967
  Planarity :  0.004   0.035   1087
  Dihedral  : 15.609  86.303   2303
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 17.88 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.31 (0.30), residues: 773
  helix:  0.43 (0.30), residues: 311
  sheet: -0.04 (0.47), residues: 134
  loop :  0.32 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 664 
 TYR   0.011   0.002   TYR B 107 
 PHE   0.018   0.001   PHE B  90 
 TRP   0.010   0.001   TRP B  86 
 HIS   0.005   0.001   HIS C 671 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 6198)
  covalent geometry    : angle       0.64298 ( 8408)
  hydrogen bonds       : bond        0.16946 (  268)
  hydrogen bonds       : angle       7.10084 (  756)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 0.239 
Fit side-chains
REVERT: B   32 MET cc_start: 0.8978 (mtm) cc_final: 0.8751 (mtm)
REVERT: B   81 ASP cc_start: 0.8273 (t70) cc_final: 0.7993 (p0)
REVERT: B  150 GLU cc_start: 0.8431 (tp30) cc_final: 0.7871 (tm-30)
REVERT: C   47 ASN cc_start: 0.8881 (t0) cc_final: 0.8638 (t0)
REVERT: C  111 HIS cc_start: 0.9031 (OUTLIER) cc_final: 0.8770 (m170)
REVERT: C  129 ARG cc_start: 0.8474 (ttm-80) cc_final: 0.8104 (ttm-80)
REVERT: C  248 ARG cc_start: 0.8276 (mtm-85) cc_final: 0.7824 (ptm-80)
REVERT: C  301 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8276 (mm-30)
REVERT: C  457 GLU cc_start: 0.8768 (tt0) cc_final: 0.8301 (tp30)
  outliers start: 5
  outliers final: 2
  residues processed: 92
  average time/residue: 0.6151
  time to fit residues: 58.9878
Evaluate side-chains
  68 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 LYS
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue  111 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.4988

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
C 451 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.128977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.086544 restraints weight = 7627.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.2951 rms_B_bonded: 2.35
r_work: 0.2804 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2665 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8801
moved from start:          0.1030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   6198  Z= 0.254
  Angle     :  0.605   6.568   8408  Z= 0.314
  Chirality :  0.045   0.156    967
  Planarity :  0.004   0.037   1087
  Dihedral  :  5.953  56.234    844
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 16.99 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.31), residues: 773
  helix:  0.86 (0.30), residues: 311
  sheet: -0.04 (0.48), residues: 138
  loop :  0.33 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  61 
 TYR   0.016   0.002   TYR C 624 
 PHE   0.014   0.002   PHE C 582 
 TRP   0.009   0.001   TRP C 639 
 HIS   0.005   0.001   HIS C 671 

Details of bonding type rmsd
  covalent geometry    : bond        0.00599 ( 6198)
  covalent geometry    : angle       0.60488 ( 8408)
  hydrogen bonds       : bond        0.05016 (  268)
  hydrogen bonds       : angle       5.49149 (  756)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.167 
Fit side-chains
REVERT: B   32 MET cc_start: 0.9092 (mtm) cc_final: 0.8823 (mtm)
REVERT: B   82 ASP cc_start: 0.7569 (m-30) cc_final: 0.7336 (p0)
REVERT: B   83 LEU cc_start: 0.7812 (mt) cc_final: 0.7529 (tp)
REVERT: B  124 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8295 (mtp)
REVERT: B  150 GLU cc_start: 0.8439 (tp30) cc_final: 0.7878 (tm-30)
REVERT: C   47 ASN cc_start: 0.8880 (t0) cc_final: 0.8614 (t0)
REVERT: C  129 ARG cc_start: 0.8430 (ttm-80) cc_final: 0.7921 (ttm-80)
REVERT: C  177 ASP cc_start: 0.7722 (m-30) cc_final: 0.7176 (m-30)
REVERT: C  248 ARG cc_start: 0.8362 (mtm-85) cc_final: 0.7829 (ptm-80)
REVERT: C  301 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8187 (mm-30)
REVERT: C  457 GLU cc_start: 0.8748 (tt0) cc_final: 0.8237 (tp30)
REVERT: C  528 LYS cc_start: 0.8498 (mttp) cc_final: 0.8139 (mttp)
  outliers start: 20
  outliers final: 12
  residues processed: 85
  average time/residue: 0.5199
  time to fit residues: 46.2995
Evaluate side-chains
  80 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  173 ASP
Chi-restraints excluded: chain C residue  186 CYS
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  650 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 61 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9990
   chunk 75 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B  40 ASN
C  38 ASN
C 111 HIS
C 647 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.131605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.089526 restraints weight = 7603.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 2.34
