Starting phenix.real_space_refine
on Tue Mar  3 17:39:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pd8_13331/03_2026/7pd8_13331.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pd8_13331/03_2026/7pd8_13331.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pd8_13331/03_2026/7pd8_13331.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pd8_13331/03_2026/7pd8_13331.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pd8_13331/03_2026/7pd8_13331.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pd8_13331/03_2026/7pd8_13331.cif"
  }
  resolution = 4.2
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    4936      2.51       5
     N    1269      2.21       5
     O    1381      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7642
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 842, 6676
          Classifications: {'peptide': 842}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 20, 'TRANS': 821}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 966
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 3, 'TRANS': 124}
  Time building chain proxies: 1.63, per 1000 atoms: 0.21
  Number of scatterers: 7642
  At special positions: 0
  Unit cell: (93.15, 78.57, 144.99, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1381      8.00
     N    1269      7.00
     C    4936      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: 0.85
  Conformation dependent library (CDL) restraints added in 273.3 milliseconds
  

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1810

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 6 sheets defined
      64.2% alpha, 6.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 99 through 108
      removed outlier: 3.585A  pdb=" N   ALA A 103 " --> pdb=" O   ASN A  99 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   MET A 105 " --> pdb=" O   GLU A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 136
      removed outlier: 3.599A  pdb=" N   THR A 112 " --> pdb=" O   CYS A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 163
    Processing helix  chain 'A' and resid 171 through 193
      removed outlier: 4.020A  pdb=" N   GLN A 193 " --> pdb=" O   ALA A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 236
    Processing helix  chain 'A' and resid 241 through 260
    Processing helix  chain 'A' and resid 279 through 336
      removed outlier: 3.918A  pdb=" N   PHE A 310 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 347
    Processing helix  chain 'A' and resid 402 through 407
    Processing helix  chain 'A' and resid 413 through 434
      removed outlier: 3.796A  pdb=" N   GLU A 432 " --> pdb=" O   ARG A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 481
      removed outlier: 3.758A  pdb=" N   GLU A 479 " --> pdb=" O   GLN A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 523
      removed outlier: 3.781A  pdb=" N   ASN A 515 " --> pdb=" O   SER A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 533 through 537
    Processing helix  chain 'A' and resid 784 through 808
      removed outlier: 3.642A  pdb=" N   LEU A 788 " --> pdb=" O   THR A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 844
      removed outlier: 3.781A  pdb=" N   LEU A 821 " --> pdb=" O   PRO A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 850 through 857
      removed outlier: 3.543A  pdb=" N   ARG A 854 " --> pdb=" O   THR A 850 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 858 through 860
      No H-bonds generated for 'chain 'A' and resid 858 through 860'
    Processing helix  chain 'A' and resid 861 through 885
      removed outlier: 3.599A  pdb=" N   HIS A 866 " --> pdb=" O   TRP A 862 " (cutoff:3.500A)
      Proline residue:  A 876  - end of helix
      removed outlier: 4.058A  pdb=" N   HIS A 883 " --> pdb=" O   ALA A 879 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   VAL A 884 " --> pdb=" O   VAL A 880 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR A 885 " --> pdb=" O   TYR A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 891 through 908
      removed outlier: 3.647A  pdb=" N   THR A 895 " --> pdb=" O   ASN A 891 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 911
      No H-bonds generated for 'chain 'A' and resid 909 through 911'
    Processing helix  chain 'A' and resid 917 through 936
      Proline residue:  A 931  - end of helix
    Processing helix  chain 'A' and resid 978 through 1037
      removed outlier: 4.222A  pdb=" N   ALA A1015 " --> pdb=" O   GLY A1011 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1038 through 1048
      removed outlier: 4.949A  pdb=" N   GLN A1044 " --> pdb=" O   HIS A1040 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   LEU A1045 " --> pdb=" O   VAL A1041 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LYS A1046 " --> pdb=" O   ALA A1042 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1072
      removed outlier: 4.071A  pdb=" N   GLU A1070 " --> pdb=" O   VAL A1066 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1079 through 1098
    Processing helix  chain 'A' and resid 1099 through 1103
    Processing helix  chain 'A' and resid 1133 through 1157
      removed outlier: 4.398A  pdb=" N   GLN A1137 " --> pdb=" O   GLN A1133 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ASN A1156 " --> pdb=" O   ASP A1152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1189 through 1201
      removed outlier: 4.373A  pdb=" N   ASN A1193 " --> pdb=" O   GLY A1189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1210 through 1219
    Processing helix  chain 'B' and resid 13 through 25
    Processing helix  chain 'B' and resid 26 through 36
    Processing helix  chain 'B' and resid 49 through 58
      removed outlier: 3.549A  pdb=" N   PHE B  57 " --> pdb=" O   LEU B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 70
    Processing helix  chain 'B' and resid 82 through 89
    Processing helix  chain 'B' and resid 92 through 102
      removed outlier: 3.884A  pdb=" N   VAL B  98 " --> pdb=" O   GLU B  94 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   LEU B  99 " --> pdb=" O   ILE B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 123
      removed outlier: 3.993A  pdb=" N   LEU B 119 " --> pdb=" O   THR B 115 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ALA B 120 " --> pdb=" O   PRO B 116 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ILE B 121 " --> pdb=" O   PHE B 117 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ASN B 123 " --> pdb=" O   LEU B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 135
      removed outlier: 3.659A  pdb=" N   VAL B 131 " --> pdb=" O   ASP B 127 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ALA B 135 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 388 through 391
    Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439
      removed outlier: 4.907A  pdb=" N   LYS A 437 " --> pdb=" O   VAL A 448 " (cutoff:3.500A)
      removed outlier: 5.549A  pdb=" N   VAL A 448 " --> pdb=" O   LYS A 437 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ASP A 399 " --> pdb=" O   ARG A 487 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ARG A 487 " --> pdb=" O   ASP A 399 " (cutoff:3.500A)
      removed outlier: 8.554A  pdb=" N   HIS A 530 " --> pdb=" O   MET A 486 " (cutoff:3.500A)
      removed outlier: 7.538A  pdb=" N   VAL A 488 " --> pdb=" O   HIS A 530 " (cutoff:3.500A)
      removed outlier: 8.451A  pdb=" N   SER A 532 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1052 through 1055
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1064 through 1065
      removed outlier: 3.749A  pdb=" N   ARG A1165 " --> pdb=" O   SER A1064 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1106 through 1109
      removed outlier: 6.949A  pdb=" N   MET A1116 " --> pdb=" O   ILE A1108 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1208 through 1209
      removed outlier: 3.585A  pdb=" N   TYR A1241 " --> pdb=" O   VAL A1209 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   LEU A1242 " --> pdb=" O   TYR A1226 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   TYR A1226 " --> pdb=" O   LEU A1242 " (cutoff:3.500A)

    476 hydrogen bonds defined for protein.
