Starting phenix.real_space_refine
on Fri Aug 22 19:45:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pm6_17758/08_2025/8pm6_17758.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pm6_17758/08_2025/8pm6_17758.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pm6_17758/08_2025/8pm6_17758.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pm6_17758/08_2025/8pm6_17758.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pm6_17758/08_2025/8pm6_17758.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pm6_17758/08_2025/8pm6_17758.map"
  }
  resolution = 3.22
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     Cl      1      4.86       5
     C    4624      2.51       5
     N    1125      2.21       5
     O    1239      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7029
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 872, 6772
          Classifications: {'peptide': 872}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 24, 'TRANS': 847}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 257
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 257
          Unusual residues: {'CLR': 8, 'GBM': 1}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
  Time building chain proxies: 1.62, per 1000 atoms: 0.23
  Number of scatterers: 7029
  At special positions: 0
  Unit cell: (70.422, 103.092, 136.488, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      40     16.00
     O    1239      8.00
     N    1125      7.00
     C    4624      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: 0.48
  Conformation dependent library (CDL) restraints added in 374.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1608

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 2 sheets defined
      74.7% alpha, 1.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 55 through 101
      removed outlier: 3.777A  pdb=" N   GLN A  76 " --> pdb=" O   HIS A  72 " (cutoff:3.500A)
      Proline residue:  A  77  - end of helix
      removed outlier: 3.506A  pdb=" N   GLN A 101 " --> pdb=" O   LEU A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 183
      removed outlier: 3.804A  pdb=" N   MET A 183 " --> pdb=" O   PHE A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 214
    Processing helix  chain 'A' and resid 215 through 238
    Processing helix  chain 'A' and resid 240 through 287
      Proline residue:  A 250  - end of helix
      removed outlier: 3.810A  pdb=" N   SER A 264 " --> pdb=" O   GLY A 260 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   LYS A 276 " --> pdb=" O   LYS A 272 " (cutoff:3.500A)
      removed outlier: 4.773A  pdb=" N   ALA A 277 " --> pdb=" O   ALA A 273 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   SER A 287 " --> pdb=" O   GLU A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 294
      removed outlier: 3.718A  pdb=" N   VAL A 291 " --> pdb=" O   SER A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 350
      removed outlier: 4.187A  pdb=" N   VAL A 309 " --> pdb=" O   GLU A 305 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   PHE A 310 " --> pdb=" O   LYS A 306 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   ALA A 311 " --> pdb=" O   ASN A 307 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   TRP A 314 " --> pdb=" O   PHE A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 376
    Processing helix  chain 'A' and resid 376 through 394
    Processing helix  chain 'A' and resid 741 through 748
      removed outlier: 3.955A  pdb=" N   LEU A 745 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   LYS A 746 " --> pdb=" O   ARG A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 751 through 766
    Processing helix  chain 'A' and resid 767 through 782
    Processing helix  chain 'A' and resid 783 through 785
      No H-bonds generated for 'chain 'A' and resid 783 through 785'
    Processing helix  chain 'A' and resid 787 through 842
    Processing helix  chain 'A' and resid 843 through 848
    Processing helix  chain 'A' and resid 853 through 895
      removed outlier: 4.256A  pdb=" N   ALA A 865 " --> pdb=" O   LEU A 861 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   SER A 866 " --> pdb=" O   ALA A 862 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   GLN A 869 " --> pdb=" O   ALA A 865 " (cutoff:3.500A)
      removed outlier: 4.832A  pdb=" N   GLY A 870 " --> pdb=" O   SER A 866 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   ALA A 871 " --> pdb=" O   GLN A 867 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   SER A 874 " --> pdb=" O   GLY A 870 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   GLN A 875 " --> pdb=" O   ALA A 871 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   ILE A 876 " --> pdb=" O   ALA A 872 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 897 through 917
      removed outlier: 3.967A  pdb=" N   PHE A 907 " --> pdb=" O   VAL A 903 " (cutoff:3.500A)
      Proline residue:  A 909  - end of helix
      removed outlier: 4.165A  pdb=" N   GLY A 915 " --> pdb=" O   LEU A 911 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 917 through 923
    Processing helix  chain 'A' and resid 958 through 963
      removed outlier: 3.674A  pdb=" N   ALA A 962 " --> pdb=" O   ARG A 958 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LEU A 963 " --> pdb=" O   PHE A 959 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 958 through 963'
    Processing helix  chain 'A' and resid 964 through 966
      No H-bonds generated for 'chain 'A' and resid 964 through 966'
    Processing helix  chain 'A' and resid 967 through 1010
      removed outlier: 4.284A  pdb=" N   MET A 992 " --> pdb=" O   ALA A 988 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   PHE A 993 " --> pdb=" O   GLN A 989 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1036
      removed outlier: 3.585A  pdb=" N   VAL A1017 " --> pdb=" O   HIS A1013 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   SER A1036 " --> pdb=" O   GLY A1032 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1037 through 1056
      removed outlier: 4.400A  pdb=" N   LYS A1043 " --> pdb=" O   PRO A1039 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1120 through 1128
    Processing helix  chain 'A' and resid 1143 through 1147
    Processing helix  chain 'A' and resid 1148 through 1155
    Processing helix  chain 'A' and resid 1170 through 1174
    Processing helix  chain 'A' and resid 1188 through 1195
    Processing helix  chain 'A' and resid 1197 through 1204
      removed outlier: 3.553A  pdb=" N   LEU A1204 " --> pdb=" O   PHE A1200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1220 through 1235
      removed outlier: 3.503A  pdb=" N   LYS A1224 " --> pdb=" O   SER A1220 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   ARG A1226 " --> pdb=" O   GLY A1222 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   ARG A1235 " --> pdb=" O   ARG A1231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1250 through 1266
      removed outlier: 3.686A  pdb=" N   THR A1256 " --> pdb=" O   GLU A1252 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   GLU A1266 " --> pdb=" O   ASP A1262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1301 through 1306
      removed outlier: 4.348A  pdb=" N   ALA A1305 " --> pdb=" O   GLU A1301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1309 through 1314
      removed outlier: 3.646A  pdb=" N   LEU A1313 " --> pdb=" O   ALA A1309 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1080 through 1081
      removed outlier: 3.640A  pdb=" N   LYS A1136 " --> pdb=" O   VAL A1081 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1108 through 1110
      removed outlier: 6.355A  pdb=" N   LEU A1109 " --> pdb=" O   VAL A1272 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LEU A1242 " --> pdb=" O   ILE A1271 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL A1159 " --> pdb=" O   LEU A1241 " (cutoff:3.500A)

    481 hydrogen bonds defined for protein.
