Starting phenix.real_space_refine
on Tue Mar 11 23:55:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7crb_30449/03_2025/7crb_30449.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7crb_30449/03_2025/7crb_30449.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7crb_30449/03_2025/7crb_30449.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7crb_30449/03_2025/7crb_30449.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7crb_30449/03_2025/7crb_30449.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7crb_30449/03_2025/7crb_30449.cif"
  }
  resolution = 3.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
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      39      5.16       5
     C    4318      2.51       5
     N    1155      2.21       5
     O    1294      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6806
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "J"
      Number of atoms: 1880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1880
          Classifications: {'peptide': 235}
          Link IDs: {'PTRANS': 9, 'TRANS': 225}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 4926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 616, 4926
          Classifications: {'peptide': 616}
          Link IDs: {'PTRANS': 27, 'TRANS': 588}
  Time building chain proxies: 4.58, per 1000 atoms: 0.67
  Number of scatterers: 6806
  At special positions: 0
  Unit cell: (84.5383, 114.182, 93.3215, 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      39     16.00
     O    1294      8.00
     N    1155      7.00
     C    4318      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.90
  Conformation dependent library (CDL) restraints added in 961.0 milliseconds
  

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1650

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 9 sheets defined
      31.0% alpha, 13.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'J' and resid 68 through 84
      removed outlier: 4.227A  pdb=" N   SER J  84 " --> pdb=" O   HIS J  80 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 86 through 102
      removed outlier: 4.607A  pdb=" N   VAL J  95 " --> pdb=" O   MET J  91 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ARG J  96 " --> pdb=" O   LYS J  92 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 107 through 118
    Processing helix  chain 'J' and resid 125 through 138
      removed outlier: 3.531A  pdb=" N   ALA J 129 " --> pdb=" O   THR J 125 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 139 through 149
    Processing helix  chain 'J' and resid 157 through 177
    Processing helix  chain 'J' and resid 180 through 189
    Processing helix  chain 'J' and resid 194 through 197
    Processing helix  chain 'J' and resid 198 through 210
      removed outlier: 4.319A  pdb=" N   PHE J 204 " --> pdb=" O   THR J 200 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 211 through 223
    Processing helix  chain 'J' and resid 226 through 239
      removed outlier: 3.674A  pdb=" N   GLU J 239 " --> pdb=" O   LEU J 235 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 244 through 261
    Processing helix  chain 'J' and resid 268 through 277
    Processing helix  chain 'J' and resid 302 through 309
      removed outlier: 3.877A  pdb=" N   TYR J 309 " --> pdb=" O   TYR J 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 597 through 601
      removed outlier: 3.618A  pdb=" N   SER A 600 " --> pdb=" O   THR A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 626
      removed outlier: 3.671A  pdb=" N   LEU A 624 " --> pdb=" O   SER A 620 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   GLU A 625 " --> pdb=" O   GLU A 621 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ARG A 626 " --> pdb=" O   LYS A 622 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 620 through 626'
    Processing helix  chain 'A' and resid 643 through 652
      removed outlier: 3.616A  pdb=" N   GLN A 647 " --> pdb=" O   HIS A 643 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   GLN A 652 " --> pdb=" O   GLY A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 745
      removed outlier: 3.919A  pdb=" N   GLU A 743 " --> pdb=" O   SER A 740 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 838
    Processing helix  chain 'A' and resid 858 through 862
    Processing helix  chain 'A' and resid 880 through 886
      removed outlier: 3.732A  pdb=" N   ILE A 883 " --> pdb=" O   PRO A 880 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   GLY A 884 " --> pdb=" O   SER A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 947 through 953
      removed outlier: 3.889A  pdb=" N   ILE A 950 " --> pdb=" O   PRO A 947 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   MET A 951 " --> pdb=" O   LEU A 948 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 964 through 968
      removed outlier: 4.097A  pdb=" N   LYS A 968 " --> pdb=" O   GLU A 965 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 975
      removed outlier: 3.609A  pdb=" N   LEU A 974 " --> pdb=" O   PHE A 970 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   ASP A 975 " --> pdb=" O   PRO A 971 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 970 through 975'
    Processing helix  chain 'A' and resid 990 through 996
      removed outlier: 3.652A  pdb=" N   LYS A 994 " --> pdb=" O   PRO A 991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1054 through 1064
    Processing sheet with id=AA1, first strand: chain 'A' and resid 584 through 585
      removed outlier: 3.513A  pdb=" N   GLY A 585 " --> pdb=" O   ASN A 607 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 680 through 682
      removed outlier: 6.400A  pdb=" N   LEU A 681 " --> pdb=" O   ASP A 705 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   MET A 704 " --> pdb=" O   LYS A 728 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   LEU A 797 " --> pdb=" O   ASN A 821 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 788 through 789
      removed outlier: 3.583A  pdb=" N   ILE A 789 " --> pdb=" O   ALA A 810 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 843 through 845
      removed outlier: 3.530A  pdb=" N   ILE A 939 " --> pdb=" O   LEU A 917 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 979 through 982
      removed outlier: 6.707A  pdb=" N   LEU A 980 " --> pdb=" O   ARG A1003 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1012 through 1013
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1091 through 1094
      removed outlier: 3.653A  pdb=" N   VAL A1129 " --> pdb=" O   GLU A1176 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   ILE A1130 " --> pdb=" O   VAL A1139 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LEU A1137 " --> pdb=" O   ASP A1132 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1091 through 1094
      removed outlier: 3.653A  pdb=" N   VAL A1129 " --> pdb=" O   GLU A1176 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1159 through 1164