r_work: 0.2851 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2711 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8763
moved from start:          0.1191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6198  Z= 0.133
  Angle     :  0.525   8.398   8408  Z= 0.270
  Chirality :  0.041   0.143    967
  Planarity :  0.004   0.035   1087
  Dihedral  :  5.191  52.100    840
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 17.59 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.73 (0.31), residues: 773
  helix:  1.10 (0.30), residues: 313
  sheet: -0.09 (0.48), residues: 134
  loop :  0.31 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  61 
 TYR   0.013   0.001   TYR C 624 
 PHE   0.011   0.001   PHE C 582 
 TRP   0.009   0.001   TRP B  86 
 HIS   0.005   0.001   HIS C 671 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6198)
  covalent geometry    : angle       0.52486 ( 8408)
  hydrogen bonds       : bond        0.03845 (  268)
  hydrogen bonds       : angle       5.10562 (  756)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.237 
Fit side-chains
REVERT: B   32 MET cc_start: 0.9116 (mtm) cc_final: 0.8859 (mtm)
REVERT: B   83 LEU cc_start: 0.7872 (mt) cc_final: 0.7587 (tp)
REVERT: B  150 GLU cc_start: 0.8414 (tp30) cc_final: 0.7848 (tm-30)
REVERT: C   47 ASN cc_start: 0.8845 (t0) cc_final: 0.8566 (t0)
REVERT: C  248 ARG cc_start: 0.8340 (mtm-85) cc_final: 0.7896 (ptm-80)
REVERT: C  301 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8101 (mm-30)
REVERT: C  457 GLU cc_start: 0.8715 (tt0) cc_final: 0.8202 (tp30)
  outliers start: 19
  outliers final: 7
  residues processed: 82
  average time/residue: 0.5201
  time to fit residues: 44.6415
Evaluate side-chains
  69 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  173 ASP
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  650 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 70 optimal weight:    0.0010
   chunk 12 optimal weight:    0.0070
   chunk 51 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 47 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 3 optimal weight:   10.0000
   chunk 49 optimal weight:    0.2980
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.3604

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
C 111 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.132965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.091372 restraints weight = 7591.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3029 rms_B_bonded: 2.32
r_work: 0.2884 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2744 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8740
moved from start:          0.1395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6198  Z= 0.105
  Angle     :  0.501   7.027   8408  Z= 0.260
  Chirality :  0.041   0.154    967
  Planarity :  0.004   0.034   1087
  Dihedral  :  4.811  46.918    838
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 17.44 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.81 (0.31), residues: 773
  helix:  1.25 (0.30), residues: 315
  sheet: -0.20 (0.47), residues: 134
  loop :  0.33 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 129 
 TYR   0.010   0.001   TYR C 624 
 PHE   0.014   0.001   PHE B  90 
 TRP   0.016   0.001   TRP B  86 
 HIS   0.004   0.000   HIS C 671 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 6198)
  covalent geometry    : angle       0.50076 ( 8408)
  hydrogen bonds       : bond        0.03513 (  268)
  hydrogen bonds       : angle       4.97715 (  756)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 70
  time to evaluate  : 0.248 
Fit side-chains
REVERT: B   32 MET cc_start: 0.9152 (mtm) cc_final: 0.8861 (mtm)
REVERT: B  150 GLU cc_start: 0.8409 (tp30) cc_final: 0.7838 (tm-30)
REVERT: C   47 ASN cc_start: 0.8817 (t0) cc_final: 0.8542 (t0)
REVERT: C  248 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7913 (ptm-80)
REVERT: C  271 SER cc_start: 0.9079 (m) cc_final: 0.8800 (p)
REVERT: C  301 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8108 (mm-30)
REVERT: C  457 GLU cc_start: 0.8717 (tt0) cc_final: 0.8196 (tp30)
  outliers start: 22
  outliers final: 9
  residues processed: 85
  average time/residue: 0.6015
  time to fit residues: 53.5434
Evaluate side-chains
  75 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain C residue   84 ASN
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  173 ASP
Chi-restraints excluded: chain C residue  248 ARG
Chi-restraints excluded: chain C residue  388 ILE
Chi-restraints excluded: chain C residue  574 LEU
Chi-restraints excluded: chain C residue  650 SER