    1422 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.13

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1096
        1.32 -     1.44: 1905
        1.44 -     1.57: 4126
        1.57 -     1.69: 1
        1.69 -     1.82: 64
  Bond restraints: 7192
  Sorted by residual:
  bond pdb=" N   ILE A 393 "
       pdb=" CA  ILE A 393 "
    ideal  model  delta    sigma   weight residual
    1.457  1.510 -0.053 1.29e-02 6.01e+03 1.68e+01
  bond pdb=" N   PRO A 740 "
       pdb=" CA  PRO A 740 "
    ideal  model  delta    sigma   weight residual
    1.469  1.423  0.046 1.28e-02 6.10e+03 1.27e+01
  bond pdb=" CA  SER A 377 "
       pdb=" CB  SER A 377 "
    ideal  model  delta    sigma   weight residual
    1.531  1.485  0.046 1.33e-02 5.65e+03 1.19e+01
  bond pdb=" C   TRP A 752 "
       pdb=" O   TRP A 752 "
    ideal  model  delta    sigma   weight residual
    1.244  1.211  0.032 9.80e-03 1.04e+04 1.10e+01
  bond pdb=" C   PRO A1184 "
       pdb=" O   PRO A1184 "
    ideal  model  delta    sigma   weight residual
    1.232  1.192  0.041 1.25e-02 6.40e+03 1.06e+01
  ... (remaining 7187 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 9490
        2.03 -     4.06: 216
        4.06 -     6.09: 48
        6.09 -     8.12: 11
        8.12 -    10.15: 7
  Bond angle restraints: 9772
  Sorted by residual:
  angle pdb=" N   THR A 391 "
        pdb=" CA  THR A 391 "
        pdb=" C   THR A 391 "
      ideal   model   delta    sigma   weight residual
     111.82  102.14    9.68 1.16e+00 7.43e-01 6.96e+01
  angle pdb=" N   GLU A 395 "
        pdb=" CA  GLU A 395 "
        pdb=" C   GLU A 395 "
      ideal   model   delta    sigma   weight residual
     112.88  102.73   10.15 1.29e+00 6.01e-01 6.19e+01
  angle pdb=" N   ARG A 201 "
        pdb=" CA  ARG A 201 "
        pdb=" C   ARG A 201 "
      ideal   model   delta    sigma   weight residual
     111.36  103.90    7.46 1.09e+00 8.42e-01 4.68e+01
  angle pdb=" N   LEU A 745 "
        pdb=" CA  LEU A 745 "
        pdb=" C   LEU A 745 "
      ideal   model   delta    sigma   weight residual
     111.14  104.42    6.72 1.08e+00 8.57e-01 3.87e+01
  angle pdb=" N   THR A 396 "
        pdb=" CA  THR A 396 "
        pdb=" C   THR A 396 "
      ideal   model   delta    sigma   weight residual
     113.16  105.86    7.30 1.24e+00 6.50e-01 3.47e+01
  ... (remaining 9767 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.41: 4200
       24.41 -    48.81: 343
       48.81 -    73.22: 47
       73.22 -    97.62: 17
       97.62 -   122.03: 11
  Dihedral angle restraints: 4618
    sinusoidal: 2115
      harmonic: 2503
  Sorted by residual:
  dihedral pdb=" C   PRO A 378 "
           pdb=" N   PRO A 378 "
           pdb=" CA  PRO A 378 "
           pdb=" CB  PRO A 378 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -109.77  -10.93     0      2.50e+00 1.60e-01 1.91e+01
  dihedral pdb=" C1  CLR A1404 "
           pdb=" C2  CLR A1404 "
           pdb=" C3  CLR A1404 "
           pdb=" O1  CLR A1404 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.04   58.01  122.03     1      3.00e+01 1.11e-03 1.63e+01
  dihedral pdb=" C10 CLR A1405 "
           pdb=" C1  CLR A1405 "
           pdb=" C2  CLR A1405 "
           pdb=" C3  CLR A1405 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.83   64.17 -121.00     1      3.00e+01 1.11e-03 1.62e+01
  ... (remaining 4615 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 922
       0.055 -    0.109: 170
       0.109 -    0.163: 31
       0.163 -    0.218: 6
       0.218 -    0.272: 2
  Chirality restraints: 1131
  Sorted by residual:
  chirality pdb=" CA  ARG A 387 "
            pdb=" N   ARG A 387 "
            pdb=" C   ARG A 387 "
            pdb=" CB  ARG A 387 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.85e+00
  chirality pdb=" CB  ILE A 213 "
            pdb=" CA  ILE A 213 "
            pdb=" CG1 ILE A 213 "
            pdb=" CG2 ILE A 213 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CA  ILE A 206 "
            pdb=" N   ILE A 206 "
            pdb=" C   ILE A 206 "
            pdb=" CB  ILE A 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 1128 not shown)

  Planarity restraints: 1184
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C11 GBM A1409 "    0.493 2.00e-02 2.50e+03   3.37e-01 1.71e+03
        pdb=" C17 GBM A1409 "   -0.175 2.00e-02 2.50e+03
        pdb=" N8  GBM A1409 "   -0.494 2.00e-02 2.50e+03
        pdb=" N9  GBM A1409 "   -0.257 2.00e-02 2.50e+03
        pdb=" O3  GBM A1409 "    0.167 2.00e-02 2.50e+03
        pdb=" S2  GBM A1409 "    0.266 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A1070 "    0.019 2.00e-02 2.50e+03   3.79e-02 1.44e+01
        pdb=" C   LYS A1070 "   -0.066 2.00e-02 2.50e+03
        pdb=" O   LYS A1070 "    0.025 2.00e-02 2.50e+03
        pdb=" N   TRP A1071 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C25 GBM A1409 "   -0.037 2.00e-02 2.50e+03   3.21e-02 1.29e+01
        pdb=" C26 GBM A1409 "   -0.012 2.00e-02 2.50e+03
        pdb=" C27 GBM A1409 "   -0.022 2.00e-02 2.50e+03
        pdb=" N10 GBM A1409 "    0.053 2.00e-02 2.50e+03
        pdb=" O6  GBM A1409 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1181 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 656
        2.74 -     3.28: 7409
        3.28 -     3.82: 11725
        3.82 -     4.36: 13312
        4.36 -     4.90: 23081
  Nonbonded interactions: 56183
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A  88 "
            pdb=" OG1 THR A 355 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   LEU A 198 "
            pdb=" CD2 PHE A 202 "
     model   vdw
     2.215 3.340
  nonbonded pdb=" O   ALA A 995 "
            pdb=" OG  SER A 999 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   PHE A1018 "
            pdb=" OG  SER A1022 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   SER A 897 "
            pdb=" OG  SER A 901 "
     model   vdw
     2.272 3.040
  ... (remaining 56178 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.240
  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:          0.160
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.060
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
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   0.060   7192  Z= 0.303
  Angle     :  0.800  10.146   9772  Z= 0.510
  Chirality :  0.046   0.272   1131
  Planarity :  0.011   0.337   1184
  Dihedral  : 18.408 122.028   3010
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 22.73 %
    Favored  : 76.85 %
  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 aren not related in a simple way.