    216 hydrogen bonds defined for protein.
    585 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.93

  Time building geometry restraints manager: 2.03 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1139
        1.31 -     1.43: 1761
        1.43 -     1.56: 3987
        1.56 -     1.68: 0
        1.68 -     1.81: 53
  Bond restraints: 6940
  Sorted by residual:
  bond pdb=" C   PRO A 947 "
       pdb=" O   PRO A 947 "
    ideal  model  delta    sigma   weight residual
    1.233  1.184  0.049 1.18e-02 7.18e+03 1.71e+01
  bond pdb=" CA  SER J 296 "
       pdb=" CB  SER J 296 "
    ideal  model  delta    sigma   weight residual
    1.531  1.467  0.063 1.62e-02 3.81e+03 1.54e+01
  bond pdb=" N   LEU A1121 "
       pdb=" CA  LEU A1121 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.039 1.29e-02 6.01e+03 9.33e+00
  bond pdb=" N   LYS A1122 "
       pdb=" CA  LYS A1122 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.14e-02 7.69e+03 9.31e+00
  bond pdb=" N   VAL A1113 "
       pdb=" CA  VAL A1113 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.27e-02 6.20e+03 8.04e+00
  ... (remaining 6935 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 9169
        2.23 -     4.45: 191
        4.45 -     6.68: 32
        6.68 -     8.91: 8
        8.91 -    11.13: 1
  Bond angle restraints: 9401
  Sorted by residual:
  angle pdb=" N   SER J 294 "
        pdb=" CA  SER J 294 "
        pdb=" C   SER J 294 "
      ideal   model   delta    sigma   weight residual
     113.38  102.25   11.13 1.23e+00 6.61e-01 8.19e+01
  angle pdb=" C   PRO A 947 "
        pdb=" CA  PRO A 947 "
        pdb=" CB  PRO A 947 "
      ideal   model   delta    sigma   weight residual
     110.95  103.18    7.77 1.31e+00 5.83e-01 3.52e+01
  angle pdb=" N   GLU J 300 "
        pdb=" CA  GLU J 300 "
        pdb=" C   GLU J 300 "
      ideal   model   delta    sigma   weight residual
     111.14  105.10    6.04 1.08e+00 8.57e-01 3.13e+01
  angle pdb=" N   LEU J 301 "
        pdb=" CA  LEU J 301 "
        pdb=" C   LEU J 301 "
      ideal   model   delta    sigma   weight residual
     112.92  106.21    6.71 1.23e+00 6.61e-01 2.97e+01
  angle pdb=" CA  PRO J 265 "
        pdb=" N   PRO J 265 "
        pdb=" CD  PRO J 265 "
      ideal   model   delta    sigma   weight residual
     112.00  104.54    7.46 1.40e+00 5.10e-01 2.84e+01
  ... (remaining 9396 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.76: 3817
       16.76 -    33.52: 364
       33.52 -    50.27: 57
       50.27 -    67.03: 15
       67.03 -    83.79: 8
  Dihedral angle restraints: 4261
    sinusoidal: 1737
      harmonic: 2524
  Sorted by residual:
  dihedral pdb=" N   LEU J 295 "
           pdb=" C   LEU J 295 "
           pdb=" CA  LEU J 295 "
           pdb=" CB  LEU J 295 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  110.43   12.37     0      2.50e+00 1.60e-01 2.45e+01
  dihedral pdb=" CA  LEU A 753 "
           pdb=" C   LEU A 753 "
           pdb=" N   HIS A 754 "
           pdb=" CA  HIS A 754 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.74  -22.26     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" C   PRO A 947 "
           pdb=" N   PRO A 947 "
           pdb=" CA  PRO A 947 "
           pdb=" CB  PRO A 947 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -110.26  -10.44     0      2.50e+00 1.60e-01 1.74e+01
  ... (remaining 4258 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 970
       0.077 -    0.153: 102
       0.153 -    0.230: 10
       0.230 -    0.307: 2
       0.307 -    0.384: 1
  Chirality restraints: 1085
  Sorted by residual:
  chirality pdb=" CA  LEU J 295 "
            pdb=" N   LEU J 295 "
            pdb=" C   LEU J 295 "
            pdb=" CB  LEU J 295 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.89   -0.38 2.00e-01 2.50e+01 3.68e+00
  chirality pdb=" CA  GLN J 297 "
            pdb=" N   GLN J 297 "
            pdb=" C   GLN J 297 "
            pdb=" CB  GLN J 297 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.25e+00
  chirality pdb=" CA  ILE J 298 "
            pdb=" N   ILE J 298 "
            pdb=" C   ILE J 298 "
            pdb=" CB  ILE J 298 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.26 2.00e-01 2.50e+01 1.71e+00
  ... (remaining 1082 not shown)

