Starting phenix.real_space_refine
on Sat Jun  7 07:23:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qju_18449/06_2025/8qju_18449.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qju_18449/06_2025/8qju_18449.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qju_18449/06_2025/8qju_18449.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qju_18449/06_2025/8qju_18449.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qju_18449/06_2025/8qju_18449.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qju_18449/06_2025/8qju_18449.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      43      5.16       5
     C    5470      2.51       5
     N    1470      2.21       5
     O    1595      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 75 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8578
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 8578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1045, 8578
          Classifications: {'peptide': 1045}
          Link IDs: {'PTRANS': 46, 'TRANS': 998}
          Chain breaks: 4
  Time building chain proxies: 5.49, per 1000 atoms: 0.64
  Number of scatterers: 8578
  At special positions: 0
  Unit cell: (85.412, 104.32, 115.404, 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      43     16.00
     O    1595      8.00
     N    1470      7.00
     C    5470      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 348 " - pdb=" SG  CYS A 353 " distance=2.07

  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: 2.09
  Conformation dependent library (CDL) restraints added in 937.5 milliseconds
  

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2004

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 15 sheets defined
      34.9% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 25
    Processing helix  chain 'A' and resid 79 through 83
      removed outlier: 3.768A  pdb=" N   PHE A  82 " --> pdb=" O   SER A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 136
      removed outlier: 3.919A  pdb=" N   ALA A 119 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LYS A 127 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 154
      removed outlier: 3.558A  pdb=" N   GLU A 143 " --> pdb=" O   PRO A 139 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER A 144 " --> pdb=" O   THR A 140 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   ASP A 154 " --> pdb=" O   ILE A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 173
      Proline residue:  A 171  - end of helix
    Processing helix  chain 'A' and resid 179 through 191
      removed outlier: 3.736A  pdb=" N   LEU A 183 " --> pdb=" O   SER A 179 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LYS A 184 " --> pdb=" O   ALA A 180 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLU A 189 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 222
      removed outlier: 3.580A  pdb=" N   PHE A 211 " --> pdb=" O   LYS A 207 " (cutoff:3.500A)
      removed outlier: 5.533A  pdb=" N   SER A 216 " --> pdb=" O   GLU A 212 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   ILE A 217 " --> pdb=" O   GLN A 213 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   LEU A 218 " --> pdb=" O   GLN A 214 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASP A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLU A 220 " --> pdb=" O   SER A 216 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   PHE A 221 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   LYS A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 252
    Processing helix  chain 'A' and resid 256 through 260
    Processing helix  chain 'A' and resid 261 through 274
    Processing helix  chain 'A' and resid 286 through 295
      removed outlier: 3.539A  pdb=" N   LEU A 291 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 300
    Processing helix  chain 'A' and resid 304 through 308
      removed outlier: 3.733A  pdb=" N   ALA A 308 " --> pdb=" O   LYS A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 315
      removed outlier: 3.623A  pdb=" N   ASN A 315 " --> pdb=" O   GLN A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 321
    Processing helix  chain 'A' and resid 341 through 352
      removed outlier: 3.976A  pdb=" N   TYR A 345 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 394
      removed outlier: 3.506A  pdb=" N   HIS A 392 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   PHE A 394 " --> pdb=" O   LYS A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 426
      removed outlier: 4.005A  pdb=" N   HIS A 416 " --> pdb=" O   GLU A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 429
      No H-bonds generated for 'chain 'A' and resid 427 through 429'
    Processing helix  chain 'A' and resid 526 through 530
    Processing helix  chain 'A' and resid 539 through 555
      removed outlier: 3.559A  pdb=" N   THR A 554 " --> pdb=" O   TYR A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 620
    Processing helix  chain 'A' and resid 639 through 644
      removed outlier: 3.835A  pdb=" N   SER A 643 " --> pdb=" O   ASN A 639 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   LYS A 644 " --> pdb=" O   PRO A 640 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 639 through 644'
    Processing helix  chain 'A' and resid 652 through 663
      removed outlier: 3.997A  pdb=" N   ILE A 663 " --> pdb=" O   MET A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 723
    Processing helix  chain 'A' and resid 736 through 743
      removed outlier: 3.753A  pdb=" N   ARG A 742 " --> pdb=" O   GLU A 738 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 843
      removed outlier: 3.624A  pdb=" N   ASP A 842 " --> pdb=" O   GLN A 838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 849
    Processing helix  chain 'A' and resid 892 through 908
    Processing helix  chain 'A' and resid 927 through 934
      removed outlier: 3.604A  pdb=" N   VAL A 934 " --> pdb=" O   LEU A 930 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 959 through 970
    Processing helix  chain 'A' and resid 970 through 979
      removed outlier: 4.660A  pdb=" N   LEU A 974 " --> pdb=" O   LYS A 970 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LEU A 975 " --> pdb=" O   PRO A 971 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 999 through 1005
    Processing helix  chain 'A' and resid 1018 through 1030
    Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 66
      removed outlier: 3.968A  pdb=" N   GLY A  63 " --> pdb=" O   TRP A  54 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLU A  39 " --> pdb=" O   VAL A  30 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   ARG A  41 " --> pdb=" O   MET A  28 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   MET A  28 " --> pdb=" O   ARG A  41 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   SER A 110 " --> pdb=" O   PHE A  31 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   SER A 107 " --> pdb=" O   TYR A 100 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLU A  72 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 162
    Processing sheet with id=AA3, first strand: chain 'A' and resid 241 through 242
    Processing sheet with id=AA4, first strand: chain 'A' and resid 331 through 332
      removed outlier: 3.665A  pdb=" N   THR A 332 " --> pdb=" O   GLU A 339 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLU A 339 " --> pdb=" O   THR A 332 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 369 through 370
    Processing sheet with id=AA6, first strand: chain 'A' and resid 851 through 854
    Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 565
    Processing sheet with id=AA8, first strand: chain 'A' and resid 622 through 624
    Processing sheet with id=AA9, first strand: chain 'A' and resid 647 through 648
      removed outlier: 3.866A  pdb=" N   ALA A 668 " --> pdb=" O   ARG A 685 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   TYR A 680 " --> pdb=" O   ILE A 695 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE A 682 " --> pdb=" O   CYS A 693 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   PHE A 684 " --> pdb=" O   LYS A 691 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LYS A 691 " --> pdb=" O   PHE A 684 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ASN A 696 " --> pdb=" O   VAL A 703 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 647 through 648
    Processing sheet with id=AB2, first strand: chain 'A' and resid 858 through 862
      removed outlier: 3.662A  pdb=" N   GLU A 877 " --> pdb=" O   ASN A 859 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 938 through 939
      removed outlier: 5.077A  pdb=" N   LYS A 938 " --> pdb=" O   ILE A 955 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   GLU A 954 " --> pdb=" O   LEU A 982 " (cutoff:3.500A)
      removed outlier: 8.333A  pdb=" N   ARG A 984 " --> pdb=" O   GLU A 954 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   ARG A 956 " --> pdb=" O   ARG A 984 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   THR A 983 " --> pdb=" O   MET A1009 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1061 through 1063
      removed outlier: 4.292A  pdb=" N   ARG A1187 " --> pdb=" O   THR A1062 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1098 through 1100
      removed outlier: 3.997A  pdb=" N   VAL A1087 " --> pdb=" O   PHE A1099 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   CYS A1082 " --> pdb=" O   GLU A1139 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   GLU A1138 " --> pdb=" O   PHE A1147 " (cutoff:3.500A)
      removed outlier: 5.337A  pdb=" N   PHE A1147 " --> pdb=" O   GLU A1138 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   ASP A1140 " --> pdb=" O   PRO A1145 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1163 through 1164