  whole:  0.94 (0.29), residues: 862
  helix:  1.65 (0.21), residues: 593
  sheet: -2.87 (1.00), residues: 17
  loop : -1.65 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1033 
 TYR   0.014   0.001   TYR A1041 
 PHE   0.016   0.001   PHE A 202 
 TRP   0.014   0.001   TRP A1071 
 HIS   0.003   0.001   HIS A1198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 ( 7192)
  covalent geometry    : angle       0.79982 ( 9772)
  hydrogen bonds       : bond        0.12295 (  481)
  hydrogen bonds       : angle       5.38861 ( 1422)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 139
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 LYS cc_start: 0.6747 (mmmm) cc_final: 0.6030 (tmtt)
REVERT: A  268 ASP cc_start: 0.7274 (t0) cc_final: 0.6984 (t0)
REVERT: A  322 MET cc_start: 0.7571 (ttm) cc_final: 0.7364 (ttm)
REVERT: A  743 ARG cc_start: 0.7170 (ptp-110) cc_final: 0.6560 (ttm110)
REVERT: A  744 ILE cc_start: 0.7072 (mm) cc_final: 0.6704 (mt)
REVERT: A  789 GLU cc_start: 0.7519 (pt0) cc_final: 0.6819 (mt-10)
REVERT: A  891 ILE cc_start: 0.8551 (mm) cc_final: 0.8348 (mt)
REVERT: A 1010 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6390 (tt0)
REVERT: A 1033 ARG cc_start: 0.7314 (ttm110) cc_final: 0.6982 (mmm160)
REVERT: A 1050 ARG cc_start: 0.7642 (mtp180) cc_final: 0.7374 (mtm110)
REVERT: A 1175 LYS cc_start: 0.7609 (pttp) cc_final: 0.6762 (mttt)
REVERT: A 1194 GLN cc_start: 0.8423 (mt0) cc_final: 0.7980 (mt0)
REVERT: A 1262 ASP cc_start: 0.8020 (m-30) cc_final: 0.7790 (m-30)
  outliers start: 3
  outliers final: 1
  residues processed: 139
  average time/residue: 0.0908
  time to fit residues: 16.7252
Evaluate side-chains
  103 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 170 GLN
A 210 ASN
A 375 ASN
A 813 GLN
** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1155 ASN
A1198 HIS
A1218 GLN
A1258 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.201607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.158553 restraints weight = 8839.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3887 rms_B_bonded: 2.01
r_work: 0.3705 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3572 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   7192  Z= 0.147
  Angle     :  0.590  11.561   9772  Z= 0.295
  Chirality :  0.041   0.189   1131
  Planarity :  0.004   0.049   1184
  Dihedral  :  8.365 107.436   1477
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 21.48 %
    Favored  : 74.62 %
  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 aren not related in a simple way.
  whole:  1.25 (0.29), residues: 862
  helix:  1.83 (0.21), residues: 608
  sheet: -2.90 (0.98), residues: 17
  loop : -1.57 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1033 
 TYR   0.015   0.001   TYR A 754 
 PHE   0.013   0.001   PHE A 776 
 TRP   0.011   0.001   TRP A1071 
 HIS   0.002   0.001   HIS A1198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 7192)
  covalent geometry    : angle       0.58963 ( 9772)
  hydrogen bonds       : bond        0.04189 (  481)
  hydrogen bonds       : angle       4.00432 ( 1422)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 110
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  743 ARG cc_start: 0.7039 (ptp-110) cc_final: 0.6716 (ttm110)
REVERT: A  789 GLU cc_start: 0.7687 (pt0) cc_final: 0.7116 (mt-10)
REVERT: A  875 GLN cc_start: 0.8600 (tp40) cc_final: 0.8167 (tp40)
REVERT: A 1010 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6721 (tt0)
REVERT: A 1033 ARG cc_start: 0.7736 (ttm110) cc_final: 0.7431 (mmm160)
REVERT: A 1050 ARG cc_start: 0.7889 (mtp180) cc_final: 0.7683 (mtp85)
REVERT: A 1175 LYS cc_start: 0.7873 (pttp) cc_final: 0.7258 (ptpt)
REVERT: A 1194 GLN cc_start: 0.8612 (mt0) cc_final: 0.8399 (mt0)
REVERT: A 1218 GLN cc_start: 0.4979 (OUTLIER) cc_final: 0.4684 (pm20)
REVERT: A 1244 GLU cc_start: 0.6049 (tp30) cc_final: 0.5588 (tt0)
REVERT: A 1258 GLN cc_start: 0.6819 (OUTLIER) cc_final: 0.6485 (tm-30)
REVERT: A 1262 ASP cc_start: 0.8228 (m-30) cc_final: 0.7766 (m-30)
  outliers start: 28
  outliers final: 14
  residues processed: 126
  average time/residue: 0.0867
  time to fit residues: 14.8518
Evaluate side-chains
  112 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  170 GLN
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  812 THR
Chi-restraints excluded: chain A residue  992 MET
Chi-restraints excluded: chain A residue 1061 ILE
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1164 VAL
Chi-restraints excluded: chain A residue 1218 GLN
Chi-restraints excluded: chain A residue 1258 GLN
Chi-restraints excluded: chain A residue 1263 LYS
Chi-restraints excluded: chain A residue 1269 THR
Chi-restraints excluded: chain A residue 1272 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 59 optimal weight:    4.9990
   chunk 64 optimal weight:    0.0570
   chunk 13 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0670
   chunk 44 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9980
   chunk 43 optimal weight:    0.2980
   chunk 79 optimal weight:    0.6980
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.3436

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

Flipped N/Q/H residues before XYZ refinement:
** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 842 GLN
** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 996 ASN
A1155 ASN
A1196 GLN
A1215 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.203842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.161539 restraints weight = 8750.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3928 rms_B_bonded: 2.03
r_work: 0.3739 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.061   7192  Z= 0.114
  Angle     :  0.523   6.965   9772  Z= 0.267
  Chirality :  0.040   0.157   1131
  Planarity :  0.004   0.049   1184
  Dihedral  :  7.606  93.342   1474
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 22.32 %
    Favored  : 74.34 %
  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 aren not related in a simple way.