  Planarity restraints: 1198
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP J  98 "    0.021 2.00e-02 2.50e+03   2.04e-02 1.04e+01
        pdb=" CG  TRP J  98 "   -0.054 2.00e-02 2.50e+03
        pdb=" CD1 TRP J  98 "    0.028 2.00e-02 2.50e+03
        pdb=" CD2 TRP J  98 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP J  98 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP J  98 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP J  98 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP J  98 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP J  98 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP J  98 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE J 298 "   -0.015 2.00e-02 2.50e+03   2.99e-02 8.92e+00
        pdb=" C   ILE J 298 "    0.052 2.00e-02 2.50e+03
        pdb=" O   ILE J 298 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   GLU J 299 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU J 300 "   -0.014 2.00e-02 2.50e+03   2.88e-02 8.27e+00
        pdb=" C   GLU J 300 "    0.050 2.00e-02 2.50e+03
        pdb=" O   GLU J 300 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LEU J 301 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1195 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1933
        2.81 -     3.33: 6277
        3.33 -     3.86: 10539
        3.86 -     4.38: 12704
        4.38 -     4.90: 21856
  Nonbonded interactions: 53309
  Sorted by model distance:
  nonbonded pdb=" O   SER A 949 "
            pdb=" OG  SER A 952 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" NZ  LYS A 690 "
            pdb=" OE2 GLU A 693 "
     model   vdw
     2.299 3.120
  nonbonded pdb=" O   LEU A1060 "
            pdb=" OG1 THR A1064 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" NH1 ARG J 151 "
            pdb=" OE1 GLU J 167 "
     model   vdw
     2.337 3.120
  nonbonded pdb=" N   SER J 294 "
            pdb=" N   LEU J 295 "
     model   vdw
     2.352 2.560
  ... (remaining 53304 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=0.43 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:             2.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     19.940
  Find NCS groups from input model:        0.070
  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:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
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      :  0.005   0.063   6940  Z= 0.349
  Angle     :  0.809  11.134   9401  Z= 0.491
  Chirality :  0.052   0.384   1085
  Planarity :  0.004   0.035   1198
  Dihedral  : 13.844  83.788   2611
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.76 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  0.89 %
    Favored  : 98.34 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.29 (0.29), residues: 845
  helix: -0.88 (0.32), residues: 238
  sheet: -2.37 (0.42), residues: 162
  loop : -1.47 (0.31), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.002   TRP J  98 
 HIS   0.004   0.001   HIS A 913 
 PHE   0.022   0.002   PHE A 868 
 TYR   0.009   0.001   TYR J 305 
 ARG   0.010   0.001   ARG J 307 

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
REVERT: J  297 GLN cc_start: 0.8372 (mp10) cc_final: 0.7906 (mp10)
REVERT: A  626 ARG cc_start: 0.6789 (tpt90) cc_final: 0.6564 (tpt-90)
REVERT: A  984 LYS cc_start: 0.8705 (mptt) cc_final: 0.8495 (mptt)
REVERT: A 1011 VAL cc_start: 0.7845 (p) cc_final: 0.7615 (t)
  outliers start: 6
  outliers final: 3
  residues processed: 86
  average time/residue: 0.1814
  time to fit residues: 21.5799
Evaluate side-chains
  67 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  295 LEU
Chi-restraints excluded: chain A residue 1103 THR
Chi-restraints excluded: chain A residue 1117 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 21 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0970
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
J 183 ASN
** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 792 ASN
A 813 ASN
A1082 ASN
** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.143160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.116315 restraints weight = 8438.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 2.46
r_work: 0.3350 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3207
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.1090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   6940  Z= 0.289
  Angle     :  0.628   9.205   9401  Z= 0.328
  Chirality :  0.044   0.145   1085
  Planarity :  0.004   0.041   1198
  Dihedral  :  6.127  59.632    921
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  :  6.64 %
    Favored  : 91.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.90 (0.30), residues: 845
  helix: -0.26 (0.34), residues: 246
  sheet: -2.26 (0.42), residues: 164
  loop : -1.38 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP J  98 
 HIS   0.003   0.001   HIS A 913 
 PHE   0.014   0.001   PHE A 868 
 TYR   0.013   0.001   TYR J 305 
 ARG   0.004   0.000   ARG J 307 

