Starting phenix.real_space_refine
on Tue Mar  3 16:04:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7crb_30449/03_2026/7crb_30449.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7crb_30449/03_2026/7crb_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_2026/7crb_30449.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7crb_30449/03_2026/7crb_30449.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7crb_30449/03_2026/7crb_30449.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7crb_30449/03_2026/7crb_30449.cif"
  }
  resolution = 3.16
  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=   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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.36, per 1000 atoms: 0.20
  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: 0.59
  Conformation dependent library (CDL) restraints added in 172.9 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: 0.25
  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: 0.93

  Time building geometry restraints manager: 0.77 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:             3.790
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.170
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.290
-------------------------------------------------------------------------------
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= 0.283
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.29 (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
 ARG   0.010   0.001   ARG J 307 
 TYR   0.009   0.001   TYR J 305 
 PHE   0.022   0.002   PHE A 868 
 TRP   0.054   0.002   TRP J  98 
 HIS   0.004   0.001   HIS A 913 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 ( 6940)
  covalent geometry    : angle       0.80913 ( 9401)
  hydrogen bonds       : bond        0.22611 (  207)
  hydrogen bonds       : angle       8.38211 (  585)

*********************** 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  : 0.237 
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: 0.0751
  time to fit residues: 8.9808
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  : 0.299 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.0970
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:    0.3980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.3980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.3778

-------------------------------------------------------------------------------
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 = 0.3816 r_free = 0.3816 target = 0.146337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.119060 restraints weight = 8531.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 2.47
r_work: 0.3379 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3239
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3239 r_free = 0.3239    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3238
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   6940  Z= 0.142
  Angle     :  0.594   9.226   9401  Z= 0.311
  Chirality :  0.043   0.143   1085
  Planarity :  0.004   0.036   1198
  Dihedral  :  5.938  58.939    921
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  :  6.51 %
    Favored  : 91.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.76 (0.30), residues: 845
  helix: -0.17 (0.34), residues: 243
  sheet: -2.22 (0.42), residues: 164
  loop : -1.25 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG J 307 
 TYR   0.012   0.001   TYR J 305 
 PHE   0.012   0.001   PHE A 868 
 TRP   0.017   0.002   TRP J  98 
 HIS   0.003   0.001   HIS A 913 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6940)
  covalent geometry    : angle       0.59359 ( 9401)
  hydrogen bonds       : bond        0.04586 (  207)
  hydrogen bonds       : angle       5.51944 (  585)

*********************** 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
  95 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  270 GLU cc_start: 0.7987 (tt0) cc_final: 0.7662 (pm20)
REVERT: A  795 GLN cc_start: 0.8053 (mt0) cc_final: 0.7821 (mp10)
REVERT: A  984 LYS cc_start: 0.8618 (mptt) cc_final: 0.8404 (mptt)
REVERT: A 1029 LYS cc_start: 0.8341 (mmmt) cc_final: 0.8115 (mmmm)
REVERT: A 1124 MET cc_start: 0.8532 (ttp) cc_final: 0.8100 (ttp)
REVERT: A 1166 GLU cc_start: 0.7745 (pt0) cc_final: 0.7338 (pt0)
  outliers start: 14
  outliers final: 12
  residues processed: 86
  average time/residue: 0.0737
  time to fit residues: 8.8678
Evaluate side-chains
  85 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain A residue 1139 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 59 optimal weight:    0.0980
   chunk 70 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 79 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   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 277 GLN
** J 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 643 HIS
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 = 0.3773 r_free = 0.3773 target = 0.142351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.115520 restraints weight = 8596.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 2.48
r_work: 0.3335 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3195
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   6940  Z= 0.191
  Angle     :  0.618  11.369   9401  Z= 0.318
  Chirality :  0.044   0.154   1085
  Planarity :  0.004   0.038   1198
  Dihedral  :  5.541  46.551    918
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  :  8.30 %
    Favored  : 88.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.30), residues: 845
  helix:  0.19 (0.35), residues: 240
  sheet: -2.24 (0.42), residues: 165
  loop : -1.25 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG J 307 
 TYR   0.011   0.001   TYR J 305 
 PHE   0.021   0.002   PHE J 269 
 TRP   0.009   0.001   TRP J 254 
 HIS   0.003   0.001   HIS A 913 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 6940)
  covalent geometry    : angle       0.61836 ( 9401)
  hydrogen bonds       : bond        0.04658 (  207)
  hydrogen bonds       : angle       5.13524 (  585)