    1401 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: 1.44

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2433
        1.34 -     1.46: 1600
        1.46 -     1.58: 3684
        1.58 -     1.69: 1
        1.69 -     1.81: 88
  Bond restraints: 7806
  Sorted by residual:
  bond pdb=" CB  TRP A 862 "
       pdb=" CG  TRP A 862 "
    ideal  model  delta    sigma   weight residual
    1.498  1.620 -0.122 3.10e-02 1.04e+03 1.56e+01
  bond pdb=" CB  PHE A 232 "
       pdb=" CG  PHE A 232 "
    ideal  model  delta    sigma   weight residual
    1.502  1.437  0.065 2.30e-02 1.89e+03 7.87e+00
  bond pdb=" CB  VAL A 907 "
       pdb=" CG2 VAL A 907 "
    ideal  model  delta    sigma   weight residual
    1.521  1.437  0.084 3.30e-02 9.18e+02 6.45e+00
  bond pdb=" CB  VAL A 986 "
       pdb=" CG1 VAL A 986 "
    ideal  model  delta    sigma   weight residual
    1.521  1.439  0.082 3.30e-02 9.18e+02 6.18e+00
  bond pdb=" CG1 ILE A 291 "
       pdb=" CD1 ILE A 291 "
    ideal  model  delta    sigma   weight residual
    1.513  1.422  0.091 3.90e-02 6.57e+02 5.50e+00
  ... (remaining 7801 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.72: 10284
        2.72 -     5.45: 238
        5.45 -     8.17: 27
        8.17 -    10.90: 9
       10.90 -    13.62: 5
  Bond angle restraints: 10563
  Sorted by residual:
  angle pdb=" CA  TYR A1072 "
        pdb=" C   TYR A1072 "
        pdb=" O   TYR A1072 "
      ideal   model   delta    sigma   weight residual
     119.49  113.57    5.92 1.21e+00 6.83e-01 2.39e+01
  angle pdb=" N   ASN A 356 "
        pdb=" CA  ASN A 356 "
        pdb=" C   ASN A 356 "
      ideal   model   delta    sigma   weight residual
     114.31  108.05    6.26 1.29e+00 6.01e-01 2.35e+01
  angle pdb=" C   ASP A 344 "
        pdb=" N   ASP A 345 "
        pdb=" CA  ASP A 345 "
      ideal   model   delta    sigma   weight residual
     120.38  126.61   -6.23 1.37e+00 5.33e-01 2.07e+01
  angle pdb=" C   SER A 813 "
        pdb=" N   THR A 814 "
        pdb=" CA  THR A 814 "
      ideal   model   delta    sigma   weight residual
     120.69  107.60   13.09 2.95e+00 1.15e-01 1.97e+01
  angle pdb=" CA  LEU A 231 "
        pdb=" CB  LEU A 231 "
        pdb=" CG  LEU A 231 "
      ideal   model   delta    sigma   weight residual
     116.30  102.68   13.62 3.50e+00 8.16e-02 1.51e+01
  ... (remaining 10558 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.11: 3969
       17.11 -    34.23: 513
       34.23 -    51.34: 89
       51.34 -    68.46: 18
       68.46 -    85.57: 6
  Dihedral angle restraints: 4595
    sinusoidal: 1788
      harmonic: 2807
  Sorted by residual:
  dihedral pdb=" CA  PRO A 816 "
           pdb=" C   PRO A 816 "
           pdb=" N   PRO A 817 "
           pdb=" CA  PRO A 817 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.46  -27.54     0      5.00e+00 4.00e-02 3.03e+01
  dihedral pdb=" CA  LEU A 978 "
           pdb=" C   LEU A 978 "
           pdb=" N   ILE A 979 "
           pdb=" CA  ILE A 979 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.68   27.32     0      5.00e+00 4.00e-02 2.99e+01
  dihedral pdb=" CA  GLU A1043 "
           pdb=" C   GLU A1043 "
           pdb=" N   GLN A1044 "
           pdb=" CA  GLN A1044 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.54  -25.46     0      5.00e+00 4.00e-02 2.59e+01
  ... (remaining 4592 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 672
       0.036 -    0.072: 351
       0.072 -    0.108: 144
       0.108 -    0.144: 29
       0.144 -    0.180: 13
  Chirality restraints: 1209
  Sorted by residual:
  chirality pdb=" CB  ILE A1022 "
            pdb=" CA  ILE A1022 "
            pdb=" CG1 ILE A1022 "
            pdb=" CG2 ILE A1022 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.18 2.00e-01 2.50e+01 8.10e-01
  chirality pdb=" CA  LEU A 875 "
            pdb=" N   LEU A 875 "
            pdb=" C   LEU A 875 "
            pdb=" CB  LEU A 875 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.18 2.00e-01 2.50e+01 7.66e-01
  chirality pdb=" CA  PHE A 987 "
            pdb=" N   PHE A 987 "
            pdb=" C   PHE A 987 "
            pdb=" CB  PHE A 987 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.53e-01
  ... (remaining 1206 not shown)

  Planarity restraints: 1323
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 918 "    0.020 2.00e-02 2.50e+03   1.51e-02 5.67e+00
        pdb=" CG  TRP A 918 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 918 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 918 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 918 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 918 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 918 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 918 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 918 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 918 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 994 "   -0.010 2.00e-02 2.50e+03   1.98e-02 3.91e+00
        pdb=" C   VAL A 994 "    0.034 2.00e-02 2.50e+03
        pdb=" O   VAL A 994 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   TRP A 995 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 987 "   -0.014 2.00e-02 2.50e+03   1.33e-02 3.09e+00