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  795 GLN cc_start: 0.8075 (mt0) cc_final: 0.7806 (mp10)
REVERT: A  984 LYS cc_start: 0.8627 (mptt) cc_final: 0.8410 (mptt)
REVERT: A 1029 LYS cc_start: 0.8384 (mmmt) cc_final: 0.8153 (mmmm)
  outliers start: 15
  outliers final: 11
  residues processed: 81
  average time/residue: 0.1766
  time to fit residues: 19.9679
Evaluate side-chains
  78 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   83 VAL
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain J residue  258 CYS
Chi-restraints excluded: chain J residue  268 VAL
Chi-restraints excluded: chain J residue  276 TYR
Chi-restraints excluded: chain J residue  295 LEU
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  948 LEU
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1080 CYS
Chi-restraints excluded: chain A residue 1103 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 63 optimal weight:    0.4980
   chunk 73 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 9 optimal weight:    0.3980
   chunk 12 optimal weight:    0.6980
   chunk 22 optimal weight:    0.4980
   chunk 65 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0770
   chunk 83 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
J 261 GLN
J 277 GLN
** J 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 643 HIS
A1140 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.145330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.118158 restraints weight = 8540.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 2.47
r_work: 0.3367 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3231
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3231
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6940  Z= 0.221
  Angle     :  0.564   8.729   9401  Z= 0.293
  Chirality :  0.043   0.148   1085
  Planarity :  0.003   0.033   1198
  Dihedral  :  5.340  46.817    918
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  :  7.66 %
    Favored  : 89.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.30), residues: 845
  helix:  0.29 (0.35), residues: 236
  sheet: -2.24 (0.41), residues: 164
  loop : -1.09 (0.32), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP J 254 
 HIS   0.003   0.001   HIS A 913 
 PHE   0.012   0.001   PHE J 269 
 TYR   0.009   0.001   TYR J 305 
 ARG   0.002   0.000   ARG J 307 

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.749 
Fit side-chains
REVERT: J  277 GLN cc_start: 0.7613 (pt0) cc_final: 0.7388 (pt0)
REVERT: J  295 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.6773 (pt)
REVERT: J  297 GLN cc_start: 0.8599 (mp10) cc_final: 0.8286 (mp10)
REVERT: A  795 GLN cc_start: 0.8025 (mt0) cc_final: 0.7757 (mp10)
REVERT: A  887 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.8005 (mtt90)
REVERT: A  939 ILE cc_start: 0.8821 (mm) cc_final: 0.8620 (mm)
REVERT: A  969 GLU cc_start: 0.8585 (mp0) cc_final: 0.8277 (mp0)
REVERT: A  984 LYS cc_start: 0.8659 (mptt) cc_final: 0.8454 (mptt)
REVERT: A 1029 LYS cc_start: 0.8376 (mmmt) cc_final: 0.8151 (mmmm)
REVERT: A 1140 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7609 (pp30)
  outliers start: 20
  outliers final: 13
  residues processed: 85
  average time/residue: 0.1744
  time to fit residues: 20.5187
Evaluate side-chains
  84 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   83 VAL
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain J residue  258 CYS
Chi-restraints excluded: chain J residue  276 TYR
Chi-restraints excluded: chain J residue  295 LEU
Chi-restraints excluded: chain A residue  914 THR
Chi-restraints excluded: chain A residue  948 LEU
Chi-restraints excluded: chain A residue  996 MET
Chi-restraints excluded: chain A residue 1009 ASN
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1080 CYS
Chi-restraints excluded: chain A residue 1103 THR
Chi-restraints excluded: chain A residue 1105 THR
Chi-restraints excluded: chain A residue 1140 GLN
Chi-restraints excluded: chain A residue 1180 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   chunk 82 optimal weight:    0.8980
   chunk 79 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
J 261 GLN
** J 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 647 GLN
A 916 ASN
A1140 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.141243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.114262 restraints weight = 8656.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 2.46
r_work: 0.3326 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3193
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3193
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   6940  Z= 0.348
  Angle     :  0.624   8.570   9401  Z= 0.324
  Chirality :  0.045   0.157   1085
  Planarity :  0.004   0.041   1198
  Dihedral  :  5.472  45.764    918
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  :  9.20 %
    Favored  : 87.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.30), residues: 845
  helix:  0.23 (0.35), residues: 236
  sheet: -2.29 (0.41), residues: 165
  loop : -1.17 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP J 254 
 HIS   0.003   0.001   HIS A 913 
 PHE   0.019   0.002   PHE J 269 
 TYR   0.014   0.001   TYR J 305 
 ARG   0.002   0.000   ARG A 645 