*********************** 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
  95 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: A  916 ASN cc_start: 0.8969 (OUTLIER) cc_final: 0.8726 (t0)
REVERT: A  939 ILE cc_start: 0.8877 (mm) cc_final: 0.8674 (mm)
REVERT: A  969 GLU cc_start: 0.8583 (mp0) cc_final: 0.8264 (mp0)
REVERT: A  984 LYS cc_start: 0.8666 (mptt) cc_final: 0.8457 (mptt)
REVERT: A 1029 LYS cc_start: 0.8408 (mmmt) cc_final: 0.8172 (mmmm)
  outliers start: 22
  outliers final: 16
  residues processed: 83
  average time/residue: 0.0799
  time to fit residues: 8.9350
Evaluate side-chains
  81 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
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  914 THR
Chi-restraints excluded: chain A residue  916 ASN
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 1156 GLU
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 14 optimal weight:    0.3980
   chunk 68 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   chunk 45 optimal weight:    0.4980
   chunk 18 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0870
   chunk 33 optimal weight:    0.0980
   chunk 82 optimal weight:    0.7980
   overall best weight:    0.3758

-------------------------------------------------------------------------------
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**
A1140 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.146436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.118612 restraints weight = 8576.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 2.51
r_work: 0.3366 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3230
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3230
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.1554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6940  Z= 0.131
  Angle     :  0.565  10.587   9401  Z= 0.291
  Chirality :  0.042   0.158   1085
  Planarity :  0.003   0.034   1198
  Dihedral  :  4.967  45.570    916
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  :  9.58 %
    Favored  : 87.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.41 (0.31), residues: 845
  helix:  0.36 (0.35), residues: 237
  sheet: -2.22 (0.42), residues: 165
  loop : -1.06 (0.32), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 995 
 TYR   0.011   0.001   TYR J 305 
 PHE   0.019   0.001   PHE J 269 
 TRP   0.008   0.001   TRP J 254 
 HIS   0.003   0.001   HIS A 913 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6940)
  covalent geometry    : angle       0.56540 ( 9401)
  hydrogen bonds       : bond        0.03965 (  207)
  hydrogen bonds       : angle       4.85612 (  585)

*********************** 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
  96 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
REVERT: J  291 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7414 (tm-30)
REVERT: J  297 GLN cc_start: 0.8554 (mp10) cc_final: 0.8324 (mp10)
REVERT: J  304 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7087 (tp30)
REVERT: A  626 ARG cc_start: 0.6580 (tpt90) cc_final: 0.6372 (tpt-90)
REVERT: A  811 ILE cc_start: 0.8479 (mt) cc_final: 0.8144 (mm)
REVERT: A  887 ARG cc_start: 0.8316 (mtm-85) cc_final: 0.7945 (mtt90)
REVERT: A  945 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6472 (pm20)
REVERT: A  969 GLU cc_start: 0.8569 (mp0) cc_final: 0.8260 (mp0)
REVERT: A  984 LYS cc_start: 0.8662 (mptt) cc_final: 0.8457 (mptt)
REVERT: A 1029 LYS cc_start: 0.8383 (mmmt) cc_final: 0.8152 (mmmm)
REVERT: A 1140 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7618 (pp30)
  outliers start: 21
  outliers final: 14
  residues processed: 84
  average time/residue: 0.0867
  time to fit residues: 9.7505
Evaluate side-chains
  85 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
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  276 TYR
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  837 THR
Chi-restraints excluded: chain A residue  878 GLU
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 1103 THR
Chi-restraints excluded: chain A residue 1140 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0020
   chunk 17 optimal weight:    3.9990
   chunk 81 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.5588