        pdb=" CG  PHE A 987 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 987 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 987 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 987 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 987 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 987 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1320 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 139
        2.58 -     3.16: 7866
        3.16 -     3.74: 13057
        3.74 -     4.32: 17552
        4.32 -     4.90: 26012
  Nonbonded interactions: 64626
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 912 "
            pdb=" NH1 ARG A 920 "
     model   vdw
     2.003 3.120
  nonbonded pdb=" OH  TYR A1226 "
            pdb=" OG1 THR A1229 "
     model   vdw
     2.098 3.040
  nonbonded pdb=" O   SER A 532 "
            pdb=" OG1 THR A 535 "
     model   vdw
     2.123 3.040
  nonbonded pdb=" O   PRO A1100 "
            pdb=" OG  SER A1103 "
     model   vdw
     2.134 3.040
  nonbonded pdb=" NE2 GLN A 389 "
            pdb=" OG1 THR A 494 "
     model   vdw
     2.154 3.120
  ... (remaining 64621 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.660
  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:             0.020
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.010
  Find NCS groups from input model:        0.040
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
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      :  0.009   0.122   7806  Z= 0.436
  Angle     :  1.080  13.622  10563  Z= 0.612
  Chirality :  0.051   0.180   1209
  Planarity :  0.005   0.042   1323
  Dihedral  : 15.646  85.573   2785
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 34.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.22 %
    Favored  : 88.78 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 13.82 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.82 (0.20), residues: 954
  helix: -2.69 (0.16), residues: 569
  sheet: -4.06 (0.40), residues: 84
  loop : -3.52 (0.29), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 920 
 TYR   0.018   0.003   TYR A1185 
 PHE   0.030   0.003   PHE A 987 
 TRP   0.041   0.003   TRP A 918 
 HIS   0.009   0.002   HIS A 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00896 ( 7806)
  covalent geometry    : angle       1.07995 (10563)
  hydrogen bonds       : bond        0.13594 (  476)
  hydrogen bonds       : angle       7.70021 ( 1401)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 193
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 MET cc_start: 0.8257 (mmt) cc_final: 0.7691 (mmt)
REVERT: A  167 LEU cc_start: 0.8320 (tp) cc_final: 0.7928 (tt)
REVERT: A  288 HIS cc_start: 0.7954 (m90) cc_final: 0.7671 (m90)
REVERT: A  446 TYR cc_start: 0.7975 (p90) cc_final: 0.7670 (p90)
REVERT: A  465 MET cc_start: 0.8638 (ttt) cc_final: 0.8263 (ttt)
REVERT: A  793 LEU cc_start: 0.9331 (tp) cc_final: 0.9010 (tp)
REVERT: A  798 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.8090 (t80)
REVERT: A 1095 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8050 (mt-10)
REVERT: A 1107 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8068 (ttmt)
REVERT: A 1115 TYR cc_start: 0.7761 (t80) cc_final: 0.6679 (t80)
REVERT: A 1147 MET cc_start: 0.9248 (ttm) cc_final: 0.8775 (tmm)
  outliers start: 9
  outliers final: 5
  residues processed: 201
  average time/residue: 0.0940
  time to fit residues: 25.4267
Evaluate side-chains
  161 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 155
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 262 HIS
A 319 HIS
A 389 GLN
A 883 HIS
** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1028 GLN
A1075 ASN
A1135 HIS
A1154 ASN
A1155 ASN
B  48 HIS
B 107 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.129921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.093503 restraints weight = 19878.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.093742 restraints weight = 13643.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.094106 restraints weight = 8790.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.094579 restraints weight = 7782.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.094794 restraints weight = 7086.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.2850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7806  Z= 0.153
  Angle     :  0.698   9.536  10563  Z= 0.359
  Chirality :  0.042   0.189   1209
  Planarity :  0.004   0.052   1323
  Dihedral  :  5.392  29.359   1036
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 15.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  4.97 %
    Favored  : 94.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.18 (0.25), residues: 954
  helix: -0.58 (0.20), residues: 586
  sheet: -3.47 (0.45), residues: 86
  loop : -2.36 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 920 
 TYR   0.015   0.002   TYR A 261 
 PHE   0.020   0.002   PHE A 232 
 TRP   0.012   0.001   TRP A 918 
 HIS   0.007   0.001   HIS A 530 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 7806)
  covalent geometry    : angle       0.69764 (10563)
  hydrogen bonds       : bond        0.04902 (  476)
  hydrogen bonds       : angle       5.43261 ( 1401)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 225