  whole:  1.46 (0.29), residues: 862
  helix:  2.00 (0.21), residues: 611
  sheet: -2.96 (0.99), residues: 17
  loop : -1.59 (0.40), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1033 
 TYR   0.015   0.001   TYR A 754 
 PHE   0.010   0.001   PHE A  63 
 TRP   0.008   0.001   TRP A 314 
 HIS   0.002   0.000   HIS A1198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 7192)
  covalent geometry    : angle       0.52315 ( 9772)
  hydrogen bonds       : bond        0.03761 (  481)
  hydrogen bonds       : angle       3.86866 ( 1422)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A  185 MET cc_start: 0.1117 (OUTLIER) cc_final: 0.0641 (ppp)
REVERT: A  743 ARG cc_start: 0.6919 (ptp-110) cc_final: 0.6631 (ttm110)
REVERT: A  789 GLU cc_start: 0.7517 (pt0) cc_final: 0.7045 (mt-10)
REVERT: A 1050 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7559 (mtm110)
REVERT: A 1051 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7351 (t80)
REVERT: A 1175 LYS cc_start: 0.7621 (pttp) cc_final: 0.7052 (ptpt)
REVERT: A 1194 GLN cc_start: 0.8542 (mt0) cc_final: 0.8311 (mt0)
REVERT: A 1201 VAL cc_start: 0.3505 (OUTLIER) cc_final: 0.2932 (p)
REVERT: A 1243 ASP cc_start: 0.8253 (t0) cc_final: 0.8009 (m-30)
REVERT: A 1262 ASP cc_start: 0.8310 (m-30) cc_final: 0.7893 (m-30)
  outliers start: 24
  outliers final: 13
  residues processed: 119
  average time/residue: 0.0878
  time to fit residues: 13.9927
Evaluate side-chains
  109 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  921 MET
Chi-restraints excluded: chain A residue  992 MET
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1051 PHE
Chi-restraints excluded: chain A residue 1126 LEU
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1164 VAL
Chi-restraints excluded: chain A residue 1201 VAL
Chi-restraints excluded: chain A residue 1269 THR
Chi-restraints excluded: chain A residue 1272 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 54 optimal weight:    0.6980
   chunk 65 optimal weight:   10.0000
   chunk 64 optimal weight:    5.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 170 GLN
** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 842 GLN
** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1155 ASN
A1196 GLN
A1218 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.200990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.159129 restraints weight = 8903.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3889 rms_B_bonded: 1.95
r_work: 0.3698 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3562 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080   7192  Z= 0.141
  Angle     :  0.541   6.769   9772  Z= 0.275
  Chirality :  0.040   0.175   1131
  Planarity :  0.004   0.048   1184
  Dihedral  :  7.494  85.936   1474
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 21.62 %
    Favored  : 74.34 %
  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 aren not related in a simple way.
  whole:  1.45 (0.29), residues: 862
  helix:  2.00 (0.21), residues: 611
  sheet: -3.02 (0.98), residues: 17
  loop : -1.60 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 184 
 TYR   0.016   0.001   TYR A 754 
 PHE   0.023   0.001   PHE A  63 
 TRP   0.008   0.001   TRP A 898 
 HIS   0.003   0.001   HIS A1198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 7192)
  covalent geometry    : angle       0.54129 ( 9772)
  hydrogen bonds       : bond        0.03844 (  481)
  hydrogen bonds       : angle       3.86343 ( 1422)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 99
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A  185 MET cc_start: 0.1311 (OUTLIER) cc_final: 0.0760 (ppp)
REVERT: A  743 ARG cc_start: 0.7057 (ptp-110) cc_final: 0.6749 (ttm110)
REVERT: A  789 GLU cc_start: 0.7800 (pt0) cc_final: 0.7136 (mt-10)
REVERT: A 1050 ARG cc_start: 0.7919 (mtp180) cc_final: 0.7691 (mtp85)
REVERT: A 1051 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7600 (t80)
REVERT: A 1175 LYS cc_start: 0.7852 (pttp) cc_final: 0.7271 (ptpt)
REVERT: A 1194 GLN cc_start: 0.8610 (mt0) cc_final: 0.8336 (mt0)
REVERT: A 1199 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6617 (t0)
REVERT: A 1218 GLN cc_start: 0.4749 (OUTLIER) cc_final: 0.4509 (pm20)
REVERT: A 1243 ASP cc_start: 0.8441 (t0) cc_final: 0.8175 (m-30)
REVERT: A 1244 GLU cc_start: 0.5769 (tp30) cc_final: 0.5317 (tt0)
REVERT: A 1258 GLN cc_start: 0.7840 (tm-30) cc_final: 0.7561 (tp-100)
  outliers start: 29
  outliers final: 21
  residues processed: 117
  average time/residue: 0.0852
  time to fit residues: 13.5290
Evaluate side-chains
  118 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  921 MET
Chi-restraints excluded: chain A residue  992 MET
Chi-restraints excluded: chain A residue 1012 LEU
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1051 PHE
Chi-restraints excluded: chain A residue 1061 ILE
Chi-restraints excluded: chain A residue 1078 ILE
Chi-restraints excluded: chain A residue 1100 SER
Chi-restraints excluded: chain A residue 1126 LEU
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1164 VAL
Chi-restraints excluded: chain A residue 1180 THR
Chi-restraints excluded: chain A residue 1199 ASP
Chi-restraints excluded: chain A residue 1218 GLN
Chi-restraints excluded: chain A residue 1269 THR
Chi-restraints excluded: chain A residue 1272 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 63 optimal weight:    0.4980
   chunk 70 optimal weight:    0.9990
   chunk 83 optimal weight:    0.0030
   chunk 4 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 56 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.5590

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

Flipped N/Q/H residues before XYZ refinement:
** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 842 GLN
** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 996 ASN
A1155 ASN
A1218 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.202288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.159754 restraints weight = 8870.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3892 rms_B_bonded: 2.36
r_work: 0.3713 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   7192  Z= 0.122
  Angle     :  0.514   6.866   9772  Z= 0.263
  Chirality :  0.040   0.172   1131
  Planarity :  0.004   0.048   1184
  Dihedral  :  7.340  83.708   1474
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 19.67 %
    Favored  : 75.17 %
  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 aren not related in a simple way.