    300 hydrogen bonds defined for protein.
    816 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: 3.00

  Time building geometry restraints manager: 2.52 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1421
        1.31 -     1.44: 2389
        1.44 -     1.57: 4901
        1.57 -     1.70: 0
        1.70 -     1.83: 68
  Bond restraints: 8779
  Sorted by residual:
  bond pdb=" C   THR A1102 "
       pdb=" O   THR A1102 "
    ideal  model  delta    sigma   weight residual
    1.234  1.182  0.051 1.17e-02 7.31e+03 1.92e+01
  bond pdb=" CA  SER A1110 "
       pdb=" CB  SER A1110 "
    ideal  model  delta    sigma   weight residual
    1.528  1.487  0.040 1.14e-02 7.69e+03 1.25e+01
  bond pdb=" CA  SER A 110 "
       pdb=" CB  SER A 110 "
    ideal  model  delta    sigma   weight residual
    1.530  1.483  0.047 1.50e-02 4.44e+03 1.00e+01
  bond pdb=" N   LEU A1073 "
       pdb=" CA  LEU A1073 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.032 1.14e-02 7.69e+03 8.07e+00
  bond pdb=" CA  SER A1172 "
       pdb=" CB  SER A1172 "
    ideal  model  delta    sigma   weight residual
    1.523  1.491  0.033 1.21e-02 6.83e+03 7.25e+00
  ... (remaining 8774 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 10759
        2.42 -     4.83: 990
        4.83 -     7.25: 82
        7.25 -     9.66: 15
        9.66 -    12.08: 3
  Bond angle restraints: 11849
  Sorted by residual:
  angle pdb=" N   PRO A 400 "
        pdb=" CA  PRO A 400 "
        pdb=" C   PRO A 400 "
      ideal   model   delta    sigma   weight residual
     111.32  123.40  -12.08 1.71e+00 3.42e-01 4.99e+01
  angle pdb=" N   PRO A  75 "
        pdb=" CA  PRO A  75 "
        pdb=" C   PRO A  75 "
      ideal   model   delta    sigma   weight residual
     113.57  122.36   -8.79 1.31e+00 5.83e-01 4.50e+01
  angle pdb=" C   PRO A 400 "
        pdb=" CA  PRO A 400 "
        pdb=" CB  PRO A 400 "
      ideal   model   delta    sigma   weight residual
     110.85  101.65    9.20 1.41e+00 5.03e-01 4.25e+01
  angle pdb=" C   PRO A  75 "
        pdb=" CA  PRO A  75 "
        pdb=" CB  PRO A  75 "
      ideal   model   delta    sigma   weight residual
     112.11  103.18    8.93 1.46e+00 4.69e-01 3.74e+01
  angle pdb=" CA  PHE A 505 "
        pdb=" CB  PHE A 505 "
        pdb=" CG  PHE A 505 "
      ideal   model   delta    sigma   weight residual
     113.80  119.26   -5.46 1.00e+00 1.00e+00 2.98e+01
  ... (remaining 11844 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.12: 4702
       17.12 -    34.23: 442
       34.23 -    51.34: 96
       51.34 -    68.46: 88
       68.46 -    85.57: 2
  Dihedral angle restraints: 5330
    sinusoidal: 2245
      harmonic: 3085
  Sorted by residual:
  dihedral pdb=" CB  CYS A 348 "
           pdb=" SG  CYS A 348 "
           pdb=" SG  CYS A 353 "
           pdb=" CB  CYS A 353 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.46  -60.46     1      1.00e+01 1.00e-02 4.87e+01
  dihedral pdb=" CA  ALA A 259 "
           pdb=" C   ALA A 259 "
           pdb=" N   GLN A 260 "
           pdb=" CA  GLN A 260 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.62   27.38     0      5.00e+00 4.00e-02 3.00e+01
  dihedral pdb=" CA  THR A 706 "
           pdb=" C   THR A 706 "
           pdb=" N   SER A 707 "
           pdb=" CA  SER A 707 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.07  -25.93     0      5.00e+00 4.00e-02 2.69e+01
  ... (remaining 5327 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 902
       0.083 -    0.166: 332
       0.166 -    0.249: 34
       0.249 -    0.332: 4
       0.332 -    0.415: 1
  Chirality restraints: 1273
  Sorted by residual:
  chirality pdb=" CA  PHE A1028 "
            pdb=" N   PHE A1028 "
            pdb=" C   PHE A1028 "
            pdb=" CB  PHE A1028 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.30e+00
  chirality pdb=" CA  TYR A1020 "
            pdb=" N   TYR A1020 "
            pdb=" C   TYR A1020 "
            pdb=" CB  TYR A1020 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.23e+00
  chirality pdb=" CA  ARG A 248 "
            pdb=" N   ARG A 248 "
            pdb=" C   ARG A 248 "
            pdb=" CB  ARG A 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.05e+00
  ... (remaining 1270 not shown)