Chi-restraints excluded: chain C residue  683 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
C 111 HIS
C 364 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.129065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.087027 restraints weight = 7697.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 2.31
r_work: 0.2807 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2667 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8798
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   6198  Z= 0.228
  Angle     :  0.580   8.211   8408  Z= 0.300
  Chirality :  0.044   0.155    967
  Planarity :  0.004   0.031   1087
  Dihedral  :  4.584  18.785    835
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 16.54 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.73 (0.31), residues: 773
  helix:  1.19 (0.30), residues: 313
  sheet: -0.16 (0.47), residues: 136
  loop :  0.24 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 433 
 TYR   0.017   0.002   TYR C 624 
 PHE   0.012   0.002   PHE C 582 
 TRP   0.008   0.001   TRP C 639 
 HIS   0.004   0.001   HIS C 671 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 ( 6198)
  covalent geometry    : angle       0.58008 ( 8408)
  hydrogen bonds       : bond        0.04385 (  268)
  hydrogen bonds       : angle       5.17886 (  756)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 68
  time to evaluate  : 0.188 
Fit side-chains
REVERT: B   32 MET cc_start: 0.9161 (mtm) cc_final: 0.8920 (mtm)
REVERT: B  124 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8286 (mtp)
REVERT: B  150 GLU cc_start: 0.8444 (tp30) cc_final: 0.7815 (tm-30)
REVERT: C   47 ASN cc_start: 0.8831 (t0) cc_final: 0.8568 (t0)
REVERT: C  248 ARG cc_start: 0.8313 (mtm-85) cc_final: 0.7889 (ptm-80)
REVERT: C  301 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8117 (mm-30)
REVERT: C  375 ASP cc_start: 0.8688 (p0) cc_final: 0.8104 (p0)
REVERT: C  428 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.8965 (ttt)
REVERT: C  457 GLU cc_start: 0.8735 (tt0) cc_final: 0.8237 (tp30)
REVERT: C  528 LYS cc_start: 0.8538 (mttp) cc_final: 0.8154 (mttp)
  outliers start: 22
  outliers final: 10
  residues processed: 81
  average time/residue: 0.6123
  time to fit residues: 51.9253
Evaluate side-chains
  77 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  173 ASP
Chi-restraints excluded: chain C residue  388 ILE
Chi-restraints excluded: chain C residue  428 MET
Chi-restraints excluded: chain C residue  573 VAL
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  650 SER
Chi-restraints excluded: chain C residue  683 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0570
   chunk 38 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 2 optimal weight:    6.9990
   chunk 65 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
C 111 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.131720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.089919 restraints weight = 7655.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 2.32
r_work: 0.2856 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8768
moved from start:          0.1499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6198  Z= 0.128
  Angle     :  0.512   7.238   8408  Z= 0.264
  Chirality :  0.041   0.143    967
  Planarity :  0.003   0.032   1087
  Dihedral  :  4.348  19.012    835
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 18.33 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.82 (0.31), residues: 773
  helix:  1.29 (0.30), residues: 314
  sheet: -0.21 (0.47), residues: 136
  loop :  0.30 (0.36), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 433 
 TYR   0.012   0.001   TYR C 624 
 PHE   0.014   0.001   PHE B  90 
 TRP   0.008   0.001   TRP B  86 
 HIS   0.005   0.001   HIS C 671 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6198)
  covalent geometry    : angle       0.51206 ( 8408)
  hydrogen bonds       : bond        0.03606 (  268)
  hydrogen bonds       : angle       4.97512 (  756)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.158 
Fit side-chains
REVERT: B   32 MET cc_start: 0.9161 (mtm) cc_final: 0.8884 (mtm)
REVERT: B  150 GLU cc_start: 0.8426 (tp30) cc_final: 0.7827 (tm-30)
REVERT: C   47 ASN cc_start: 0.8786 (t0) cc_final: 0.8509 (t0)
REVERT: C  129 ARG cc_start: 0.8431 (tmm-80) cc_final: 0.7420 (tpp-160)
REVERT: C  248 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7915 (ptm-80)
REVERT: C  271 SER cc_start: 0.9052 (m) cc_final: 0.8752 (p)
REVERT: C  301 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8132 (mm-30)
REVERT: C  375 ASP cc_start: 0.8666 (p0) cc_final: 0.8074 (p0)
REVERT: C  457 GLU cc_start: 0.8672 (tt0) cc_final: 0.8206 (tp30)