  whole:  1.59 (0.29), residues: 862
  helix:  2.08 (0.21), residues: 611
  sheet: -3.00 (0.99), residues: 17
  loop : -1.47 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 832 
 TYR   0.014   0.001   TYR A 754 
 PHE   0.015   0.001   PHE A  63 
 TRP   0.007   0.001   TRP A 898 
 HIS   0.003   0.001   HIS A1198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 7192)
  covalent geometry    : angle       0.51398 ( 9772)
  hydrogen bonds       : bond        0.03669 (  481)
  hydrogen bonds       : angle       3.81089 ( 1422)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 99
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A  185 MET cc_start: 0.1061 (OUTLIER) cc_final: 0.0585 (ppp)
REVERT: A  743 ARG cc_start: 0.7001 (ptp-110) cc_final: 0.6723 (ttm110)
REVERT: A  744 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7555 (mt)
REVERT: A  789 GLU cc_start: 0.7655 (pt0) cc_final: 0.7075 (mt-10)
REVERT: A  842 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7828 (mm110)
REVERT: A 1050 ARG cc_start: 0.7826 (mtp180) cc_final: 0.7536 (mtm110)
REVERT: A 1051 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7562 (t80)
REVERT: A 1175 LYS cc_start: 0.7673 (pttp) cc_final: 0.6951 (mttt)
REVERT: A 1194 GLN cc_start: 0.8599 (mt0) cc_final: 0.8307 (mt0)
REVERT: A 1199 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6628 (t0)
REVERT: A 1218 GLN cc_start: 0.4565 (OUTLIER) cc_final: 0.4324 (pm20)
REVERT: A 1243 ASP cc_start: 0.8302 (t0) cc_final: 0.8003 (m-30)
REVERT: A 1244 GLU cc_start: 0.5673 (tp30) cc_final: 0.5269 (tt0)
REVERT: A 1262 ASP cc_start: 0.8114 (m-30) cc_final: 0.7820 (m-30)
  outliers start: 37
  outliers final: 21
  residues processed: 124
  average time/residue: 0.0776
  time to fit residues: 12.7299
Evaluate side-chains
  117 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 91
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  744 ILE
Chi-restraints excluded: chain A residue  921 MET
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1035 PHE
Chi-restraints excluded: chain A residue 1051 PHE
Chi-restraints excluded: chain A residue 1061 ILE
Chi-restraints excluded: chain A residue 1100 SER
Chi-restraints excluded: chain A residue 1126 LEU
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1139 ILE
Chi-restraints excluded: chain A residue 1142 HIS
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1164 VAL
Chi-restraints excluded: chain A residue 1180 THR
Chi-restraints excluded: chain A residue 1199 ASP
Chi-restraints excluded: chain A residue 1204 LEU
Chi-restraints excluded: chain A residue 1218 GLN
Chi-restraints excluded: chain A residue 1269 THR
Chi-restraints excluded: chain A residue 1272 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0470
   chunk 81 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0030
   overall best weight:    1.1692

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

Flipped N/Q/H residues before XYZ refinement:
A 307 ASN
** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1155 ASN
A1218 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.199162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.155356 restraints weight = 8862.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3837 rms_B_bonded: 2.07
r_work: 0.3658 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.096   7192  Z= 0.165
  Angle     :  0.557   7.017   9772  Z= 0.287
  Chirality :  0.041   0.165   1131
  Planarity :  0.004   0.048   1184
  Dihedral  :  7.482  83.991   1474
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 19.94 %
    Favored  : 75.31 %
  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 aren not related in a simple way.