  Planarity restraints: 1521
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 679 "   -0.015 2.00e-02 2.50e+03   3.10e-02 9.63e+00
        pdb=" C   SER A 679 "    0.054 2.00e-02 2.50e+03
        pdb=" O   SER A 679 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   TYR A 680 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 147 "   -0.260 9.50e-02 1.11e+02   1.17e-01 8.71e+00
        pdb=" NE  ARG A 147 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 147 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 147 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 147 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A1153 "    0.039 2.00e-02 2.50e+03   2.01e-02 8.05e+00
        pdb=" CG  TYR A1153 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR A1153 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD2 TYR A1153 "   -0.018 2.00e-02 2.50e+03
        pdb=" CE1 TYR A1153 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 TYR A1153 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR A1153 "    0.008 2.00e-02 2.50e+03
        pdb=" OH  TYR A1153 "    0.022 2.00e-02 2.50e+03
  ... (remaining 1518 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1683
        2.77 -     3.31: 8974
        3.31 -     3.84: 13878
        3.84 -     4.37: 16841
        4.37 -     4.90: 27064
  Nonbonded interactions: 68440
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 647 "
            pdb=" NZ  LYS A 673 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" O   PRO A 400 "
            pdb=" OH  TYR A1036 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   THR A 332 "
            pdb=" OG  SER A 338 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   ARG A 700 "
            pdb=" ND1 HIS A 701 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" O   GLU A 279 "
            pdb=" OG1 THR A 280 "
     model   vdw
     2.285 3.040
  ... (remaining 68435 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.970
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
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      :  0.007   0.051   8780  Z= 0.500
  Angle     :  1.446  12.078  11851  Z= 0.979
  Chirality :  0.078   0.415   1273
  Planarity :  0.010   0.117   1521
  Dihedral  : 16.446  85.571   3323
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 31.96
  Ramachandran Plot:
    Outliers :  2.13 %
    Allowed  :  8.79 %
    Favored  : 89.08 %
  Rotamer:
    Outliers : 10.42 %
    Allowed  : 12.21 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.58 (0.23), residues: 1035
  helix: -1.69 (0.25), residues: 284
  sheet: -1.34 (0.37), residues: 198
  loop : -1.84 (0.23), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.005   TRP A 322 
 HIS   0.008   0.002   HIS A 252 
 PHE   0.036   0.004   PHE A 505 
 TYR   0.039   0.006   TYR A1153 
 ARG   0.018   0.002   ARG A 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.26608 (  298)
  hydrogen bonds       : angle       9.82690 (  816)
  SS BOND              : bond        0.03762 (    1)
  SS BOND              : angle       2.00407 (    2)
  covalent geometry    : bond        0.00732 ( 8779)
  covalent geometry    : angle       1.44624 (11849)

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

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

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  401 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 99
    poor density    : 302
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLN cc_start: 0.8445 (tp40) cc_final: 0.7998 (tm-30)
REVERT: A   20 ARG cc_start: 0.8323 (tpp-160) cc_final: 0.7910 (tmm-80)
REVERT: A   28 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8139 (mtp)
REVERT: A   68 MET cc_start: 0.8701 (mmm) cc_final: 0.8441 (mtt)
REVERT: A   93 ASP cc_start: 0.8354 (t0) cc_final: 0.7788 (p0)
REVERT: A  164 ARG cc_start: 0.9134 (ttt-90) cc_final: 0.8926 (ttm110)
REVERT: A  186 LYS cc_start: 0.6226 (OUTLIER) cc_final: 0.5787 (mmtp)
REVERT: A  196 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8412 (tp30)
REVERT: A  200 GLU cc_start: 0.9032 (mp0) cc_final: 0.8692 (tp30)
REVERT: A  249 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.8298 (t80)
REVERT: A  289 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8184 (mp0)
REVERT: A  314 MET cc_start: 0.8018 (mmm) cc_final: 0.7160 (mmm)
REVERT: A  320 HIS cc_start: 0.8230 (m90) cc_final: 0.7656 (m-70)
REVERT: A  409 CYS cc_start: 0.8826 (m) cc_final: 0.8431 (m)
REVERT: A  484 TRP cc_start: 0.7483 (t-100) cc_final: 0.7224 (t-100)
REVERT: A  592 MET cc_start: -0.3752 (mtt) cc_final: -0.3980 (pmm)
REVERT: A  646 TRP cc_start: 0.8388 (p-90) cc_final: 0.7670 (p-90)
REVERT: A  651 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8762 (tp)
REVERT: A  652 SER cc_start: 0.8620 (t) cc_final: 0.8225 (p)
REVERT: A  693 CYS cc_start: 0.8484 (t) cc_final: 0.8098 (p)
REVERT: A  728 LYS cc_start: 0.9237 (mptm) cc_final: 0.8857 (tmtt)
REVERT: A  729 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.9018 (ppp)
REVERT: A  859 ASN cc_start: 0.8504 (m-40) cc_final: 0.8278 (p0)
REVERT: A  868 ASN cc_start: 0.8457 (m-40) cc_final: 0.8117 (m-40)
REVERT: A  873 VAL cc_start: 0.9324 (p) cc_final: 0.9105 (t)
REVERT: A  886 VAL cc_start: 0.8619 (t) cc_final: 0.8394 (m)
REVERT: A  938 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7882 (ttmm)
REVERT: A  953 ARG cc_start: 0.8846 (ptp-110) cc_final: 0.8504 (mtm-85)
REVERT: A  970 LYS cc_start: 0.5774 (OUTLIER) cc_final: 0.4597 (pptt)
REVERT: A  997 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7773 (p90)
REVERT: A 1039 GLN cc_start: 0.8916 (mt0) cc_final: 0.8674 (mt0)
REVERT: A 1051 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8999 (mmm)
REVERT: A 1110 SER cc_start: 0.9044 (p) cc_final: 0.8843 (t)
REVERT: A 1141 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8746 (mtm)
REVERT: A 1164 SER cc_start: 0.8829 (t) cc_final: 0.8407 (p)
REVERT: A 1176 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8208 (mm-30)
REVERT: A 1186 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.9009 (mtm)
  outliers start: 99
  outliers final: 42
  residues processed: 361
  average time/residue: 0.2419
  time to fit residues: 117.7305
Evaluate side-chains
  279 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 225
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   89 ARG
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  118 ASP
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  157 ARG
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  186 LYS
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  242 TYR
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  249 PHE
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  477 GLN
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  496 CYS
Chi-restraints excluded: chain A residue  636 PRO
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  680 TYR
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  692 HIS
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  970 LYS
Chi-restraints excluded: chain A residue  997 TYR
Chi-restraints excluded: chain A residue 1014 PHE
Chi-restraints excluded: chain A residue 1021 MET
Chi-restraints excluded: chain A residue 1025 HIS
Chi-restraints excluded: chain A residue 1051 MET
Chi-restraints excluded: chain A residue 1096 ASN
Chi-restraints excluded: chain A residue 1102 THR
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain A residue 1120 VAL
Chi-restraints excluded: chain A residue 1138 GLU
Chi-restraints excluded: chain A residue 1141 MET
Chi-restraints excluded: chain A residue 1142 PHE
Chi-restraints excluded: chain A residue 1155 ILE
Chi-restraints excluded: chain A residue 1158 VAL
Chi-restraints excluded: chain A residue 1186 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 78 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 53 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 60 optimal weight:    5.9990
   chunk 94 optimal weight:    5.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A  51 GLN
A 121 ASN
A 201 GLN
A 247 GLN
A 260 GLN
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 372 HIS
A 387 GLN
A 413 GLN
A 446 GLN
A 616 HIS
A 637 ASN
A 856 ASN
A 868 ASN
A 979 GLN
** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1031 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.132820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.099559 restraints weight = 14335.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.103555 restraints weight = 6633.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.106151 restraints weight = 4001.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.3202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8780  Z= 0.169
  Angle     :  0.746   9.146  11851  Z= 0.403
  Chirality :  0.046   0.220   1273
  Planarity :  0.006   0.104   1521
  Dihedral  : 10.912  62.272   1262
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  6.38 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  : 17.37 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.25), residues: 1035
  helix:  0.64 (0.28), residues: 311
  sheet: -0.92 (0.36), residues: 209
  loop : -1.61 (0.25), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  54 
 HIS   0.006   0.001   HIS A 692 
 PHE   0.021   0.002   PHE A 272 
 TYR   0.017   0.002   TYR A1137 
 ARG   0.007   0.001   ARG A1057 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05206 (  298)
  hydrogen bonds       : angle       5.81182 (  816)
  SS BOND              : bond        0.00185 (    1)
  SS BOND              : angle       1.39124 (    2)
  covalent geometry    : bond        0.00372 ( 8779)
  covalent geometry    : angle       0.74563 (11849)