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 LEU cc_start: 0.8429 (tp) cc_final: 0.8076 (tt)
REVERT: A  181 LEU cc_start: 0.9210 (mm) cc_final: 0.8957 (mm)
REVERT: A  233 LEU cc_start: 0.9376 (mm) cc_final: 0.8940 (mm)
REVERT: A  288 HIS cc_start: 0.7680 (m90) cc_final: 0.7364 (m90)
REVERT: A  419 LEU cc_start: 0.9605 (tp) cc_final: 0.9279 (tp)
REVERT: A  445 TYR cc_start: 0.7934 (t80) cc_final: 0.7671 (t80)
REVERT: A  465 MET cc_start: 0.8999 (ttt) cc_final: 0.8451 (ttp)
REVERT: A  545 MET cc_start: 0.7781 (mpp) cc_final: 0.7511 (mmt)
REVERT: A  854 ARG cc_start: 0.7862 (tpm170) cc_final: 0.7644 (tpm170)
REVERT: A  865 ARG cc_start: 0.7952 (ttp-170) cc_final: 0.7670 (ttp-170)
REVERT: A  996 PHE cc_start: 0.8040 (m-10) cc_final: 0.7829 (m-80)
REVERT: A 1107 LYS cc_start: 0.8336 (ttpt) cc_final: 0.8048 (ttmt)
REVERT: A 1147 MET cc_start: 0.9008 (ttm) cc_final: 0.8433 (tmm)
REVERT: A 1149 VAL cc_start: 0.9245 (t) cc_final: 0.8672 (t)
REVERT: A 1198 MET cc_start: 0.8153 (tpp) cc_final: 0.7662 (tpp)
REVERT: B   34 MET cc_start: 0.7805 (ttt) cc_final: 0.7256 (mmm)
REVERT: B   78 TRP cc_start: 0.7493 (t-100) cc_final: 0.6892 (t-100)
  outliers start: 2
  outliers final: 1
  residues processed: 226
  average time/residue: 0.0847
  time to fit residues: 26.4103
Evaluate side-chains
  177 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 176
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 47 optimal weight:    0.0670
   chunk 5 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 23 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 84 optimal weight:    5.9990
   chunk 43 optimal weight:    7.9990
   chunk 61 optimal weight:    0.7980
   chunk 28 optimal weight:    8.9990
   chunk 48 optimal weight:    0.4980
   chunk 80 optimal weight:    5.9990
   overall best weight:    1.0320

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

Flipped N/Q/H residues before XYZ refinement:
A 297 HIS
A 335 HIS
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1237 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.131880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.089269 restraints weight = 20039.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.092292 restraints weight = 11301.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.094341 restraints weight = 7438.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.095632 restraints weight = 5563.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.096589 restraints weight = 4617.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.3780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7806  Z= 0.143
  Angle     :  0.648   9.564  10563  Z= 0.334
  Chirality :  0.042   0.211   1209
  Planarity :  0.004   0.038   1323
  Dihedral  :  4.943  27.257   1036
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  4.36 %
    Favored  : 95.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.26), residues: 954
  helix:  0.23 (0.20), residues: 591
  sheet: -2.85 (0.46), residues: 92
  loop : -2.11 (0.38), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 920 
 TYR   0.024   0.002   TYR A1083 
 PHE   0.046   0.002   PHE A 184 
 TRP   0.006   0.001   TRP A 918 
 HIS   0.014   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 7806)
  covalent geometry    : angle       0.64785 (10563)
  hydrogen bonds       : bond        0.04370 (  476)
  hydrogen bonds       : angle       5.01028 ( 1401)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 209
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 LEU cc_start: 0.8420 (tp) cc_final: 0.8038 (tt)
REVERT: A  446 TYR cc_start: 0.7751 (p90) cc_final: 0.7490 (p90)
REVERT: A  465 MET cc_start: 0.9095 (ttt) cc_final: 0.8563 (ttp)
REVERT: A  854 ARG cc_start: 0.7902 (tpm170) cc_final: 0.7679 (tpm170)
REVERT: A 1025 MET cc_start: 0.8015 (tpp) cc_final: 0.7717 (tpp)
REVERT: A 1085 VAL cc_start: 0.9590 (t) cc_final: 0.9345 (t)
REVERT: A 1107 LYS cc_start: 0.8319 (ttpt) cc_final: 0.8044 (ttmt)
REVERT: A 1147 MET cc_start: 0.9105 (ttm) cc_final: 0.8516 (tmm)
REVERT: A 1198 MET cc_start: 0.8286 (tpp) cc_final: 0.7819 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 210
  average time/residue: 0.0829
  time to fit residues: 24.1678
Evaluate side-chains
  170 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 72 optimal weight:    7.9990
   chunk 29 optimal weight:    9.9990
   chunk 90 optimal weight:   30.0000
   chunk 64 optimal weight:    0.4980
   chunk 55 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 37 optimal weight:   20.0000
   chunk 50 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 335 HIS
** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.132341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.095904 restraints weight = 19837.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.095948 restraints weight = 12585.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.096647 restraints weight = 9480.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.096517 restraints weight = 8340.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.096948 restraints weight = 7581.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.4261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7806  Z= 0.137
  Angle     :  0.656   9.459  10563  Z= 0.333