-------------------------------------------------------------------------------
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 277 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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.143267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.116356 restraints weight = 8615.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.45
r_work: 0.3359 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3211
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    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 = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3211
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6940  Z= 0.168
  Angle     :  0.587   9.976   9401  Z= 0.300
  Chirality :  0.043   0.162   1085
  Planarity :  0.003   0.040   1198
  Dihedral  :  4.998  43.744    916
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  :  9.83 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.31), residues: 845
  helix:  0.36 (0.35), residues: 237
  sheet: -2.27 (0.41), residues: 166
  loop : -1.02 (0.32), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 995 
 TYR   0.012   0.001   TYR J 305 
 PHE   0.019   0.001   PHE J 269 
 TRP   0.008   0.001   TRP J 254 
 HIS   0.003   0.001   HIS A 913 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 6940)
  covalent geometry    : angle       0.58677 ( 9401)
  hydrogen bonds       : bond        0.04158 (  207)
  hydrogen bonds       : angle       4.78310 (  585)

*********************** 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
  100 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 72
  time to evaluate  : 0.255 
Fit side-chains
REVERT: J  297 GLN cc_start: 0.8620 (mp10) cc_final: 0.8388 (mp10)
REVERT: A  811 ILE cc_start: 0.8493 (mt) cc_final: 0.8146 (mm)
REVERT: A  887 ARG cc_start: 0.8358 (mtm-85) cc_final: 0.7980 (mtt90)
REVERT: A  945 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6506 (pm20)
REVERT: A  969 GLU cc_start: 0.8567 (mp0) cc_final: 0.8253 (mp0)
REVERT: A  981 GLN cc_start: 0.8719 (tt0) cc_final: 0.8486 (tt0)
REVERT: A  984 LYS cc_start: 0.8715 (mptt) cc_final: 0.8513 (mptt)
REVERT: A 1029 LYS cc_start: 0.8422 (mmmt) cc_final: 0.8184 (mmmm)
REVERT: A 1140 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7681 (pp30)
  outliers start: 28
  outliers final: 18
  residues processed: 89
  average time/residue: 0.0816
  time to fit residues: 9.7296
Evaluate side-chains
  87 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 67
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
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  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  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
Chi-restraints excluded: chain A residue 1156 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 60 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 33 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 916 ASN
A1140 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.141576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.114628 restraints weight = 8711.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.49
r_work: 0.3335 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.1663

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= 0.201
  Angle     :  0.617  10.276   9401  Z= 0.316
  Chirality :  0.044   0.165   1085
  Planarity :  0.004   0.039   1198
  Dihedral  :  4.917  20.473    915
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 10.98 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.30), residues: 845
  helix:  0.32 (0.35), residues: 236
  sheet: -2.28 (0.41), residues: 166
  loop : -1.07 (0.32), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 995 
 TYR   0.016   0.001   TYR J 305 
 PHE   0.019   0.002   PHE J 269 
 TRP   0.008   0.001   TRP J 254 
 HIS   0.003   0.001   HIS A 913 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 ( 6940)
  covalent geometry    : angle       0.61745 ( 9401)
  hydrogen bonds       : bond        0.04404 (  207)
  hydrogen bonds       : angle       4.83631 (  585)