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

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

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 226
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLN cc_start: 0.7815 (tp40) cc_final: 0.7363 (tm-30)
REVERT: A   20 ARG cc_start: 0.8005 (tpp-160) cc_final: 0.7346 (tmm-80)
REVERT: A   28 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7664 (ptp)
REVERT: A   89 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8237 (tpm170)
REVERT: A  214 GLN cc_start: 0.8213 (mt0) cc_final: 0.7723 (mt0)
REVERT: A  314 MET cc_start: 0.7744 (mmm) cc_final: 0.6703 (mmt)
REVERT: A  320 HIS cc_start: 0.7799 (m90) cc_final: 0.7026 (m-70)
REVERT: A  355 CYS cc_start: 0.7332 (t) cc_final: 0.6782 (t)
REVERT: A  449 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7382 (tt0)
REVERT: A  477 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7560 (tp-100)
REVERT: A  548 GLN cc_start: 0.8827 (pt0) cc_final: 0.8505 (pm20)
REVERT: A  646 TRP cc_start: 0.7904 (p-90) cc_final: 0.7241 (p-90)
REVERT: A  651 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8412 (tp)
REVERT: A  658 ASP cc_start: 0.8890 (m-30) cc_final: 0.8515 (m-30)
REVERT: A  693 CYS cc_start: 0.7341 (t) cc_final: 0.7131 (p)
REVERT: A  843 ASN cc_start: 0.7968 (m-40) cc_final: 0.7744 (m-40)
REVERT: A  859 ASN cc_start: 0.7640 (m-40) cc_final: 0.7434 (p0)
REVERT: A  873 VAL cc_start: 0.9316 (p) cc_final: 0.9041 (t)
REVERT: A  886 VAL cc_start: 0.8081 (t) cc_final: 0.7828 (m)
REVERT: A  895 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7238 (mp0)
REVERT: A  897 PHE cc_start: 0.8565 (t80) cc_final: 0.8219 (t80)
REVERT: A  898 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8374 (mt-10)
REVERT: A  930 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8832 (tp)
REVERT: A  946 ASN cc_start: 0.7935 (t0) cc_final: 0.7547 (t0)
REVERT: A  960 GLU cc_start: 0.7449 (pt0) cc_final: 0.6986 (pt0)
REVERT: A  964 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7925 (t0)
REVERT: A  978 ASN cc_start: 0.8111 (m-40) cc_final: 0.7456 (t0)
REVERT: A  996 ASN cc_start: 0.8450 (m-40) cc_final: 0.8002 (m-40)
REVERT: A 1009 MET cc_start: 0.7493 (mtt) cc_final: 0.6961 (mtt)
REVERT: A 1039 GLN cc_start: 0.8429 (mt0) cc_final: 0.8126 (mt0)
REVERT: A 1045 THR cc_start: 0.7591 (p) cc_final: 0.7299 (p)
REVERT: A 1061 MET cc_start: 0.7192 (mtt) cc_final: 0.6724 (ttt)
REVERT: A 1105 ASN cc_start: 0.8172 (t0) cc_final: 0.7938 (m-40)
REVERT: A 1110 SER cc_start: 0.8477 (p) cc_final: 0.8230 (t)
REVERT: A 1152 THR cc_start: 0.8673 (m) cc_final: 0.8310 (p)
  outliers start: 61
  outliers final: 24
  residues processed: 267
  average time/residue: 0.2004
  time to fit residues: 73.6958
Evaluate side-chains
  229 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 198
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   89 ARG
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  157 ARG
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  237 ASP
Chi-restraints excluded: chain A residue  242 TYR
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  477 GLN
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  692 HIS
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  895 GLU
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  964 ASP
Chi-restraints excluded: chain A residue 1096 ASN
Chi-restraints excluded: chain A residue 1102 THR
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain A residue 1138 GLU
Chi-restraints excluded: chain A residue 1142 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0770
   chunk 44 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 58 optimal weight:    7.9990
   chunk 42 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 74 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.9542

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 455 HIS
A 868 ASN
** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.131789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.099114 restraints weight = 14460.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.102903 restraints weight = 6847.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.105453 restraints weight = 4167.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.4124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8780  Z= 0.152
  Angle     :  0.659   8.659  11851  Z= 0.350
  Chirality :  0.043   0.296   1273
  Planarity :  0.004   0.041   1521
  Dihedral  :  8.588  59.409   1193
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  7.15 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 20.21 %
    Favored  : 74.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.17 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.26), residues: 1035
  helix:  1.51 (0.29), residues: 305
  sheet: -0.80 (0.35), residues: 219
  loop : -1.55 (0.26), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  54 
 HIS   0.012   0.001   HIS A 327 
 PHE   0.025   0.002   PHE A 272 
 TYR   0.013   0.001   TYR A1137 
 ARG   0.007   0.001   ARG A 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04162 (  298)
  hydrogen bonds       : angle       5.13873 (  816)
  SS BOND              : bond        0.00323 (    1)
  SS BOND              : angle       0.72400 (    2)
  covalent geometry    : bond        0.00343 ( 8779)
  covalent geometry    : angle       0.65876 (11849)