  outliers start: 19
  outliers final: 10
  residues processed: 87
  average time/residue: 0.5830
  time to fit residues: 53.3533
Evaluate side-chains
  80 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  173 ASP
Chi-restraints excluded: chain C residue  248 ARG
Chi-restraints excluded: chain C residue  388 ILE
Chi-restraints excluded: chain C residue  573 VAL
Chi-restraints excluded: chain C residue  574 LEU
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  650 SER
Chi-restraints excluded: chain C residue  683 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 28 optimal weight:    0.7980
   chunk 69 optimal weight:    0.0070
   chunk 55 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 54 optimal weight:    0.5980
   chunk 5 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 63 optimal weight:    0.0980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.4398

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
C 111 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.132753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.090990 restraints weight = 7680.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3022 rms_B_bonded: 2.32
r_work: 0.2876 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2738 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8752
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6198  Z= 0.110
  Angle     :  0.508   7.103   8408  Z= 0.259
  Chirality :  0.041   0.176    967
  Planarity :  0.004   0.032   1087
  Dihedral  :  4.207  19.878    835
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 19.08 %
    Favored  : 78.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.88 (0.31), residues: 773
  helix:  1.39 (0.31), residues: 314
  sheet: -0.25 (0.47), residues: 136
  loop :  0.32 (0.36), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 433 
 TYR   0.011   0.001   TYR B 107 
 PHE   0.008   0.001   PHE C 582 
 TRP   0.007   0.001   TRP B  86 
 HIS   0.004   0.001   HIS C 671 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 6198)
  covalent geometry    : angle       0.50755 ( 8408)
  hydrogen bonds       : bond        0.03403 (  268)
  hydrogen bonds       : angle       4.88197 (  756)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.259 
Fit side-chains
REVERT: B   32 MET cc_start: 0.9084 (mtm) cc_final: 0.8789 (mtm)
REVERT: B  150 GLU cc_start: 0.8406 (tp30) cc_final: 0.7797 (tm-30)
REVERT: C   47 ASN cc_start: 0.8822 (t0) cc_final: 0.8550 (t0)
REVERT: C  129 ARG cc_start: 0.8434 (tmm-80) cc_final: 0.7428 (tpp-160)
REVERT: C  248 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7892 (ptm-80)
REVERT: C  271 SER cc_start: 0.9043 (m) cc_final: 0.8770 (p)
REVERT: C  301 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8130 (mm-30)
REVERT: C  413 GLU cc_start: 0.8767 (tt0) cc_final: 0.8525 (tt0)
REVERT: C  457 GLU cc_start: 0.8696 (tt0) cc_final: 0.8201 (tp30)
REVERT: C  622 ARG cc_start: 0.8501 (mtp-110) cc_final: 0.8254 (mtp85)
  outliers start: 19
  outliers final: 13
  residues processed: 90
  average time/residue: 0.5790
  time to fit residues: 54.6180
Evaluate side-chains
  87 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   62 HIS
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  173 ASP
Chi-restraints excluded: chain C residue  248 ARG
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  388 ILE
Chi-restraints excluded: chain C residue  573 VAL
Chi-restraints excluded: chain C residue  574 LEU
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  650 SER
Chi-restraints excluded: chain C residue  683 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 15 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 69 optimal weight:    0.1980
   chunk 71 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
C 111 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.131300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.089328 restraints weight = 7657.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 2.31
r_work: 0.2847 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2707 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8772
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   0.032   6198  Z= 0.150
  Angle     :  0.537   7.557   8408  Z= 0.275
  Chirality :  0.042   0.178    967
  Planarity :  0.004   0.031   1087
  Dihedral  :  4.314  19.815    835
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.23 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.82 (0.31), residues: 773
  helix:  1.31 (0.30), residues: 314
  sheet: -0.18 (0.47), residues: 136
  loop :  0.29 (0.35), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 433 
 TYR   0.013   0.002   TYR C 624 