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 69
  time to evaluate  : 0.831 
Fit side-chains
REVERT: J  295 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.6536 (pp)
REVERT: J  297 GLN cc_start: 0.8595 (mp10) cc_final: 0.8206 (mp10)
REVERT: A  811 ILE cc_start: 0.8503 (mt) cc_final: 0.8161 (mm)
REVERT: A  916 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8768 (t0)
REVERT: A  945 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6510 (pm20)
REVERT: A  969 GLU cc_start: 0.8579 (mp0) cc_final: 0.8247 (mp0)
REVERT: A  984 LYS cc_start: 0.8682 (mptt) cc_final: 0.8464 (mptt)
REVERT: A 1029 LYS cc_start: 0.8432 (mmmt) cc_final: 0.8191 (mmmm)
REVERT: A 1120 ASP cc_start: 0.7731 (m-30) cc_final: 0.7328 (m-30)
REVERT: A 1140 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7704 (pp30)
  outliers start: 25
  outliers final: 16
  residues processed: 85
  average time/residue: 0.2018
  time to fit residues: 23.3420
Evaluate side-chains
  89 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   83 VAL
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain J residue  258 CYS
Chi-restraints excluded: chain J residue  276 TYR
Chi-restraints excluded: chain J residue  295 LEU
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  837 THR
Chi-restraints excluded: chain A residue  914 THR
Chi-restraints excluded: chain A residue  916 ASN
Chi-restraints excluded: chain A residue  945 GLU
Chi-restraints excluded: chain A residue  948 LEU
Chi-restraints excluded: chain A residue 1009 ASN
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1080 CYS
Chi-restraints excluded: chain A residue 1103 THR
Chi-restraints excluded: chain A residue 1105 THR
Chi-restraints excluded: chain A residue 1140 GLN
Chi-restraints excluded: chain A residue 1156 GLU
Chi-restraints excluded: chain A residue 1180 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0980
   chunk 73 optimal weight:    0.4980
   chunk 15 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   chunk 79 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0970
   chunk 34 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
J 261 GLN
** J 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1140 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.144955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.116826 restraints weight = 8581.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 2.57
r_work: 0.3346 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3204
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3204
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.1598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6940  Z= 0.232
  Angle     :  0.575  12.787   9401  Z= 0.296
  Chirality :  0.043   0.161   1085
  Planarity :  0.003   0.036   1198
  Dihedral  :  5.231  44.688    918
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  :  9.96 %
    Favored  : 86.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.31), residues: 845
  helix:  0.34 (0.35), residues: 237
  sheet: -2.26 (0.41), residues: 165
  loop : -1.08 (0.32), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP J 254 
 HIS   0.003   0.001   HIS A 913 
 PHE   0.020   0.001   PHE J 269 
 TYR   0.013   0.001   TYR J 305 
 ARG   0.002   0.000   ARG A 937 

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 76
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
REVERT: J  270 GLU cc_start: 0.8065 (tt0) cc_final: 0.7793 (pm20)
REVERT: J  304 GLU cc_start: 0.7930 (mt-10) cc_final: 0.6988 (tp30)
REVERT: A  626 ARG cc_start: 0.6589 (tpt90) cc_final: 0.6381 (tpt-90)
REVERT: A  811 ILE cc_start: 0.8486 (mt) cc_final: 0.8138 (mm)
REVERT: A  887 ARG cc_start: 0.8348 (mtm-85) cc_final: 0.8056 (mtt90)
REVERT: A  945 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6444 (pm20)
REVERT: A  969 GLU cc_start: 0.8584 (mp0) cc_final: 0.8242 (mp0)
REVERT: A  981 GLN cc_start: 0.8735 (tt0) cc_final: 0.8502 (tt0)
REVERT: A  984 LYS cc_start: 0.8673 (mptt) cc_final: 0.8467 (mptt)
REVERT: A 1029 LYS cc_start: 0.8442 (mmmt) cc_final: 0.8200 (mmmm)
REVERT: A 1140 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7551 (pp30)
  outliers start: 27
  outliers final: 17
  residues processed: 92
  average time/residue: 0.2060
  time to fit residues: 25.4505
Evaluate side-chains
  91 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   83 VAL
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain J residue  258 CYS
Chi-restraints excluded: chain J residue  276 TYR
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  837 THR
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue  878 GLU
Chi-restraints excluded: chain A residue  914 THR
Chi-restraints excluded: chain A residue  945 GLU
Chi-restraints excluded: chain A residue  948 LEU
Chi-restraints excluded: chain A residue  996 MET
Chi-restraints excluded: chain A residue 1009 ASN
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1080 CYS
Chi-restraints excluded: chain A residue 1091 LEU
Chi-restraints excluded: chain A residue 1105 THR
Chi-restraints excluded: chain A residue 1140 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 13 optimal weight:    0.1980
   chunk 46 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0060
   chunk 23 optimal weight:    0.0070
   chunk 41 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0980
   chunk 27 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 38 optimal weight:    0.3980
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.1414