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

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

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 208
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLN cc_start: 0.7739 (tp40) cc_final: 0.7309 (tm-30)
REVERT: A   20 ARG cc_start: 0.7969 (tpp-160) cc_final: 0.7301 (tmm-80)
REVERT: A   41 ARG cc_start: 0.8199 (mmt90) cc_final: 0.7956 (mmt90)
REVERT: A  164 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7268 (ttp80)
REVERT: A  235 ARG cc_start: 0.8179 (ttp-110) cc_final: 0.7901 (ptp90)
REVERT: A  320 HIS cc_start: 0.7822 (m90) cc_final: 0.7328 (m-70)
REVERT: A  359 ASP cc_start: 0.6324 (m-30) cc_final: 0.5872 (m-30)
REVERT: A  361 TRP cc_start: 0.8180 (m100) cc_final: 0.7733 (m100)
REVERT: A  379 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7443 (mmtt)
REVERT: A  423 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7819 (tm-30)
REVERT: A  449 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7536 (tt0)
REVERT: A  477 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7785 (tp-100)
REVERT: A  548 GLN cc_start: 0.8941 (pt0) cc_final: 0.8530 (pm20)
REVERT: A  658 ASP cc_start: 0.8886 (m-30) cc_final: 0.8440 (m-30)
REVERT: A  700 ARG cc_start: 0.9013 (ttp80) cc_final: 0.8501 (ttp80)
REVERT: A  843 ASN cc_start: 0.8091 (m-40) cc_final: 0.7805 (m-40)
REVERT: A  886 VAL cc_start: 0.8073 (t) cc_final: 0.7802 (m)
REVERT: A  895 GLU cc_start: 0.7919 (mp0) cc_final: 0.7253 (mp0)
REVERT: A  897 PHE cc_start: 0.8519 (t80) cc_final: 0.8260 (t80)
REVERT: A  901 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8378 (mm110)
REVERT: A  938 LYS cc_start: 0.7931 (ttmm) cc_final: 0.7320 (ttmm)
REVERT: A  946 ASN cc_start: 0.7827 (t0) cc_final: 0.7457 (t0)
REVERT: A  951 ASP cc_start: 0.7668 (t0) cc_final: 0.6952 (t0)
REVERT: A  960 GLU cc_start: 0.7559 (pt0) cc_final: 0.7065 (pt0)
REVERT: A  964 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7892 (t0)
REVERT: A  978 ASN cc_start: 0.8174 (m-40) cc_final: 0.7535 (t0)
REVERT: A  996 ASN cc_start: 0.8324 (m-40) cc_final: 0.8063 (m-40)
REVERT: A 1004 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8851 (tt)
REVERT: A 1045 THR cc_start: 0.7797 (p) cc_final: 0.7552 (p)
REVERT: A 1048 TYR cc_start: 0.7994 (t80) cc_final: 0.7768 (t80)
REVERT: A 1051 MET cc_start: 0.8888 (mmm) cc_final: 0.8630 (mmm)
  outliers start: 49
  outliers final: 31
  residues processed: 240
  average time/residue: 0.2055
  time to fit residues: 68.6057
Evaluate side-chains
  208 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 172
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  164 ARG
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  477 GLN
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  692 HIS
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  722 LYS
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  868 ASN
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue  964 ASP
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1059 ILE
Chi-restraints excluded: chain A residue 1096 ASN
Chi-restraints excluded: chain A residue 1102 THR
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain A residue 1142 PHE
Chi-restraints excluded: chain A residue 1152 THR
Chi-restraints excluded: chain A residue 1182 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 58 optimal weight:    7.9990
   chunk 1 optimal weight:    4.9990
   chunk 96 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 59 optimal weight:   20.0000
   chunk 42 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 392 HIS
A 414 GLN
A 478 GLN
A 527 HIS
** A 843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 868 ASN
A1024 ASN
** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.128704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.095137 restraints weight = 14390.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.098851 restraints weight = 6783.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.101334 restraints weight = 4157.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.4501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.055   8780  Z= 0.336
  Angle     :  0.759   9.436  11851  Z= 0.402
  Chirality :  0.046   0.235   1273
  Planarity :  0.005   0.051   1521
  Dihedral  :  8.365  59.219   1174
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 15.31
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  9.08 %
    Favored  : 90.43 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 20.95 %
    Favored  : 72.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.17 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.25), residues: 1035
  helix:  1.06 (0.29), residues: 305
  sheet: -1.02 (0.35), residues: 222
  loop : -1.80 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 361 
 HIS   0.006   0.002   HIS A 327 
 PHE   0.042   0.003   PHE A 272 
 TYR   0.020   0.003   TYR A 986 
 ARG   0.006   0.001   ARG A 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04906 (  298)
  hydrogen bonds       : angle       5.41706 (  816)
  SS BOND              : bond        0.00599 (    1)
  SS BOND              : angle       0.99038 (    2)
  covalent geometry    : bond        0.00786 ( 8779)
  covalent geometry    : angle       0.75928 (11849)