 PHE   0.010   0.001   PHE C 582 
 TRP   0.006   0.001   TRP C 639 
 HIS   0.004   0.001   HIS C 671 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 6198)
  covalent geometry    : angle       0.53745 ( 8408)
  hydrogen bonds       : bond        0.03760 (  268)
  hydrogen bonds       : angle       4.96823 (  756)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 75
  time to evaluate  : 0.250 
Fit side-chains
REVERT: B   32 MET cc_start: 0.9054 (mtm) cc_final: 0.8802 (mtm)
REVERT: B  150 GLU cc_start: 0.8422 (tp30) cc_final: 0.7750 (tm-30)
REVERT: C   47 ASN cc_start: 0.8853 (t0) cc_final: 0.8589 (t0)
REVERT: C  129 ARG cc_start: 0.8454 (tmm-80) cc_final: 0.7425 (tpp-160)
REVERT: C  248 ARG cc_start: 0.8260 (mtm-85) cc_final: 0.7882 (ptm-80)
REVERT: C  271 SER cc_start: 0.9037 (m) cc_final: 0.8742 (p)
REVERT: C  287 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8900 (m)
REVERT: C  301 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8077 (mm-30)
REVERT: C  375 ASP cc_start: 0.8548 (p0) cc_final: 0.7970 (p0)
REVERT: C  428 MET cc_start: 0.9278 (OUTLIER) cc_final: 0.8953 (ttt)
REVERT: C  457 GLU cc_start: 0.8690 (tt0) cc_final: 0.8198 (tp30)
REVERT: C  615 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8172 (ptp)
REVERT: C  622 ARG cc_start: 0.8519 (mtp-110) cc_final: 0.8264 (mtp85)
  outliers start: 22
  outliers final: 13
  residues processed: 89
  average time/residue: 0.5935
  time to fit residues: 55.4554
Evaluate side-chains
  90 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   62 HIS
Chi-restraints excluded: chain C residue   84 ASN
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  173 ASP
Chi-restraints excluded: chain C residue  266 ASP
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  388 ILE
Chi-restraints excluded: chain C residue  428 MET
Chi-restraints excluded: chain C residue  573 VAL
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  615 MET
Chi-restraints excluded: chain C residue  650 SER
Chi-restraints excluded: chain C residue  683 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 53 optimal weight:    0.4980
   chunk 72 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 55 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 74 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
C 111 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.132282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.090044 restraints weight = 7657.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 2.32
r_work: 0.2864 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2725 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8760
moved from start:          0.1680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6198  Z= 0.128
  Angle     :  0.516   6.921   8408  Z= 0.264
  Chirality :  0.041   0.177    967
  Planarity :  0.004   0.032   1087
  Dihedral  :  4.220  19.659    835
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 19.37 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.87 (0.31), residues: 773
  helix:  1.36 (0.31), residues: 308
  sheet: -0.23 (0.47), residues: 136
  loop :  0.36 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 664 
 TYR   0.011   0.002   TYR C 624 
 PHE   0.009   0.001   PHE C 582 
 TRP   0.006   0.001   TRP C 639 
 HIS   0.004   0.001   HIS C 671 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6198)
  covalent geometry    : angle       0.51565 ( 8408)
  hydrogen bonds       : bond        0.03522 (  268)
  hydrogen bonds       : angle       4.89581 (  756)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.274 
Fit side-chains
REVERT: B   32 MET cc_start: 0.9051 (mtm) cc_final: 0.8845 (mtm)
REVERT: B  150 GLU cc_start: 0.8413 (tp30) cc_final: 0.7798 (tm-30)
REVERT: C   47 ASN cc_start: 0.8831 (t0) cc_final: 0.8586 (t0)
REVERT: C  129 ARG cc_start: 0.8446 (tmm-80) cc_final: 0.7426 (tpp-160)
REVERT: C  248 ARG cc_start: 0.8271 (mtm-85) cc_final: 0.7905 (ptm-80)
REVERT: C  271 SER cc_start: 0.9034 (m) cc_final: 0.8750 (p)
REVERT: C  301 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8153 (mm-30)
REVERT: C  375 ASP cc_start: 0.8654 (p0) cc_final: 0.8095 (p0)
REVERT: C  413 GLU cc_start: 0.8768 (tt0) cc_final: 0.8519 (tt0)
REVERT: C  428 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8951 (ttt)
REVERT: C  457 GLU cc_start: 0.8689 (tt0) cc_final: 0.8218 (tp30)
REVERT: C  622 ARG cc_start: 0.8503 (mtp-110) cc_final: 0.8254 (mtp85)
  outliers start: 20
  outliers final: 15
  residues processed: 92
  average time/residue: 0.5794
  time to fit residues: 56.0507
Evaluate side-chains
  92 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   62 HIS
Chi-restraints excluded: chain B residue  159 PHE