*********************** 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
  95 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 68
  time to evaluate  : 0.265 
Fit side-chains
REVERT: J  297 GLN cc_start: 0.8595 (mp10) cc_final: 0.8373 (mp10)
REVERT: J  304 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7263 (tp30)
REVERT: A  626 ARG cc_start: 0.7096 (tpt90) cc_final: 0.6647 (tpt170)
REVERT: A  811 ILE cc_start: 0.8531 (mt) cc_final: 0.8179 (mm)
REVERT: A  945 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6487 (pm20)
REVERT: A  969 GLU cc_start: 0.8577 (mp0) cc_final: 0.8247 (mp0)
REVERT: A  981 GLN cc_start: 0.8730 (tt0) cc_final: 0.8508 (tt0)
REVERT: A 1029 LYS cc_start: 0.8379 (mmmt) cc_final: 0.8134 (mmmm)
REVERT: A 1120 ASP cc_start: 0.7486 (m-30) cc_final: 0.6914 (m-30)
REVERT: A 1140 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7620 (pp30)
  outliers start: 27
  outliers final: 20
  residues processed: 87
  average time/residue: 0.0769
  time to fit residues: 9.2739
Evaluate side-chains
  89 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 67
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
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  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  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  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 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
Chi-restraints excluded: chain A residue 1180 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0870
   chunk 47 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0030
   chunk 17 optimal weight:    0.4980
   chunk 9 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0170
   chunk 69 optimal weight:    0.8980
   chunk 62 optimal weight:    0.3980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.2006

-------------------------------------------------------------------------------
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 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3820 r_free = 0.3820 target = 0.146397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.119271 restraints weight = 8444.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 2.49
r_work: 0.3385 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3260
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3260
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.1858

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= 0.102
  Angle     :  0.545   9.758   9401  Z= 0.279
  Chirality :  0.041   0.163   1085
  Planarity :  0.003   0.033   1198
  Dihedral  :  4.532  18.113    915
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 11.88 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.31), residues: 845
  helix:  0.59 (0.36), residues: 232
  sheet: -2.08 (0.43), residues: 157
  loop : -0.99 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 995 
 TYR   0.011   0.001   TYR J 305 
 PHE   0.017   0.001   PHE J 269 
 TRP   0.008   0.001   TRP J 254 
 HIS   0.003   0.001   HIS A 913 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 6940)
  covalent geometry    : angle       0.54459 ( 9401)
  hydrogen bonds       : bond        0.03496 (  207)
  hydrogen bonds       : angle       4.58446 (  585)

*********************** 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
  100 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.264 
Fit side-chains
REVERT: J  291 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7629 (tm-30)
REVERT: J  304 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7183 (tp30)
REVERT: A  626 ARG cc_start: 0.7012 (tpt90) cc_final: 0.6698 (tpt-90)
REVERT: A  811 ILE cc_start: 0.8497 (mt) cc_final: 0.8094 (mm)
REVERT: A  837 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8266 (p)
REVERT: A  887 ARG cc_start: 0.8289 (mtm-85) cc_final: 0.7922 (mtt90)
REVERT: A  945 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6417 (pm20)
REVERT: A  969 GLU cc_start: 0.8576 (mp0) cc_final: 0.8281 (mp0)
REVERT: A  981 GLN cc_start: 0.8646 (tt0) cc_final: 0.8399 (tt0)
REVERT: A 1029 LYS cc_start: 0.8263 (mmmt) cc_final: 0.8025 (mmmm)
REVERT: A 1140 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7556 (pp30)
  outliers start: 22
  outliers final: 12
  residues processed: 89
  average time/residue: 0.0794
  time to fit residues: 9.6085
Evaluate side-chains
  86 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
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  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  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 1091 LEU
Chi-restraints excluded: chain A residue 1140 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0020
   chunk 51 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0980
   chunk 25 optimal weight:    0.4980
   chunk 76 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 62 optimal weight:    0.4980
   chunk 61 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.3388

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

Flipped N/Q/H residues before XYZ refinement:
J 261 GLN
** A 594 ASN ** 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 = 0.3820 r_free = 0.3820 target = 0.146313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.118891 restraints weight = 8564.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 2.53
r_work: 0.3378 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3230 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3239
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3239 r_free = 0.3239    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3239 r_free = 0.3239    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3239
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6940  Z= 0.122
  Angle     :  0.552   9.426   9401  Z= 0.281
  Chirality :  0.042   0.163   1085
  Planarity :  0.003   0.040   1198
  Dihedral  :  4.493  19.127    915
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 11.49 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.31), residues: 845
  helix:  0.70 (0.36), residues: 231
  sheet: -2.11 (0.42), residues: 158
  loop : -0.93 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 995 
 TYR   0.011   0.001   TYR J 305 
 PHE   0.022   0.001   PHE J 269 
 TRP   0.007   0.001   TRP J 254 
 HIS   0.003   0.001   HIS A 913 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6940)
  covalent geometry    : angle       0.55162 ( 9401)
  hydrogen bonds       : bond        0.03597 (  207)
  hydrogen bonds       : angle       4.51660 (  585)