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

Flipped N/Q/H residues before XYZ refinement:
J 261 GLN
J 297 GLN
** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1140 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.148338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.121347 restraints weight = 8539.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.45
r_work: 0.3418 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3278
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3278
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.054   6940  Z= 0.139
  Angle     :  0.529  11.658   9401  Z= 0.271
  Chirality :  0.041   0.160   1085
  Planarity :  0.003   0.037   1198
  Dihedral  :  4.400  18.981    915
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 11.11 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.31), residues: 845
  helix:  0.65 (0.36), residues: 232
  sheet: -2.14 (0.43), residues: 159
  loop : -0.96 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP J 254 
 HIS   0.003   0.001   HIS A 913 
 PHE   0.021   0.001   PHE J 269 
 TYR   0.009   0.001   TYR J 305 
 ARG   0.001   0.000   ARG J 177 

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
REVERT: J  291 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7618 (tm-30)
REVERT: J  304 GLU cc_start: 0.7892 (mt-10) cc_final: 0.6989 (tp30)
REVERT: A  811 ILE cc_start: 0.8489 (mt) cc_final: 0.8146 (mm)
REVERT: A  887 ARG cc_start: 0.8252 (mtm-85) cc_final: 0.7940 (mtt90)
REVERT: A  945 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6418 (pm20)
REVERT: A  969 GLU cc_start: 0.8577 (mp0) cc_final: 0.8292 (mp0)
REVERT: A  981 GLN cc_start: 0.8661 (tt0) cc_final: 0.8402 (tt0)
REVERT: A  984 LYS cc_start: 0.8708 (mptt) cc_final: 0.8497 (mptt)
REVERT: A 1029 LYS cc_start: 0.8283 (mmmt) cc_final: 0.8049 (mmmm)
REVERT: A 1140 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7489 (pp30)
  outliers start: 24
  outliers final: 10
  residues processed: 95
  average time/residue: 0.2158
  time to fit residues: 27.3469
Evaluate side-chains
  84 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   83 VAL
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain J residue  257 GLN
Chi-restraints excluded: chain J residue  276 TYR
Chi-restraints excluded: chain J residue  297 GLN
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain A residue  945 GLU
Chi-restraints excluded: chain A residue  948 LEU
Chi-restraints excluded: chain A residue  996 MET
Chi-restraints excluded: chain A residue 1009 ASN
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1140 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 34 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
J 149 HIS
J 261 GLN
** J 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 916 ASN
A1082 ASN
** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.143293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.116297 restraints weight = 8527.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.44
r_work: 0.3346 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3206
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3206
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6940  Z= 0.303
  Angle     :  0.611  11.216   9401  Z= 0.311
  Chirality :  0.044   0.238   1085
  Planarity :  0.004   0.042   1198
  Dihedral  :  4.742  21.625    915
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 11.62 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.31), residues: 845
  helix:  0.50 (0.35), residues: 238
  sheet: -2.22 (0.42), residues: 161
  loop : -1.06 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP J 254 
 HIS   0.004   0.001   HIS A 913 
 PHE   0.016   0.001   PHE J 269 
 TYR   0.013   0.001   TYR J 305 
 ARG   0.002   0.000   ARG A1033 

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 71
  time to evaluate  : 0.858 
Fit side-chains
REVERT: J  291 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7686 (tm-30)
REVERT: J  304 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7048 (tp30)
REVERT: A  626 ARG cc_start: 0.7034 (tpt90) cc_final: 0.6645 (tpt170)
REVERT: A  811 ILE cc_start: 0.8590 (mt) cc_final: 0.8190 (mm)
REVERT: A  887 ARG cc_start: 0.8346 (mtm-85) cc_final: 0.8064 (mtt90)
REVERT: A  945 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6442 (pm20)
REVERT: A  969 GLU cc_start: 0.8563 (mp0) cc_final: 0.8220 (mp0)
REVERT: A  984 LYS cc_start: 0.8724 (mptt) cc_final: 0.8519 (mptt)
REVERT: A 1029 LYS cc_start: 0.8308 (mmmt) cc_final: 0.8072 (mmmm)
  outliers start: 24
  outliers final: 18
  residues processed: 86
  average time/residue: 0.2142
  time to fit residues: 24.7389
Evaluate side-chains
  90 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   83 VAL
Chi-restraints excluded: chain J residue  105 ASP
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain J residue  257 GLN
Chi-restraints excluded: chain J residue  258 CYS
Chi-restraints excluded: chain J residue  276 TYR
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  837 THR
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue  945 GLU
Chi-restraints excluded: chain A residue  948 LEU
Chi-restraints excluded: chain A residue  996 MET
Chi-restraints excluded: chain A residue 1009 ASN
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1080 CYS
Chi-restraints excluded: chain A residue 1091 LEU
Chi-restraints excluded: chain A residue 1156 GLU
Chi-restraints excluded: chain A residue 1166 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0870
   chunk 35 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0970
   chunk 28 optimal weight:    0.4980
   chunk 63 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 71 optimal weight:    0.5980
   overall best weight:    0.3956