  whole:  1.43 (0.29), residues: 862
  helix:  1.97 (0.21), residues: 611
  sheet: -3.06 (0.93), residues: 18
  loop : -1.55 (0.42), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 832 
 TYR   0.016   0.002   TYR A 754 
 PHE   0.014   0.001   PHE A  63 
 TRP   0.009   0.001   TRP A 898 
 HIS   0.004   0.001   HIS A1198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 7192)
  covalent geometry    : angle       0.55699 ( 9772)
  hydrogen bonds       : bond        0.03963 (  481)
  hydrogen bonds       : angle       3.93560 ( 1422)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 92
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A   61 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7806 (mp)
REVERT: A  169 ARG cc_start: 0.7036 (mtt180) cc_final: 0.6740 (mtt-85)
REVERT: A  743 ARG cc_start: 0.7065 (ptp-110) cc_final: 0.6798 (ttm110)
REVERT: A  789 GLU cc_start: 0.7666 (pt0) cc_final: 0.7113 (mt-10)
REVERT: A 1050 ARG cc_start: 0.7806 (mtp180) cc_final: 0.7526 (mtm110)
REVERT: A 1051 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7630 (t80)
REVERT: A 1171 MET cc_start: 0.4946 (mmt) cc_final: 0.4709 (mmt)
REVERT: A 1175 LYS cc_start: 0.7745 (pttp) cc_final: 0.7166 (ptpt)
REVERT: A 1194 GLN cc_start: 0.8702 (mt0) cc_final: 0.8479 (mt0)
REVERT: A 1199 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.6709 (t0)
REVERT: A 1218 GLN cc_start: 0.4944 (OUTLIER) cc_final: 0.4724 (pm20)
REVERT: A 1243 ASP cc_start: 0.8300 (t0) cc_final: 0.7976 (m-30)
REVERT: A 1244 GLU cc_start: 0.5710 (tp30) cc_final: 0.5327 (tt0)
REVERT: A 1262 ASP cc_start: 0.8200 (m-30) cc_final: 0.7883 (m-30)
  outliers start: 34
  outliers final: 25
  residues processed: 115
  average time/residue: 0.0881
  time to fit residues: 13.6030
Evaluate side-chains
  117 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 88
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  812 THR
Chi-restraints excluded: chain A residue  921 MET
Chi-restraints excluded: chain A residue  992 MET
Chi-restraints excluded: chain A residue 1012 LEU
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1035 PHE
Chi-restraints excluded: chain A residue 1051 PHE
Chi-restraints excluded: chain A residue 1061 ILE
Chi-restraints excluded: chain A residue 1100 SER
Chi-restraints excluded: chain A residue 1126 LEU
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1164 VAL
Chi-restraints excluded: chain A residue 1180 THR
Chi-restraints excluded: chain A residue 1199 ASP
Chi-restraints excluded: chain A residue 1218 GLN
Chi-restraints excluded: chain A residue 1269 THR
Chi-restraints excluded: chain A residue 1272 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 50 optimal weight:    8.9990
   chunk 14 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 307 ASN
** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 842 GLN
** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1155 ASN
A1218 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.197641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.155618 restraints weight = 8862.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3855 rms_B_bonded: 2.02
r_work: 0.3654 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3521 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.101   7192  Z= 0.175
  Angle     :  0.567   7.777   9772  Z= 0.292
  Chirality :  0.042   0.162   1131
  Planarity :  0.004   0.048   1184
  Dihedral  :  7.596  83.436   1474
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 20.08 %
    Favored  : 74.90 %
  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 aren not related in a simple way.
  whole:  1.36 (0.29), residues: 862
  helix:  1.92 (0.21), residues: 611
  sheet: -2.99 (0.93), residues: 18
  loop : -1.57 (0.42), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 313 
 TYR   0.016   0.002   TYR A 754 
 PHE   0.014   0.002   PHE A  63 
 TRP   0.009   0.001   TRP A 898 
 HIS   0.003   0.001   HIS A1198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 7192)
  covalent geometry    : angle       0.56743 ( 9772)
  hydrogen bonds       : bond        0.04031 (  481)
  hydrogen bonds       : angle       3.95184 ( 1422)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 95
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A  169 ARG cc_start: 0.7193 (mtt180) cc_final: 0.6900 (mtt-85)
REVERT: A  282 ASP cc_start: 0.7951 (m-30) cc_final: 0.7629 (m-30)
REVERT: A  743 ARG cc_start: 0.7127 (ptp-110) cc_final: 0.6874 (ttm110)
REVERT: A  789 GLU cc_start: 0.7881 (pt0) cc_final: 0.7256 (mt-10)
REVERT: A 1050 ARG cc_start: 0.7852 (mtp180) cc_final: 0.7571 (mtm110)
REVERT: A 1051 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7593 (t80)
REVERT: A 1171 MET cc_start: 0.5428 (mmt) cc_final: 0.5185 (mmt)
REVERT: A 1175 LYS cc_start: 0.7933 (pttp) cc_final: 0.7349 (ptpt)
REVERT: A 1199 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.6883 (t0)
REVERT: A 1202 MET cc_start: 0.5655 (mmm) cc_final: 0.5111 (mmt)
REVERT: A 1218 GLN cc_start: 0.5261 (OUTLIER) cc_final: 0.4942 (pm20)
REVERT: A 1243 ASP cc_start: 0.8463 (t0) cc_final: 0.8150 (m-30)
REVERT: A 1244 GLU cc_start: 0.5821 (tp30) cc_final: 0.5442 (tt0)
REVERT: A 1262 ASP cc_start: 0.8295 (m-30) cc_final: 0.7984 (m-30)
REVERT: A 1304 MET cc_start: 0.4275 (mmm) cc_final: 0.3274 (mtp)
  outliers start: 36
  outliers final: 29
  residues processed: 118
  average time/residue: 0.0861
  time to fit residues: 13.7760
Evaluate side-chains
  122 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 90
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  812 THR
Chi-restraints excluded: chain A residue  921 MET
Chi-restraints excluded: chain A residue  992 MET
Chi-restraints excluded: chain A residue 1012 LEU
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1035 PHE
Chi-restraints excluded: chain A residue 1051 PHE
Chi-restraints excluded: chain A residue 1061 ILE
Chi-restraints excluded: chain A residue 1100 SER
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1139 ILE
Chi-restraints excluded: chain A residue 1142 HIS
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1164 VAL
Chi-restraints excluded: chain A residue 1180 THR
Chi-restraints excluded: chain A residue 1199 ASP
Chi-restraints excluded: chain A residue 1204 LEU
Chi-restraints excluded: chain A residue 1218 GLN
Chi-restraints excluded: chain A residue 1256 THR
Chi-restraints excluded: chain A residue 1269 THR
Chi-restraints excluded: chain A residue 1270 CYS
Chi-restraints excluded: chain A residue 1272 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 77 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 79 optimal weight:    0.1980
   chunk 66 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9980
   chunk 85 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 842 GLN
** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 996 ASN
A1155 ASN
A1218 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.199903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.157050 restraints weight = 8893.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3860 rms_B_bonded: 2.00
r_work: 0.3680 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3543 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076   7192  Z= 0.132
  Angle     :  0.535   8.336   9772  Z= 0.277
  Chirality :  0.041   0.166   1131
  Planarity :  0.004   0.048   1184
  Dihedral  :  7.367  82.057   1474
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 20.92 %
    Favored  : 74.62 %
  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 aren not related in a simple way.