  Chirality :  0.042   0.145   1209
  Planarity :  0.004   0.038   1323
  Dihedral  :  4.751  25.678   1036
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.27 %
    Favored  : 96.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.80 (0.27), residues: 954
  helix:  0.50 (0.20), residues: 593
  sheet: -2.59 (0.49), residues: 87
  loop : -1.95 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  23 
 TYR   0.023   0.001   TYR A1083 
 PHE   0.050   0.002   PHE A 184 
 TRP   0.008   0.001   TRP A 510 
 HIS   0.004   0.001   HIS A 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7806)
  covalent geometry    : angle       0.65576 (10563)
  hydrogen bonds       : bond        0.04215 (  476)
  hydrogen bonds       : angle       4.73521 ( 1401)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 208
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 CYS cc_start: 0.8961 (m) cc_final: 0.8400 (p)
REVERT: A  167 LEU cc_start: 0.8457 (tp) cc_final: 0.8029 (tt)
REVERT: A  446 TYR cc_start: 0.7696 (p90) cc_final: 0.7381 (p90)
REVERT: A  465 MET cc_start: 0.9115 (ttt) cc_final: 0.8579 (ttp)
REVERT: A  545 MET cc_start: 0.7717 (mpp) cc_final: 0.7439 (mmt)
REVERT: A  854 ARG cc_start: 0.7972 (tpm170) cc_final: 0.7755 (tpm170)
REVERT: A  996 PHE cc_start: 0.7719 (m-10) cc_final: 0.7409 (m-80)
REVERT: A 1107 LYS cc_start: 0.8226 (ttpt) cc_final: 0.7870 (ttmt)
REVERT: A 1139 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9134 (pp)
REVERT: A 1147 MET cc_start: 0.9062 (ttm) cc_final: 0.8533 (tmm)
REVERT: A 1198 MET cc_start: 0.8248 (tpp) cc_final: 0.7951 (tpp)
REVERT: B   78 TRP cc_start: 0.7585 (t-100) cc_final: 0.6970 (t-100)
  outliers start: 1
  outliers final: 0
  residues processed: 209
  average time/residue: 0.0761
  time to fit residues: 22.4696
Evaluate side-chains
  164 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 163
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 20 optimal weight:    0.0370
   chunk 68 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 66 optimal weight:    6.9990
   chunk 75 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   chunk 89 optimal weight:   20.0000
   chunk 71 optimal weight:    0.1980
   chunk 87 optimal weight:    6.9990
   chunk 59 optimal weight:    0.6980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1131 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.133672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.096942 restraints weight = 19850.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.096414 restraints weight = 12021.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.097109 restraints weight = 8952.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.097577 restraints weight = 8294.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.097686 restraints weight = 7713.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.4727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7806  Z= 0.128
  Angle     :  0.666   9.624  10563  Z= 0.332
  Chirality :  0.042   0.170   1209
  Planarity :  0.004   0.038   1323
  Dihedral  :  4.597  22.608   1036
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.27), residues: 954
  helix:  0.73 (0.20), residues: 595
  sheet: -2.44 (0.47), residues: 102
  loop : -1.87 (0.39), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1026 
 TYR   0.013   0.001   TYR A 252 
 PHE   0.037   0.001   PHE A 184 
 TRP   0.028   0.001   TRP A 995 
 HIS   0.004   0.001   HIS B  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 7806)
  covalent geometry    : angle       0.66561 (10563)
  hydrogen bonds       : bond        0.04027 (  476)
  hydrogen bonds       : angle       4.54014 ( 1401)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 CYS cc_start: 0.8920 (m) cc_final: 0.8372 (p)
REVERT: A  167 LEU cc_start: 0.8433 (tp) cc_final: 0.8009 (tt)
REVERT: A  446 TYR cc_start: 0.7628 (p90) cc_final: 0.7243 (p90)
REVERT: A  465 MET cc_start: 0.9170 (ttt) cc_final: 0.8551 (ttp)
REVERT: A  516 LEU cc_start: 0.9406 (mt) cc_final: 0.9180 (mt)
REVERT: A  519 LEU cc_start: 0.9448 (mt) cc_final: 0.9245 (pp)
REVERT: A  520 MET cc_start: 0.7915 (ttm) cc_final: 0.7699 (ttp)
REVERT: A  545 MET cc_start: 0.7645 (mpp) cc_final: 0.7331 (mmt)
REVERT: A  854 ARG cc_start: 0.8010 (tpm170) cc_final: 0.7797 (tpm170)
REVERT: A  862 TRP cc_start: -0.0354 (m-10) cc_final: -0.1699 (t60)
REVERT: A  996 PHE cc_start: 0.7575 (m-10) cc_final: 0.7242 (m-80)
REVERT: A 1025 MET cc_start: 0.8131 (tpp) cc_final: 0.7886 (tpt)
REVERT: A 1083 TYR cc_start: 0.8454 (m-10) cc_final: 0.8238 (m-10)
REVERT: A 1088 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8859 (mt-10)
REVERT: A 1147 MET cc_start: 0.9082 (ttm) cc_final: 0.8551 (tmm)
REVERT: B   81 ASP cc_start: 0.8475 (m-30) cc_final: 0.7685 (p0)
REVERT: B   82 THR cc_start: 0.8100 (p) cc_final: 0.7879 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.0771
  time to fit residues: 23.4168
Evaluate side-chains
  170 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 82 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 92 optimal weight:   30.0000
   chunk 4 optimal weight:   10.0000
   chunk 11 optimal weight:    0.5980
   chunk 26 optimal weight:    7.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 914 GLN