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

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

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 179
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8078 (tpp-160) cc_final: 0.7349 (tmm-80)
REVERT: A   41 ARG cc_start: 0.8342 (mmt90) cc_final: 0.8049 (mmm-85)
REVERT: A  154 ASP cc_start: 0.7198 (t0) cc_final: 0.6891 (t0)
REVERT: A  210 MET cc_start: 0.8244 (mmm) cc_final: 0.7930 (mmm)
REVERT: A  214 GLN cc_start: 0.8171 (mt0) cc_final: 0.7929 (mt0)
REVERT: A  359 ASP cc_start: 0.6827 (m-30) cc_final: 0.6418 (m-30)
REVERT: A  361 TRP cc_start: 0.8219 (m100) cc_final: 0.7711 (m100)
REVERT: A  405 ILE cc_start: 0.9071 (mm) cc_final: 0.8852 (mm)
REVERT: A  477 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7072 (tm130)
REVERT: A  658 ASP cc_start: 0.8932 (m-30) cc_final: 0.8501 (m-30)
REVERT: A  700 ARG cc_start: 0.9143 (ttp80) cc_final: 0.8818 (ttp80)
REVERT: A  843 ASN cc_start: 0.8180 (m-40) cc_final: 0.7836 (m110)
REVERT: A  886 VAL cc_start: 0.8059 (t) cc_final: 0.7828 (m)
REVERT: A  897 PHE cc_start: 0.8691 (t80) cc_final: 0.8451 (t80)
REVERT: A  946 ASN cc_start: 0.8064 (t0) cc_final: 0.7645 (t0)
REVERT: A  978 ASN cc_start: 0.8234 (m-40) cc_final: 0.7563 (t0)
REVERT: A  997 TYR cc_start: 0.8359 (p90) cc_final: 0.8043 (p90)
REVERT: A 1004 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8834 (tt)
REVERT: A 1009 MET cc_start: 0.7723 (mtt) cc_final: 0.7362 (mtt)
REVERT: A 1039 GLN cc_start: 0.8731 (mt0) cc_final: 0.8309 (mt0)
REVERT: A 1045 THR cc_start: 0.8204 (p) cc_final: 0.7945 (p)
REVERT: A 1048 TYR cc_start: 0.8195 (t80) cc_final: 0.7823 (t80)
REVERT: A 1051 MET cc_start: 0.8885 (mmm) cc_final: 0.8612 (mmm)
REVERT: A 1057 ARG cc_start: 0.6383 (mtm-85) cc_final: 0.5447 (ptp-170)
REVERT: A 1061 MET cc_start: 0.7087 (ttt) cc_final: 0.6866 (ttt)
REVERT: A 1087 VAL cc_start: 0.8069 (OUTLIER) cc_final: 0.7687 (m)
REVERT: A 1186 MET cc_start: 0.8053 (mtm) cc_final: 0.7599 (mtm)
  outliers start: 60
  outliers final: 40
  residues processed: 220
  average time/residue: 0.2041
  time to fit residues: 62.7465
Evaluate side-chains
  210 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 167
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  477 GLN
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  496 CYS
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  868 ASN
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue  964 ASP
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1059 ILE
Chi-restraints excluded: chain A residue 1087 VAL
Chi-restraints excluded: chain A residue 1096 ASN
Chi-restraints excluded: chain A residue 1102 THR
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain A residue 1123 GLU
Chi-restraints excluded: chain A residue 1142 PHE
Chi-restraints excluded: chain A residue 1152 THR
Chi-restraints excluded: chain A residue 1177 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 57 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1025 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.132743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.099003 restraints weight = 14059.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.102939 restraints weight = 6596.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.105571 restraints weight = 3999.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.4899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8780  Z= 0.156
  Angle     :  0.639  10.109  11851  Z= 0.338
  Chirality :  0.043   0.281   1273
  Planarity :  0.005   0.053   1521
  Dihedral  :  7.658  58.952   1170
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  8.50 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 22.63 %
    Favored  : 72.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.17 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.26), residues: 1035
  helix:  1.49 (0.29), residues: 304
  sheet: -0.85 (0.35), residues: 227
  loop : -1.77 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 258 
 HIS   0.005   0.001   HIS A 327 
 PHE   0.039   0.002   PHE A 272 
 TYR   0.025   0.002   TYR A 371 
 ARG   0.006   0.001   ARG A 742 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03942 (  298)
  hydrogen bonds       : angle       4.96740 (  816)
  SS BOND              : bond        0.00256 (    1)
  SS BOND              : angle       0.87424 (    2)
  covalent geometry    : bond        0.00356 ( 8779)
  covalent geometry    : angle       0.63857 (11849)

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

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

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 184
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLN cc_start: 0.7735 (tp40) cc_final: 0.7406 (tm-30)
REVERT: A   20 ARG cc_start: 0.8011 (tpp-160) cc_final: 0.7284 (tmm-80)
REVERT: A   57 THR cc_start: 0.8572 (t) cc_final: 0.8245 (p)
REVERT: A  154 ASP cc_start: 0.7195 (t0) cc_final: 0.6873 (t0)
REVERT: A  160 SER cc_start: 0.8306 (m) cc_final: 0.7838 (p)
REVERT: A  214 GLN cc_start: 0.7981 (mt0) cc_final: 0.7607 (mt0)
REVERT: A  359 ASP cc_start: 0.6396 (m-30) cc_final: 0.6055 (m-30)
REVERT: A  379 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7818 (mmtp)
REVERT: A  405 ILE cc_start: 0.8926 (mm) cc_final: 0.8694 (mt)
REVERT: A  423 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7944 (tm-30)
REVERT: A  477 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7694 (tp-100)
REVERT: A  548 GLN cc_start: 0.9036 (pt0) cc_final: 0.8562 (pm20)
REVERT: A  658 ASP cc_start: 0.8921 (m-30) cc_final: 0.8469 (m-30)
REVERT: A  690 VAL cc_start: 0.7648 (OUTLIER) cc_final: 0.7395 (p)
REVERT: A  700 ARG cc_start: 0.9130 (ttp80) cc_final: 0.8862 (ttp80)
REVERT: A  843 ASN cc_start: 0.8177 (m-40) cc_final: 0.7787 (m110)
REVERT: A  886 VAL cc_start: 0.7977 (t) cc_final: 0.7709 (m)
REVERT: A  897 PHE cc_start: 0.8672 (t80) cc_final: 0.8455 (t80)
REVERT: A  946 ASN cc_start: 0.7983 (t0) cc_final: 0.7570 (t0)
REVERT: A  964 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7941 (t0)
REVERT: A  978 ASN cc_start: 0.8138 (m-40) cc_final: 0.7463 (t0)
REVERT: A 1004 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8837 (tt)
REVERT: A 1009 MET cc_start: 0.7418 (mtt) cc_final: 0.7137 (mtt)
REVERT: A 1045 THR cc_start: 0.8198 (p) cc_final: 0.7918 (p)
REVERT: A 1048 TYR cc_start: 0.8129 (t80) cc_final: 0.7846 (t80)
REVERT: A 1051 MET cc_start: 0.8925 (mmm) cc_final: 0.8652 (mmm)
REVERT: A 1152 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8324 (p)
  outliers start: 44
  outliers final: 33
  residues processed: 212
  average time/residue: 0.2012
  time to fit residues: 60.2932
Evaluate side-chains
  211 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 172
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  477 GLN
Chi-restraints excluded: chain A residue  485 ASP
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  689 LYS
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  728 LYS
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  868 ASN
Chi-restraints excluded: chain A residue  964 ASP
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1043 MET
Chi-restraints excluded: chain A residue 1059 ILE
Chi-restraints excluded: chain A residue 1096 ASN
Chi-restraints excluded: chain A residue 1102 THR
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain A residue 1142 PHE
Chi-restraints excluded: chain A residue 1152 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 58 optimal weight:   20.0000
   chunk 90 optimal weight:    7.9990
   chunk 72 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0020
   chunk 70 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 9 optimal weight:    0.1980
   chunk 53 optimal weight:   30.0000
   chunk 34 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 843 ASN
A 868 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.138081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.104994 restraints weight = 13881.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.109172 restraints weight = 6183.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.111901 restraints weight = 3641.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.5125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8780  Z= 0.125
  Angle     :  0.616  10.240  11851  Z= 0.323
  Chirality :  0.041   0.264   1273
  Planarity :  0.004   0.052   1521
  Dihedral  :  7.254  57.028   1170
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  7.54 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 23.68 %
    Favored  : 71.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.26), residues: 1035
  helix:  1.68 (0.30), residues: 304
  sheet: -0.70 (0.35), residues: 227
  loop : -1.63 (0.27), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A 258 
 HIS   0.005   0.001   HIS A 641 
 PHE   0.038   0.002   PHE A 272 
 TYR   0.032   0.001   TYR A 371 
 ARG   0.006   0.000   ARG A  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03636 (  298)
  hydrogen bonds       : angle       4.74731 (  816)
  SS BOND              : bond        0.00209 (    1)
  SS BOND              : angle       0.81710 (    2)
  covalent geometry    : bond        0.00282 ( 8779)
  covalent geometry    : angle       0.61572 (11849)