  whole:  1.50 (0.29), residues: 862
  helix:  2.00 (0.21), residues: 612
  sheet: -3.03 (0.97), residues: 17
  loop : -1.47 (0.42), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 832 
 TYR   0.012   0.001   TYR A 754 
 PHE   0.013   0.001   PHE A  63 
 TRP   0.009   0.001   TRP A 898 
 HIS   0.003   0.001   HIS A1198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 7192)
  covalent geometry    : angle       0.53487 ( 9772)
  hydrogen bonds       : bond        0.03761 (  481)
  hydrogen bonds       : angle       3.84337 ( 1422)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 97
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A   61 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7869 (mp)
REVERT: A  169 ARG cc_start: 0.7133 (mtt180) cc_final: 0.6848 (mtt-85)
REVERT: A  282 ASP cc_start: 0.7968 (m-30) cc_final: 0.7694 (m-30)
REVERT: A  743 ARG cc_start: 0.7108 (ptp-110) cc_final: 0.6864 (ttm110)
REVERT: A  789 GLU cc_start: 0.7923 (pt0) cc_final: 0.7291 (mt-10)
REVERT: A 1050 ARG cc_start: 0.7845 (mtp180) cc_final: 0.7570 (mtm110)
REVERT: A 1051 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7609 (t80)
REVERT: A 1175 LYS cc_start: 0.7880 (pttp) cc_final: 0.7311 (ptpt)
REVERT: A 1199 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.6770 (t0)
REVERT: A 1202 MET cc_start: 0.5680 (mmm) cc_final: 0.5172 (mmt)
REVERT: A 1218 GLN cc_start: 0.5057 (OUTLIER) cc_final: 0.4765 (pm20)
REVERT: A 1243 ASP cc_start: 0.8437 (t0) cc_final: 0.8173 (m-30)
REVERT: A 1244 GLU cc_start: 0.5794 (tp30) cc_final: 0.5408 (tt0)
REVERT: A 1262 ASP cc_start: 0.8348 (m-30) cc_final: 0.8030 (m-30)
REVERT: A 1304 MET cc_start: 0.4315 (mmm) cc_final: 0.3287 (mtp)
  outliers start: 32
  outliers final: 23
  residues processed: 115
  average time/residue: 0.0814
  time to fit residues: 12.4708
Evaluate side-chains
  119 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  921 MET
Chi-restraints excluded: chain A residue  992 MET
Chi-restraints excluded: chain A residue 1012 LEU
Chi-restraints excluded: chain A residue 1035 PHE
Chi-restraints excluded: chain A residue 1051 PHE
Chi-restraints excluded: chain A residue 1061 ILE
Chi-restraints excluded: chain A residue 1100 SER
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1139 ILE
Chi-restraints excluded: chain A residue 1142 HIS
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1164 VAL
Chi-restraints excluded: chain A residue 1180 THR
Chi-restraints excluded: chain A residue 1199 ASP
Chi-restraints excluded: chain A residue 1204 LEU
Chi-restraints excluded: chain A residue 1218 GLN
Chi-restraints excluded: chain A residue 1256 THR
Chi-restraints excluded: chain A residue 1269 THR
Chi-restraints excluded: chain A residue 1272 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 85 optimal weight:    9.9990
   chunk 28 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 11 optimal weight:    0.1980
   chunk 52 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 842 GLN
** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1155 ASN
A1218 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.200056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.157334 restraints weight = 8800.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 2.28
r_work: 0.3688 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3552 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076   7192  Z= 0.134
  Angle     :  0.547   8.685   9772  Z= 0.282
  Chirality :  0.041   0.164   1131
  Planarity :  0.004   0.048   1184
  Dihedral  :  7.294  83.686   1474
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 20.78 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.29), residues: 862
  helix:  2.02 (0.21), residues: 612
  sheet: -2.99 (0.98), residues: 17
  loop : -1.44 (0.42), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 832 
 TYR   0.016   0.001   TYR A 144 
 PHE   0.013   0.001   PHE A  63 
 TRP   0.009   0.001   TRP A 898 
 HIS   0.003   0.000   HIS A1198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7192)
  covalent geometry    : angle       0.54706 ( 9772)
  hydrogen bonds       : bond        0.03709 (  481)
  hydrogen bonds       : angle       3.82557 ( 1422)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 92
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A   61 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7875 (mp)
REVERT: A  169 ARG cc_start: 0.7119 (mtt180) cc_final: 0.6834 (mtt-85)
REVERT: A  282 ASP cc_start: 0.7982 (m-30) cc_final: 0.7717 (m-30)
REVERT: A  743 ARG cc_start: 0.7117 (ptp-110) cc_final: 0.6868 (ttm110)
REVERT: A  789 GLU cc_start: 0.7916 (pt0) cc_final: 0.7286 (mt-10)
REVERT: A 1050 ARG cc_start: 0.7858 (mtp180) cc_final: 0.7569 (mtm110)
REVERT: A 1051 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7603 (t80)
REVERT: A 1175 LYS cc_start: 0.7908 (pttp) cc_final: 0.7305 (ptpt)
REVERT: A 1199 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6709 (t0)
REVERT: A 1202 MET cc_start: 0.5635 (mmm) cc_final: 0.5170 (mmt)
REVERT: A 1218 GLN cc_start: 0.5112 (OUTLIER) cc_final: 0.4858 (pm20)
REVERT: A 1243 ASP cc_start: 0.8432 (t0) cc_final: 0.8192 (m-30)
REVERT: A 1244 GLU cc_start: 0.5761 (tp30) cc_final: 0.5382 (tt0)
REVERT: A 1262 ASP cc_start: 0.8307 (m-30) cc_final: 0.7994 (m-30)
REVERT: A 1304 MET cc_start: 0.4306 (mmm) cc_final: 0.3282 (mtp)
  outliers start: 34
  outliers final: 26
  residues processed: 114
  average time/residue: 0.0779
  time to fit residues: 12.0980
Evaluate side-chains
  121 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 91
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  921 MET
Chi-restraints excluded: chain A residue  992 MET
Chi-restraints excluded: chain A residue 1012 LEU
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1035 PHE
Chi-restraints excluded: chain A residue 1051 PHE
Chi-restraints excluded: chain A residue 1061 ILE
Chi-restraints excluded: chain A residue 1100 SER
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1139 ILE
Chi-restraints excluded: chain A residue 1142 HIS
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1164 VAL
Chi-restraints excluded: chain A residue 1180 THR
Chi-restraints excluded: chain A residue 1199 ASP
Chi-restraints excluded: chain A residue 1204 LEU
Chi-restraints excluded: chain A residue 1218 GLN
Chi-restraints excluded: chain A residue 1269 THR
Chi-restraints excluded: chain A residue 1272 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 35 optimal weight:    0.3980
   chunk 47 optimal weight:    0.9980
   chunk 31 optimal weight:   10.0000
   chunk 66 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 49 optimal weight:    0.2980
   chunk 43 optimal weight:    0.0980
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 842 GLN
** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1155 ASN
A1218 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.201558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.158573 restraints weight = 8900.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3886 rms_B_bonded: 2.07
r_work: 0.3706 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   7192  Z= 0.127
  Angle     :  0.551  11.012   9772  Z= 0.282
  Chirality :  0.041   0.164   1131
  Planarity :  0.004   0.048   1184
  Dihedral  :  7.171  85.519   1474
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 20.64 %
    Favored  : 74.90 %
  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 aren not related in a simple way.