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.132519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.096999 restraints weight = 19817.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.095685 restraints weight = 12775.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.096626 restraints weight = 9406.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.096665 restraints weight = 8621.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.097016 restraints weight = 7570.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.4859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7806  Z= 0.148
  Angle     :  0.686   9.633  10563  Z= 0.346
  Chirality :  0.044   0.225   1209
  Planarity :  0.004   0.040   1323
  Dihedral  :  4.646  21.850   1036
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 14.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.27), residues: 954
  helix:  0.72 (0.21), residues: 593
  sheet: -2.30 (0.52), residues: 85
  loop : -1.77 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 284 
 TYR   0.014   0.001   TYR A1083 
 PHE   0.040   0.002   PHE A 184 
 TRP   0.021   0.001   TRP A 995 
 HIS   0.004   0.001   HIS A 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 7806)
  covalent geometry    : angle       0.68622 (10563)
  hydrogen bonds       : bond        0.04042 (  476)
  hydrogen bonds       : angle       4.67070 ( 1401)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 LEU cc_start: 0.8274 (tp) cc_final: 0.7828 (tt)
REVERT: A  446 TYR cc_start: 0.7593 (p90) cc_final: 0.7309 (p90)
REVERT: A  465 MET cc_start: 0.9073 (ttt) cc_final: 0.8727 (ttp)
REVERT: A  519 LEU cc_start: 0.9420 (mt) cc_final: 0.9220 (pp)
REVERT: A  996 PHE cc_start: 0.7495 (m-10) cc_final: 0.7141 (m-80)
REVERT: A 1083 TYR cc_start: 0.8303 (m-80) cc_final: 0.8101 (m-80)
REVERT: A 1088 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8504 (mt-10)
REVERT: A 1107 LYS cc_start: 0.9041 (tttp) cc_final: 0.8841 (tptp)
REVERT: A 1142 PHE cc_start: 0.9036 (t80) cc_final: 0.8753 (t80)
REVERT: A 1147 MET cc_start: 0.8937 (ttm) cc_final: 0.8507 (tmm)
REVERT: A 1148 ARG cc_start: 0.9096 (ptp-170) cc_final: 0.8711 (ptp90)
REVERT: B   32 ILE cc_start: 0.9434 (mt) cc_final: 0.9153 (mt)
REVERT: B   78 TRP cc_start: 0.7058 (t-100) cc_final: 0.6731 (t-100)
REVERT: B   81 ASP cc_start: 0.8461 (m-30) cc_final: 0.7722 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 209
  average time/residue: 0.0750
  time to fit residues: 22.2184
Evaluate side-chains
  164 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 88 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 41 optimal weight:    0.4980
   chunk 13 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 48 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 23 optimal weight:    6.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.134904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.098495 restraints weight = 19758.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.098778 restraints weight = 12980.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.098785 restraints weight = 9242.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.099107 restraints weight = 8768.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.099208 restraints weight = 8473.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.5264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7806  Z= 0.129
  Angle     :  0.673   9.657  10563  Z= 0.337
  Chirality :  0.042   0.192   1209
  Planarity :  0.004   0.039   1323
  Dihedral  :  4.544  21.253   1036
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.27), residues: 954
  helix:  0.86 (0.21), residues: 592
  sheet: -2.38 (0.48), residues: 102
  loop : -1.72 (0.39), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 487 
 TYR   0.015   0.001   TYR A1083 
 PHE   0.031   0.001   PHE A 184 
 TRP   0.025   0.001   TRP A 995 
 HIS   0.012   0.001   HIS B  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7806)
  covalent geometry    : angle       0.67340 (10563)
  hydrogen bonds       : bond        0.03975 (  476)
  hydrogen bonds       : angle       4.50660 ( 1401)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 LEU cc_start: 0.8355 (tp) cc_final: 0.7866 (tt)
REVERT: A  446 TYR cc_start: 0.7577 (p90) cc_final: 0.7288 (p90)
REVERT: A  465 MET cc_start: 0.9132 (ttt) cc_final: 0.8705 (ttp)
REVERT: A  486 MET cc_start: 0.7902 (tpt) cc_final: 0.7645 (tpt)
REVERT: A  516 LEU cc_start: 0.9383 (mt) cc_final: 0.9157 (mt)
REVERT: A  519 LEU cc_start: 0.9429 (mt) cc_final: 0.9218 (pp)
REVERT: A  831 GLU cc_start: 0.8594 (pp20) cc_final: 0.8329 (pp20)
REVERT: A  862 TRP cc_start: -0.0117 (m-10) cc_final: -0.1530 (t60)
REVERT: A  996 PHE cc_start: 0.7465 (m-10) cc_final: 0.6910 (m-10)
REVERT: A 1083 TYR cc_start: 0.8465 (m-80) cc_final: 0.8177 (m-80)
REVERT: A 1088 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8748 (tm-30)
REVERT: A 1089 LEU cc_start: 0.9432 (tp) cc_final: 0.8955 (tp)
REVERT: A 1107 LYS cc_start: 0.9067 (tttp) cc_final: 0.8802 (tptp)
REVERT: A 1147 MET cc_start: 0.9067 (ttm) cc_final: 0.8593 (tmm)
REVERT: A 1148 ARG cc_start: 0.9177 (ptp-170) cc_final: 0.8930 (ptp-170)
REVERT: A 1153 PHE cc_start: 0.8756 (t80) cc_final: 0.7233 (t80)