*********************** 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
  95 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 71
  time to evaluate  : 0.182 
Fit side-chains
REVERT: J  291 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7693 (tm-30)
REVERT: J  304 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7213 (tp30)
REVERT: A  811 ILE cc_start: 0.8597 (mt) cc_final: 0.8140 (mm)
REVERT: A  837 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8270 (p)
REVERT: A  887 ARG cc_start: 0.8311 (mtm-85) cc_final: 0.7952 (mtt90)
REVERT: A  945 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6415 (pm20)
REVERT: A  969 GLU cc_start: 0.8570 (mp0) cc_final: 0.8276 (mp0)
REVERT: A 1029 LYS cc_start: 0.8246 (mmmt) cc_final: 0.8025 (mmmm)
  outliers start: 24
  outliers final: 16
  residues processed: 86
  average time/residue: 0.0726
  time to fit residues: 8.3954
Evaluate side-chains
  87 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
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  276 TYR
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 1080 CYS
Chi-restraints excluded: chain A residue 1091 LEU
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1156 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 24 optimal weight:    0.0670
   chunk 36 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0030
   chunk 60 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0870
   chunk 27 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 81 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0870
   overall best weight:    0.1684

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

Flipped N/Q/H residues before XYZ refinement:
J 261 GLN
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 = 0.3853 r_free = 0.3853 target = 0.149211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.122200 restraints weight = 8498.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 2.50
r_work: 0.3427 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3281 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3303
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3303 r_free = 0.3303    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3303 r_free = 0.3303    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3303
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2215

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= 0.094
  Angle     :  0.522   9.249   9401  Z= 0.265
  Chirality :  0.041   0.164   1085
  Planarity :  0.003   0.039   1198
  Dihedral  :  4.204  17.170    915
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 12.77 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.31), residues: 845
  helix:  0.81 (0.36), residues: 233
  sheet: -2.25 (0.41), residues: 161
  loop : -0.88 (0.31), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 995 
 TYR   0.008   0.001   TYR J 305 
 PHE   0.020   0.001   PHE J 269 
 TRP   0.006   0.001   TRP J 254 
 HIS   0.004   0.001   HIS A 913 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 6940)
  covalent geometry    : angle       0.52240 ( 9401)
  hydrogen bonds       : bond        0.03091 (  207)
  hydrogen bonds       : angle       4.27330 (  585)