  whole:  1.67 (0.29), residues: 862
  helix:  2.13 (0.21), residues: 610
  sheet: -3.00 (0.98), residues: 17
  loop : -1.37 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 832 
 TYR   0.011   0.001   TYR A 754 
 PHE   0.013   0.001   PHE A1151 
 TRP   0.009   0.001   TRP A 898 
 HIS   0.002   0.000   HIS A1198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7192)
  covalent geometry    : angle       0.55061 ( 9772)
  hydrogen bonds       : bond        0.03609 (  481)
  hydrogen bonds       : angle       3.79773 ( 1422)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 90
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A   61 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7789 (mp)
REVERT: A  169 ARG cc_start: 0.7015 (mtt180) cc_final: 0.6745 (mtt-85)
REVERT: A  282 ASP cc_start: 0.7834 (m-30) cc_final: 0.7611 (m-30)
REVERT: A  743 ARG cc_start: 0.7002 (ptp-110) cc_final: 0.6777 (ttm110)
REVERT: A  789 GLU cc_start: 0.7648 (pt0) cc_final: 0.7221 (mt-10)
REVERT: A 1050 ARG cc_start: 0.7804 (mtp180) cc_final: 0.7519 (mtm110)
REVERT: A 1051 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7571 (t80)
REVERT: A 1175 LYS cc_start: 0.7771 (pttp) cc_final: 0.7059 (mttt)
REVERT: A 1199 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.6713 (t0)
REVERT: A 1202 MET cc_start: 0.5593 (mmm) cc_final: 0.5148 (mmt)
REVERT: A 1218 GLN cc_start: 0.4930 (OUTLIER) cc_final: 0.4636 (pm20)
REVERT: A 1243 ASP cc_start: 0.8252 (t0) cc_final: 0.7995 (m-30)
REVERT: A 1244 GLU cc_start: 0.5615 (tp30) cc_final: 0.5254 (tt0)
REVERT: A 1262 ASP cc_start: 0.8269 (m-30) cc_final: 0.7982 (m-30)
REVERT: A 1304 MET cc_start: 0.4351 (mmm) cc_final: 0.3313 (mtp)
  outliers start: 32
  outliers final: 25
  residues processed: 109
  average time/residue: 0.0663
  time to fit residues: 9.9410
Evaluate side-chains
  118 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 89
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  921 MET
Chi-restraints excluded: chain A residue  992 MET
Chi-restraints excluded: chain A residue 1012 LEU
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1035 PHE
Chi-restraints excluded: chain A residue 1051 PHE
Chi-restraints excluded: chain A residue 1061 ILE
Chi-restraints excluded: chain A residue 1100 SER
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1139 ILE
Chi-restraints excluded: chain A residue 1142 HIS
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain A residue 1164 VAL
Chi-restraints excluded: chain A residue 1180 THR
Chi-restraints excluded: chain A residue 1199 ASP
Chi-restraints excluded: chain A residue 1204 LEU
Chi-restraints excluded: chain A residue 1218 GLN
Chi-restraints excluded: chain A residue 1256 THR
Chi-restraints excluded: chain A residue 1272 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 85 optimal weight:   10.0000
   chunk 16 optimal weight:    0.8980
   chunk 50 optimal weight:    7.9990
   chunk 81 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0030
   chunk 43 optimal weight:    0.0970
   chunk 5 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 70 optimal weight:    0.4980
   chunk 22 optimal weight:    0.4980
   chunk 12 optimal weight:    9.9990
   overall best weight:    0.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1218 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.203428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.162504 restraints weight = 8743.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3923 rms_B_bonded: 1.94
r_work: 0.3736 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3604 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   7192  Z= 0.118
  Angle     :  0.534  10.761   9772  Z= 0.274
  Chirality :  0.040   0.165   1131
  Planarity :  0.004   0.047   1184
  Dihedral  :  7.018  87.432   1474
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 21.20 %
    Favored  : 74.62 %
  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 aren not related in a simple way.
  whole:  1.78 (0.30), residues: 862
  helix:  2.21 (0.21), residues: 610
  sheet: -3.13 (0.98), residues: 17
  loop : -1.33 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1268 
 TYR   0.019   0.001   TYR A 144 
 PHE   0.016   0.001   PHE A1151 
 TRP   0.009   0.001   TRP A 898 
 HIS   0.002   0.000   HIS A1198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 7192)
  covalent geometry    : angle       0.53409 ( 9772)
  hydrogen bonds       : bond        0.03479 (  481)
  hydrogen bonds       : angle       3.74881 ( 1422)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1986.27 seconds
wall clock time: 34 minutes 38.39 seconds (2078.39 seconds total)