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  173 ASP
Chi-restraints excluded: chain C residue  266 ASP
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  388 ILE
Chi-restraints excluded: chain C residue  428 MET
Chi-restraints excluded: chain C residue  573 VAL
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  650 SER
Chi-restraints excluded: chain C residue  683 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
C 111 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.131488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.089286 restraints weight = 7673.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 2.31
r_work: 0.2846 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2705 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8776
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6198  Z= 0.153
  Angle     :  0.534   6.813   8408  Z= 0.274
  Chirality :  0.042   0.182    967
  Planarity :  0.004   0.031   1087
  Dihedral  :  4.293  19.489    835
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 19.67 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.79 (0.31), residues: 773
  helix:  1.27 (0.30), residues: 308
  sheet: -0.22 (0.47), residues: 136
  loop :  0.31 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 664 
 TYR   0.013   0.002   TYR C 624 
 PHE   0.010   0.001   PHE C 582 
 TRP   0.007   0.001   TRP C 639 
 HIS   0.004   0.001   HIS C 671 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6198)
  covalent geometry    : angle       0.53355 ( 8408)
  hydrogen bonds       : bond        0.03761 (  268)
  hydrogen bonds       : angle       4.97123 (  756)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.267 
Fit side-chains
REVERT: B   32 MET cc_start: 0.9041 (mtm) cc_final: 0.8822 (mtm)
REVERT: B  150 GLU cc_start: 0.8426 (tp30) cc_final: 0.7754 (tm-30)
REVERT: C   47 ASN cc_start: 0.8852 (t0) cc_final: 0.8607 (t0)
REVERT: C  129 ARG cc_start: 0.8459 (tmm-80) cc_final: 0.7422 (tpp-160)
REVERT: C  248 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.7889 (ptm-80)
REVERT: C  271 SER cc_start: 0.9039 (m) cc_final: 0.8750 (p)
REVERT: C  287 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8902 (m)
REVERT: C  301 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8125 (mm-30)
REVERT: C  375 ASP cc_start: 0.8663 (p0) cc_final: 0.8083 (p0)
REVERT: C  428 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8958 (ttt)
REVERT: C  457 GLU cc_start: 0.8686 (tt0) cc_final: 0.8217 (tp30)
REVERT: C  622 ARG cc_start: 0.8526 (mtp-110) cc_final: 0.8274 (mtp85)
  outliers start: 18
  outliers final: 13
  residues processed: 94
  average time/residue: 0.5928
  time to fit residues: 58.4606
Evaluate side-chains
  92 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   62 HIS
Chi-restraints excluded: chain B residue  159 PHE
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  173 ASP
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  388 ILE
Chi-restraints excluded: chain C residue  428 MET
Chi-restraints excluded: chain C residue  573 VAL
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  650 SER
Chi-restraints excluded: chain C residue  683 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 39 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 13 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
C 111 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.131262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.088905 restraints weight = 7688.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 2.34
r_work: 0.2859 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2722 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8766
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6198  Z= 0.153
  Angle     :  0.536   6.866   8408  Z= 0.275
  Chirality :  0.042   0.183    967
  Planarity :  0.004   0.031   1087
  Dihedral  :  4.290  19.199    835
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 19.67 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.78 (0.31), residues: 773
  helix:  1.25 (0.30), residues: 308
  sheet: -0.23 (0.47), residues: 136
  loop :  0.31 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 664 
 TYR   0.013   0.002   TYR C 624 
 PHE   0.010   0.001   PHE C 582 
 TRP   0.007   0.001   TRP C 639 
 HIS   0.004   0.001   HIS C 671 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 6198)
  covalent geometry    : angle       0.53603 ( 8408)
  hydrogen bonds       : bond        0.03778 (  268)
  hydrogen bonds       : angle       4.97500 (  756)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2551.32 seconds
wall clock time: 44 minutes 7.59 seconds (2647.59 seconds total)