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

Flipped N/Q/H residues before XYZ refinement:
J 261 GLN
** J 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 916 ASN
** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.146499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.118325 restraints weight = 8644.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 2.58
r_work: 0.3373 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3369
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3369 r_free = 0.3369    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3369 r_free = 0.3369    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3369
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6940  Z= 0.212
  Angle     :  0.569  10.940   9401  Z= 0.292
  Chirality :  0.042   0.164   1085
  Planarity :  0.003   0.040   1198
  Dihedral  :  4.606  20.316    915
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 12.39 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.31), residues: 845
  helix:  0.68 (0.36), residues: 232
  sheet: -2.21 (0.41), residues: 160
  loop : -0.98 (0.31), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP J 254 
 HIS   0.003   0.001   HIS A 913 
 PHE   0.019   0.001   PHE J 269 
 TYR   0.011   0.001   TYR J 305 
 ARG   0.001   0.000   ARG A 699 

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.739 
Fit side-chains
REVERT: J  297 GLN cc_start: 0.8280 (mp10) cc_final: 0.8060 (mp10)
REVERT: J  304 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7048 (tp30)
REVERT: A  626 ARG cc_start: 0.7001 (tpt90) cc_final: 0.6549 (tpt-90)
REVERT: A  811 ILE cc_start: 0.8569 (mt) cc_final: 0.8119 (mm)
REVERT: A  837 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8250 (p)
REVERT: A  887 ARG cc_start: 0.8235 (mtm-85) cc_final: 0.7987 (mtt90)
REVERT: A  945 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6300 (pm20)
REVERT: A  969 GLU cc_start: 0.8484 (mp0) cc_final: 0.8222 (mp0)
REVERT: A  981 GLN cc_start: 0.8472 (tt0) cc_final: 0.8233 (tt0)
REVERT: A 1029 LYS cc_start: 0.8264 (mmmt) cc_final: 0.8046 (mmmm)
  outliers start: 20
  outliers final: 13
  residues processed: 85
  average time/residue: 0.2079
  time to fit residues: 23.5271
Evaluate side-chains
  84 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   83 VAL
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain J residue  257 GLN
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain A residue  837 THR
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue  945 GLU
Chi-restraints excluded: chain A residue  948 LEU
Chi-restraints excluded: chain A residue  996 MET
Chi-restraints excluded: chain A residue 1009 ASN
Chi-restraints excluded: chain A residue 1016 LEU
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1091 LEU
Chi-restraints excluded: chain A residue 1156 GLU
Chi-restraints excluded: chain A residue 1166 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 81 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 56 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
J 261 GLN
** J 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 916 ASN
** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.142496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.114659 restraints weight = 8713.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.56
r_work: 0.3325 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3175
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3175
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   6940  Z= 0.346
  Angle     :  0.638  11.369   9401  Z= 0.326
  Chirality :  0.044   0.169   1085
  Planarity :  0.004   0.044   1198
  Dihedral  :  4.952  21.901    915
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 12.01 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.30), residues: 845
  helix:  0.47 (0.35), residues: 240
  sheet: -2.31 (0.40), residues: 169
  loop : -1.05 (0.32), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP J 254 
 HIS   0.003   0.001   HIS A 913 
 PHE   0.017   0.002   PHE J 269 
 TYR   0.015   0.001   TYR J 305 
 ARG   0.002   0.000   ARG A1033 

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 72
  time to evaluate  : 0.813 
Fit side-chains
REVERT: J  297 GLN cc_start: 0.8396 (mp10) cc_final: 0.7780 (mp10)
REVERT: A  626 ARG cc_start: 0.7093 (tpt90) cc_final: 0.6677 (tpt170)
REVERT: A  811 ILE cc_start: 0.8605 (mt) cc_final: 0.8188 (mm)
REVERT: A  887 ARG cc_start: 0.8390 (mtm-85) cc_final: 0.8092 (mtt90)
REVERT: A  945 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6438 (pm20)
REVERT: A  969 GLU cc_start: 0.8582 (mp0) cc_final: 0.8222 (mp0)
REVERT: A  981 GLN cc_start: 0.8692 (tt0) cc_final: 0.8491 (tt0)
REVERT: A 1029 LYS cc_start: 0.8358 (mmmt) cc_final: 0.8129 (mmmm)
REVERT: A 1120 ASP cc_start: 0.7718 (m-30) cc_final: 0.7122 (m-30)
  outliers start: 23
  outliers final: 18
  residues processed: 89
  average time/residue: 0.2023
  time to fit residues: 24.1127
Evaluate side-chains
  87 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   83 VAL
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain J residue  257 GLN
Chi-restraints excluded: chain J residue  258 CYS
Chi-restraints excluded: chain J residue  261 GLN
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  837 THR
Chi-restraints excluded: chain A residue  914 THR
Chi-restraints excluded: chain A residue  945 GLU
Chi-restraints excluded: chain A residue  948 LEU
Chi-restraints excluded: chain A residue 1009 ASN
Chi-restraints excluded: chain A residue 1016 LEU
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1080 CYS
Chi-restraints excluded: chain A residue 1091 LEU
Chi-restraints excluded: chain A residue 1156 GLU
Chi-restraints excluded: chain A residue 1166 GLU
Chi-restraints excluded: chain A residue 1192 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 22 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9990
   chunk 72 optimal weight:    0.0020
   chunk 13 optimal weight:    0.3980
   chunk 4 optimal weight:    0.3980
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0050
   chunk 2 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0670
   overall best weight:    0.1740