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

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

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 185
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLN cc_start: 0.7686 (tp40) cc_final: 0.7399 (tm-30)
REVERT: A   20 ARG cc_start: 0.7978 (tpp-160) cc_final: 0.7261 (tmm-80)
REVERT: A   57 THR cc_start: 0.8551 (t) cc_final: 0.8217 (p)
REVERT: A   62 GLU cc_start: 0.7354 (tt0) cc_final: 0.7150 (tt0)
REVERT: A   64 PHE cc_start: 0.7766 (p90) cc_final: 0.7453 (p90)
REVERT: A  127 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7844 (ttmt)
REVERT: A  154 ASP cc_start: 0.7218 (t0) cc_final: 0.6765 (t0)
REVERT: A  160 SER cc_start: 0.8284 (m) cc_final: 0.7813 (p)
REVERT: A  190 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8031 (mp)
REVERT: A  210 MET cc_start: 0.8178 (mmm) cc_final: 0.7317 (mmm)
REVERT: A  271 LYS cc_start: 0.8332 (tptm) cc_final: 0.7990 (tppt)
REVERT: A  320 HIS cc_start: 0.7863 (m90) cc_final: 0.7319 (m-70)
REVERT: A  355 CYS cc_start: 0.7391 (t) cc_final: 0.6795 (t)
REVERT: A  359 ASP cc_start: 0.6173 (m-30) cc_final: 0.5880 (m-30)
REVERT: A  379 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7761 (mmmm)
REVERT: A  405 ILE cc_start: 0.8836 (mm) cc_final: 0.8621 (mt)
REVERT: A  423 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7949 (tm-30)
REVERT: A  477 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7666 (tp-100)
REVERT: A  548 GLN cc_start: 0.9087 (pt0) cc_final: 0.8607 (pm20)
REVERT: A  658 ASP cc_start: 0.8921 (m-30) cc_final: 0.8451 (m-30)
REVERT: A  690 VAL cc_start: 0.7580 (OUTLIER) cc_final: 0.7363 (p)
REVERT: A  700 ARG cc_start: 0.9097 (ttp80) cc_final: 0.8838 (ttp80)
REVERT: A  843 ASN cc_start: 0.8228 (m110) cc_final: 0.7778 (m-40)
REVERT: A  886 VAL cc_start: 0.7959 (t) cc_final: 0.7666 (m)
REVERT: A  897 PHE cc_start: 0.8668 (t80) cc_final: 0.8159 (t80)
REVERT: A  901 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8514 (mm-40)
REVERT: A  946 ASN cc_start: 0.7847 (t0) cc_final: 0.7314 (t0)
REVERT: A  978 ASN cc_start: 0.8113 (m-40) cc_final: 0.7471 (t0)
REVERT: A  997 TYR cc_start: 0.8180 (p90) cc_final: 0.7668 (p90)
REVERT: A 1004 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8823 (tt)
REVERT: A 1009 MET cc_start: 0.7335 (mtt) cc_final: 0.6874 (mtt)
REVERT: A 1039 GLN cc_start: 0.8572 (mt0) cc_final: 0.8085 (mt0)
REVERT: A 1045 THR cc_start: 0.8134 (p) cc_final: 0.7851 (p)
REVERT: A 1048 TYR cc_start: 0.8101 (t80) cc_final: 0.7778 (t80)
REVERT: A 1051 MET cc_start: 0.8962 (mmm) cc_final: 0.8698 (mmm)
REVERT: A 1152 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8325 (p)
REVERT: A 1186 MET cc_start: 0.7965 (mtm) cc_final: 0.7704 (mtm)
  outliers start: 43
  outliers final: 27
  residues processed: 211
  average time/residue: 0.2025
  time to fit residues: 59.5432
Evaluate side-chains
  210 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 176
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  127 LYS
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  379 LYS
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  477 GLN
Chi-restraints excluded: chain A residue  485 ASP
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  689 LYS
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1102 THR
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain A residue 1124 ILE
Chi-restraints excluded: chain A residue 1142 PHE
Chi-restraints excluded: chain A residue 1152 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 93 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0010
   chunk 31 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9980
   chunk 16 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   chunk 88 optimal weight:    0.7980
   chunk 12 optimal weight:    5.9990
   overall best weight:    0.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 880 GLN ** 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 = 0.3873 r_free = 0.3873 target = 0.134842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.101461 restraints weight = 14043.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.105489 restraints weight = 6479.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.108179 restraints weight = 3892.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.5346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8780  Z= 0.131
  Angle     :  0.623  10.201  11851  Z= 0.322
  Chirality :  0.041   0.253   1273
  Planarity :  0.004   0.050   1521
  Dihedral  :  6.767  52.782   1165
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  8.21 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 23.37 %
    Favored  : 72.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.26), residues: 1035
  helix:  1.69 (0.30), residues: 306
  sheet: -0.67 (0.37), residues: 209
  loop : -1.54 (0.26), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 258 
 HIS   0.005   0.001   HIS A 641 
 PHE   0.023   0.001   PHE A 900 
 TYR   0.032   0.001   TYR A 371 
 ARG   0.005   0.000   ARG A 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03554 (  298)
  hydrogen bonds       : angle       4.62738 (  816)
  SS BOND              : bond        0.00171 (    1)
  SS BOND              : angle       0.75262 (    2)
  covalent geometry    : bond        0.00299 ( 8779)
  covalent geometry    : angle       0.62326 (11849)