REVERT: B   78 TRP cc_start: 0.7116 (t-100) cc_final: 0.6802 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 0.0791
  time to fit residues: 23.2163
Evaluate side-chains
  158 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 95 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 67 optimal weight:    0.8980
   chunk 91 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   chunk 75 optimal weight:    8.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  92 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.134379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.097371 restraints weight = 19852.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.098566 restraints weight = 12735.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.098242 restraints weight = 9179.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.098454 restraints weight = 8598.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.098426 restraints weight = 8763.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.5506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7806  Z= 0.134
  Angle     :  0.678   9.672  10563  Z= 0.339
  Chirality :  0.043   0.174   1209
  Planarity :  0.004   0.062   1323
  Dihedral  :  4.537  21.419   1036
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.27), residues: 954
  helix:  0.86 (0.21), residues: 594
  sheet: -2.27 (0.50), residues: 96
  loop : -1.78 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 340 
 TYR   0.017   0.001   TYR A1083 
 PHE   0.056   0.002   PHE A 184 
 TRP   0.024   0.001   TRP A 995 
 HIS   0.009   0.001   HIS B  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7806)
  covalent geometry    : angle       0.67810 (10563)
  hydrogen bonds       : bond        0.03897 (  476)
  hydrogen bonds       : angle       4.49380 ( 1401)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 CYS cc_start: 0.8982 (m) cc_final: 0.8320 (p)
REVERT: A  167 LEU cc_start: 0.8427 (tp) cc_final: 0.7980 (tt)
REVERT: A  335 HIS cc_start: 0.7789 (m-70) cc_final: 0.7204 (m170)
REVERT: A  446 TYR cc_start: 0.7582 (p90) cc_final: 0.7357 (p90)
REVERT: A  465 MET cc_start: 0.9303 (ttt) cc_final: 0.8871 (ttp)
REVERT: A  516 LEU cc_start: 0.9372 (mt) cc_final: 0.9133 (mt)
REVERT: A  519 LEU cc_start: 0.9447 (mt) cc_final: 0.9232 (pp)
REVERT: A  831 GLU cc_start: 0.8677 (pp20) cc_final: 0.8122 (pp20)
REVERT: A  875 LEU cc_start: 0.8219 (pp) cc_final: 0.7915 (pp)
REVERT: A  922 SER cc_start: 0.9308 (m) cc_final: 0.9102 (m)
REVERT: A  996 PHE cc_start: 0.7581 (m-10) cc_final: 0.7011 (m-10)
REVERT: A 1083 TYR cc_start: 0.8671 (m-80) cc_final: 0.8342 (m-80)
REVERT: A 1088 GLU cc_start: 0.9293 (mt-10) cc_final: 0.8733 (mt-10)
REVERT: A 1107 LYS cc_start: 0.8927 (tttp) cc_final: 0.8701 (tptp)
REVERT: A 1115 TYR cc_start: 0.7887 (t80) cc_final: 0.7504 (t80)
REVERT: A 1147 MET cc_start: 0.9179 (ttm) cc_final: 0.8637 (tmm)
REVERT: A 1148 ARG cc_start: 0.9255 (ptp-170) cc_final: 0.8987 (ptp-170)
REVERT: B   78 TRP cc_start: 0.7181 (t-100) cc_final: 0.6720 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.0740
  time to fit residues: 21.9106
Evaluate side-chains
  162 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 88 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 6 optimal weight:    8.9990
   chunk 17 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 30 optimal weight:    9.9990
   chunk 72 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 86 optimal weight:   20.0000
   chunk 62 optimal weight:    0.9990
   chunk 37 optimal weight:   20.0000
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 914 GLN
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.131907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.093845 restraints weight = 20314.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.095365 restraints weight = 13162.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.097437 restraints weight = 8876.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.097401 restraints weight = 7326.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.097371 restraints weight = 6676.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.5407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   7806  Z= 0.174
  Angle     :  0.721   9.903  10563  Z= 0.368
  Chirality :  0.044   0.191   1209
  Planarity :  0.004   0.044   1323
  Dihedral  :  4.704  21.945   1036
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.27), residues: 954
  helix:  0.60 (0.21), residues: 595
  sheet: -2.22 (0.50), residues: 96
  loop : -1.86 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 340 
 TYR   0.019   0.002   TYR A1083 
 PHE   0.031   0.002   PHE A 184 
 TRP   0.009   0.001   TRP A1159 
 HIS   0.011   0.001   HIS B  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 7806)
  covalent geometry    : angle       0.72149 (10563)
  hydrogen bonds       : bond        0.04173 (  476)
  hydrogen bonds       : angle       4.71120 ( 1401)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 CYS cc_start: 0.9038 (m) cc_final: 0.8452 (p)
REVERT: A  167 LEU cc_start: 0.8359 (tp) cc_final: 0.7878 (tt)
REVERT: A  446 TYR cc_start: 0.7629 (p90) cc_final: 0.7388 (p90)
REVERT: A  465 MET cc_start: 0.9207 (ttt) cc_final: 0.8793 (ttp)
REVERT: A  516 LEU cc_start: 0.9377 (mt) cc_final: 0.9158 (mt)