*********************** 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
  97 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.223 
Fit side-chains
REVERT: J  297 GLN cc_start: 0.8555 (mp-120) cc_final: 0.8236 (mp10)
REVERT: J  304 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7256 (tp30)
REVERT: A  602 ARG cc_start: 0.5894 (tpt170) cc_final: 0.5078 (tpt90)
REVERT: A  699 ARG cc_start: 0.8314 (mmp-170) cc_final: 0.7838 (mmp-170)
REVERT: A  811 ILE cc_start: 0.8577 (mt) cc_final: 0.8127 (mm)
REVERT: A  887 ARG cc_start: 0.8255 (mtm-85) cc_final: 0.7958 (mtt90)
REVERT: A  945 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6461 (pm20)
REVERT: A  969 GLU cc_start: 0.8605 (mp0) cc_final: 0.8319 (mp0)
REVERT: A  981 GLN cc_start: 0.8474 (tt0) cc_final: 0.8244 (tt0)
REVERT: A 1029 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7942 (mmmm)
REVERT: A 1055 GLN cc_start: 0.7759 (tp40) cc_final: 0.7494 (tp40)
REVERT: A 1181 ASN cc_start: 0.8088 (m-40) cc_final: 0.7838 (m110)
  outliers start: 15
  outliers final: 10
  residues processed: 92
  average time/residue: 0.0803
  time to fit residues: 10.0183
Evaluate side-chains
  84 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
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  276 TYR
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 77 optimal weight:    0.2980
   chunk 75 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 39 optimal weight:    0.3980
   chunk 64 optimal weight:    0.9980
   chunk 5 optimal weight:    0.4980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
J 261 GLN
** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1082 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 = 0.3813 r_free = 0.3813 target = 0.145243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.117922 restraints weight = 8643.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 2.52
r_work: 0.3372 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3234
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3234 r_free = 0.3234    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3234 r_free = 0.3234    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3234
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.2079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6940  Z= 0.154
  Angle     :  0.578   9.836   9401  Z= 0.294
  Chirality :  0.042   0.169   1085
  Planarity :  0.003   0.043   1198
  Dihedral  :  4.482  19.811    915
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 13.41 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.05 (0.31), residues: 845
  helix:  0.78 (0.36), residues: 232
  sheet: -2.33 (0.40), residues: 172
  loop : -0.73 (0.32), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 995 
 TYR   0.012   0.001   TYR J 305 
 PHE   0.021   0.001   PHE J 269 
 TRP   0.007   0.001   TRP J 254 
 HIS   0.003   0.001   HIS A 913 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 6940)
  covalent geometry    : angle       0.57820 ( 9401)
  hydrogen bonds       : bond        0.03829 (  207)
  hydrogen bonds       : angle       4.48180 (  585)

********************** 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
  85 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.262 
Fit side-chains
REVERT: J  269 PHE cc_start: 0.6290 (t80) cc_final: 0.6075 (t80)
REVERT: J  297 GLN cc_start: 0.8587 (mp-120) cc_final: 0.8274 (mp10)
REVERT: J  304 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7274 (tp30)
REVERT: A  602 ARG cc_start: 0.5956 (tpt170) cc_final: 0.5429 (tpt90)
REVERT: A  811 ILE cc_start: 0.8552 (mt) cc_final: 0.8129 (mm)
REVERT: A  887 ARG cc_start: 0.8297 (mtm-85) cc_final: 0.8046 (mtt90)
REVERT: A  945 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6408 (pm20)
REVERT: A  969 GLU cc_start: 0.8586 (mp0) cc_final: 0.8285 (mp0)
REVERT: A 1029 LYS cc_start: 0.8240 (mmmt) cc_final: 0.8023 (mmmm)
  outliers start: 15
  outliers final: 13
  residues processed: 80
  average time/residue: 0.0744
  time to fit residues: 8.0990
Evaluate side-chains
  84 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
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  261 GLN
Chi-restraints excluded: chain J residue  276 TYR
Chi-restraints excluded: chain A residue  863 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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0970
   chunk 82 optimal weight:    0.5980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
J 261 GLN
** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1006 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 = 0.3816 r_free = 0.3816 target = 0.145363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.118013 restraints weight = 8655.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 2.52
r_work: 0.3371 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3222 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3226
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3226
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.2069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.148   6940  Z= 0.225
  Angle     :  1.038  59.200   9401  Z= 0.588
  Chirality :  0.046   0.542   1085
  Planarity :  0.003   0.042   1198
  Dihedral  :  4.485  19.765    915
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 13.41 %
    Favored  : 84.67 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.31), residues: 845
  helix:  0.78 (0.36), residues: 232
  sheet: -2.33 (0.40), residues: 172
  loop : -0.73 (0.32), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 995 
 TYR   0.012   0.001   TYR J 305 
 PHE   0.021   0.001   PHE J 269 
 TRP   0.007   0.001   TRP J 254 
 HIS   0.003   0.001   HIS A 913 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 ( 6940)
  covalent geometry    : angle       1.03779 ( 9401)
  hydrogen bonds       : bond        0.03879 (  207)
  hydrogen bonds       : angle       4.46789 (  585)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1918.85 seconds
wall clock time: 33 minutes 37.73 seconds (2017.73 seconds total)