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

Flipped N/Q/H residues before XYZ refinement:
J 261 GLN
** J 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 916 ASN
A1006 ASN
A1140 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.152205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.124324 restraints weight = 8443.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 2.56
r_work: 0.3467 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3467
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3467 r_free = 0.3467    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3467 r_free = 0.3467    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3467
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.055   6940  Z= 0.150
  Angle     :  0.562  11.287   9401  Z= 0.288
  Chirality :  0.043   0.333   1085
  Planarity :  0.003   0.041   1198
  Dihedral  :  4.529  18.709    915
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.15 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.31), residues: 845
  helix:  0.80 (0.36), residues: 231
  sheet: -2.16 (0.42), residues: 157
  loop : -0.98 (0.31), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP J 254 
 HIS   0.003   0.001   HIS A 913 
 PHE   0.022   0.001   PHE J 269 
 TYR   0.015   0.001   TYR J 305 
 ARG   0.002   0.000   ARG J 151 

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.938 
Fit side-chains
REVERT: J  297 GLN cc_start: 0.8453 (mp10) cc_final: 0.8231 (mp10)
REVERT: A  626 ARG cc_start: 0.6984 (tpt90) cc_final: 0.6523 (tpt-90)
REVERT: A  699 ARG cc_start: 0.8305 (mmp-170) cc_final: 0.7842 (mmp-170)
REVERT: A  811 ILE cc_start: 0.8578 (mt) cc_final: 0.8141 (mm)
REVERT: A  887 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7932 (mtt90)
REVERT: A  945 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6288 (pm20)
REVERT: A  969 GLU cc_start: 0.8441 (mp0) cc_final: 0.8202 (mp0)
REVERT: A  981 GLN cc_start: 0.8384 (tt0) cc_final: 0.8140 (tt0)
REVERT: A 1029 LYS cc_start: 0.8272 (mmmt) cc_final: 0.8070 (mmmm)
REVERT: A 1110 ILE cc_start: 0.8569 (mt) cc_final: 0.8290 (pt)
REVERT: A 1140 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7545 (pp30)
  outliers start: 19
  outliers final: 8
  residues processed: 85
  average time/residue: 0.2480
  time to fit residues: 29.3847
Evaluate side-chains
  79 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   83 VAL
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain J residue  258 CYS
Chi-restraints excluded: chain A residue  945 GLU
Chi-restraints excluded: chain A residue  948 LEU
Chi-restraints excluded: chain A residue 1009 ASN
Chi-restraints excluded: chain A residue 1016 LEU
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1129 VAL
Chi-restraints excluded: chain A residue 1140 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 32 optimal weight:    0.2980
   chunk 30 optimal weight:    0.4980
   chunk 33 optimal weight:    0.6980
   chunk 62 optimal weight:    0.3980
   chunk 63 optimal weight:    0.0010
   chunk 41 optimal weight:    0.0370
   chunk 22 optimal weight:    0.5980
   chunk 77 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 26 optimal weight:    0.2980
   overall best weight:    0.2064

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

Flipped N/Q/H residues before XYZ refinement:
J 261 GLN
** J 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 916 ASN
A1082 ASN
A1140 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.148322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.120992 restraints weight = 8572.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 2.53
r_work: 0.3408 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3260 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3276
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3276
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052   6940  Z= 0.156
  Angle     :  0.555  11.397   9401  Z= 0.283
  Chirality :  0.043   0.314   1085
  Planarity :  0.003   0.039   1198
  Dihedral  :  4.427  19.147    915
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 13.79 %
    Favored  : 84.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.31), residues: 845
  helix:  0.90 (0.36), residues: 231
  sheet: -2.12 (0.42), residues: 157
  loop : -0.95 (0.31), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 992 
 HIS   0.003   0.001   HIS A 913 
 PHE   0.020   0.001   PHE J 269 
 TYR   0.020   0.001   TYR J 309 
 ARG   0.001   0.000   ARG A 995 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3981.45 seconds
wall clock time: 68 minutes 54.70 seconds (4134.70 seconds total)