REVERT: A  519 LEU cc_start: 0.9444 (mt) cc_final: 0.9222 (pp)
REVERT: A  545 MET cc_start: 0.7689 (mmt) cc_final: 0.7342 (mmm)
REVERT: A  996 PHE cc_start: 0.7640 (m-10) cc_final: 0.7208 (m-10)
REVERT: A 1083 TYR cc_start: 0.8619 (m-80) cc_final: 0.8294 (m-80)
REVERT: A 1088 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8675 (mt-10)
REVERT: A 1115 TYR cc_start: 0.7861 (t80) cc_final: 0.7449 (t80)
REVERT: A 1147 MET cc_start: 0.9063 (ttm) cc_final: 0.8510 (tmm)
REVERT: B   78 TRP cc_start: 0.7188 (t-100) cc_final: 0.6802 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.0710
  time to fit residues: 20.1976
Evaluate side-chains
  163 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 89 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 84 optimal weight:    1.9990
   chunk 94 optimal weight:    0.1980
   chunk 18 optimal weight:    1.9990
   chunk 75 optimal weight:    5.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 335 HIS
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 914 GLN
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.133520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.093459 restraints weight = 19884.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.096137 restraints weight = 12098.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.097728 restraints weight = 8365.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 63)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.098888 restraints weight = 6589.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.099473 restraints weight = 5595.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.5691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7806  Z= 0.141
  Angle     :  0.702   9.620  10563  Z= 0.356
  Chirality :  0.043   0.175   1209
  Planarity :  0.004   0.041   1323
  Dihedral  :  4.712  22.862   1036
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.27), residues: 954
  helix:  0.69 (0.21), residues: 594
  sheet: -2.13 (0.49), residues: 102
  loop : -1.67 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 854 
 TYR   0.020   0.002   TYR A1083 
 PHE   0.058   0.002   PHE A 184 
 TRP   0.028   0.002   TRP A1159 
 HIS   0.012   0.001   HIS B  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 7806)
  covalent geometry    : angle       0.70208 (10563)
  hydrogen bonds       : bond        0.04067 (  476)
  hydrogen bonds       : angle       4.64064 ( 1401)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 CYS cc_start: 0.8995 (m) cc_final: 0.8259 (p)
REVERT: A  167 LEU cc_start: 0.8330 (tp) cc_final: 0.7870 (tt)
REVERT: A  446 TYR cc_start: 0.7592 (p90) cc_final: 0.7331 (p90)
REVERT: A  465 MET cc_start: 0.9087 (ttt) cc_final: 0.8706 (ttp)
REVERT: A  516 LEU cc_start: 0.9357 (mt) cc_final: 0.9132 (mt)
REVERT: A  519 LEU cc_start: 0.9412 (mt) cc_final: 0.9198 (pp)
REVERT: A  545 MET cc_start: 0.7577 (mmt) cc_final: 0.7274 (mmt)
REVERT: A  875 LEU cc_start: 0.8427 (pp) cc_final: 0.8169 (pp)
REVERT: A  996 PHE cc_start: 0.7653 (m-10) cc_final: 0.7290 (m-10)
REVERT: A 1083 TYR cc_start: 0.8691 (m-80) cc_final: 0.8337 (m-80)
REVERT: A 1088 GLU cc_start: 0.9354 (mt-10) cc_final: 0.8741 (mt-10)
REVERT: A 1115 TYR cc_start: 0.7764 (t80) cc_final: 0.7358 (t80)
REVERT: A 1142 PHE cc_start: 0.8960 (t80) cc_final: 0.8754 (t80)
REVERT: A 1147 MET cc_start: 0.9063 (ttm) cc_final: 0.8396 (tmm)
REVERT: B   78 TRP cc_start: 0.7260 (t-100) cc_final: 0.6848 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.0735
  time to fit residues: 21.0933
Evaluate side-chains
  160 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 25 optimal weight:    0.5980
   chunk 73 optimal weight:    0.8980
   chunk 64 optimal weight:    8.9990
   chunk 57 optimal weight:    0.0970
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 914 GLN
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.135214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.095226 restraints weight = 19907.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.097708 restraints weight = 12446.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.099472 restraints weight = 8734.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.100597 restraints weight = 6805.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.101415 restraints weight = 5771.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.5885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7806  Z= 0.140
  Angle     :  0.698   9.766  10563  Z= 0.353
  Chirality :  0.044   0.187   1209
  Planarity :  0.004   0.041   1323
  Dihedral  :  4.686  23.434   1036
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.27), residues: 954
  helix:  0.65 (0.21), residues: 603
  sheet: -2.17 (0.50), residues: 96
  loop : -1.80 (0.39), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  23 
 TYR   0.035   0.002   TYR A 909 
 PHE   0.033   0.002   PHE A 184 
 TRP   0.021   0.001   TRP A1159 
 HIS   0.011   0.001   HIS B  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7806)
  covalent geometry    : angle       0.69818 (10563)
  hydrogen bonds       : bond        0.04012 (  476)
  hydrogen bonds       : angle       4.64632 ( 1401)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1651.85 seconds
wall clock time: 29 minutes 13.95 seconds (1753.95 seconds total)