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

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

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 180
  time to evaluate  : 0.951 
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   20 ARG cc_start: 0.7953 (tpp-160) cc_final: 0.7210 (tmm-80)
REVERT: A   64 PHE cc_start: 0.7707 (p90) cc_final: 0.7424 (p90)
REVERT: A  127 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7850 (ttmt)
REVERT: A  154 ASP cc_start: 0.7349 (t0) cc_final: 0.7102 (t0)
REVERT: A  160 SER cc_start: 0.8282 (m) cc_final: 0.7845 (p)
REVERT: A  190 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8073 (mp)
REVERT: A  210 MET cc_start: 0.8005 (mmm) cc_final: 0.7367 (mmm)
REVERT: A  271 LYS cc_start: 0.8351 (tptm) cc_final: 0.7985 (tppt)
REVERT: A  320 HIS cc_start: 0.7797 (m90) cc_final: 0.7303 (m-70)
REVERT: A  359 ASP cc_start: 0.6119 (m-30) cc_final: 0.5835 (m-30)
REVERT: A  405 ILE cc_start: 0.8815 (mm) cc_final: 0.8599 (mt)
REVERT: A  423 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7966 (tm-30)
REVERT: A  477 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7734 (tp-100)
REVERT: A  487 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8309 (mt)
REVERT: A  548 GLN cc_start: 0.9099 (pt0) cc_final: 0.8624 (pm20)
REVERT: A  658 ASP cc_start: 0.8935 (m-30) cc_final: 0.8464 (m-30)
REVERT: A  700 ARG cc_start: 0.9076 (ttp80) cc_final: 0.8832 (ttp80)
REVERT: A  843 ASN cc_start: 0.8225 (m110) cc_final: 0.7788 (m110)
REVERT: A  886 VAL cc_start: 0.7942 (t) cc_final: 0.7639 (m)
REVERT: A  978 ASN cc_start: 0.8074 (m-40) cc_final: 0.7516 (t0)
REVERT: A  997 TYR cc_start: 0.8097 (p90) cc_final: 0.7603 (p90)
REVERT: A 1039 GLN cc_start: 0.8452 (mt0) cc_final: 0.8057 (mt0)
REVERT: A 1045 THR cc_start: 0.8119 (p) cc_final: 0.7844 (p)
REVERT: A 1051 MET cc_start: 0.8952 (mmm) cc_final: 0.8675 (mmm)
REVERT: A 1152 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8323 (p)
  outliers start: 40
  outliers final: 27
  residues processed: 206
  average time/residue: 0.1944
  time to fit residues: 56.3776
Evaluate side-chains
  199 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 167
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  127 LYS
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  477 GLN
Chi-restraints excluded: chain A residue  485 ASP
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  689 LYS
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1124 ILE
Chi-restraints excluded: chain A residue 1142 PHE
Chi-restraints excluded: chain A residue 1152 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 6 optimal weight:    0.1980
   chunk 60 optimal weight:    0.0870
   chunk 15 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0040
   chunk 37 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 93 optimal weight:    0.4980
   overall best weight:    0.2970

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 GLN ** 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 = 0.3987 r_free = 0.3987 target = 0.142056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.109217 restraints weight = 13784.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.113548 restraints weight = 5918.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.116419 restraints weight = 3430.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.5638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8780  Z= 0.115
  Angle     :  0.619  10.120  11851  Z= 0.318
  Chirality :  0.041   0.238   1273
  Planarity :  0.004   0.047   1521
  Dihedral  :  6.380  53.487   1161
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  7.63 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 24.11 %
    Favored  : 72.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.27), residues: 1035
  helix:  1.67 (0.30), residues: 312
  sheet: -0.60 (0.37), residues: 215
  loop : -1.52 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 258 
 HIS   0.004   0.001   HIS A 641 
 PHE   0.026   0.002   PHE A 272 
 TYR   0.026   0.001   TYR A 371 
 ARG   0.009   0.000   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03287 (  298)
  hydrogen bonds       : angle       4.49456 (  816)
  SS BOND              : bond        0.00065 (    1)
  SS BOND              : angle       0.70589 (    2)
  covalent geometry    : bond        0.00255 ( 8779)
  covalent geometry    : angle       0.61880 (11849)

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

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

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 186
  time to evaluate  : 1.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLN cc_start: 0.7599 (tp40) cc_final: 0.7308 (tm-30)
REVERT: A   64 PHE cc_start: 0.7634 (p90) cc_final: 0.7373 (p90)
REVERT: A  127 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7832 (ttmt)
REVERT: A  144 SER cc_start: 0.8656 (p) cc_final: 0.8345 (t)
REVERT: A  154 ASP cc_start: 0.7333 (t0) cc_final: 0.7101 (t0)
REVERT: A  210 MET cc_start: 0.7958 (mmm) cc_final: 0.7378 (mmm)
REVERT: A  359 ASP cc_start: 0.5908 (m-30) cc_final: 0.5633 (m-30)
REVERT: A  405 ILE cc_start: 0.8674 (mm) cc_final: 0.8471 (mt)
REVERT: A  417 MET cc_start: 0.7974 (ttm) cc_final: 0.7766 (ttm)
REVERT: A  419 LYS cc_start: 0.8554 (ttmm) cc_final: 0.8259 (ttpt)
REVERT: A  477 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7594 (tp-100)
REVERT: A  487 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8197 (mt)
REVERT: A  548 GLN cc_start: 0.9114 (pt0) cc_final: 0.8643 (pm20)
REVERT: A  658 ASP cc_start: 0.8897 (m-30) cc_final: 0.8406 (m-30)
REVERT: A  661 MET cc_start: 0.8573 (mmm) cc_final: 0.8300 (tpp)
REVERT: A  680 TYR cc_start: 0.7145 (m-10) cc_final: 0.6852 (m-10)
REVERT: A  689 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7711 (pttt)
REVERT: A  700 ARG cc_start: 0.9054 (ttp80) cc_final: 0.8834 (ttp80)
REVERT: A  843 ASN cc_start: 0.8213 (m110) cc_final: 0.7763 (m110)
REVERT: A  886 VAL cc_start: 0.7864 (t) cc_final: 0.7542 (m)
REVERT: A  901 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8545 (mm110)
REVERT: A  936 TYR cc_start: 0.7301 (m-80) cc_final: 0.7041 (m-80)
REVERT: A  978 ASN cc_start: 0.8064 (m-40) cc_final: 0.7539 (t0)
REVERT: A 1039 GLN cc_start: 0.8376 (mt0) cc_final: 0.8083 (mt0)
REVERT: A 1045 THR cc_start: 0.8068 (p) cc_final: 0.7803 (p)
REVERT: A 1051 MET cc_start: 0.8913 (mmm) cc_final: 0.8519 (mmt)
  outliers start: 35
  outliers final: 21
  residues processed: 210
  average time/residue: 0.1896
  time to fit residues: 58.2262
Evaluate side-chains
  194 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 169
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  127 LYS
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  477 GLN
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  689 LYS
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  728 LYS
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1096 ASN
Chi-restraints excluded: chain A residue 1142 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   chunk 97 optimal weight:    4.9990
   chunk 48 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0970
   chunk 103 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 GLN ** 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 = 0.3944 r_free = 0.3944 target = 0.139105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.106208 restraints weight = 13914.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.110400 restraints weight = 6110.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.113233 restraints weight = 3578.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.5718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8780  Z= 0.166
  Angle     :  0.653  10.130  11851  Z= 0.337
  Chirality :  0.042   0.229   1273
  Planarity :  0.004   0.047   1521
  Dihedral  :  6.409  53.267   1161
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  8.12 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 25.05 %
    Favored  : 71.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.26), residues: 1035
  helix:  1.74 (0.30), residues: 307
  sheet: -0.61 (0.38), residues: 194
  loop : -1.55 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.002   TRP A 145 
 HIS   0.008   0.001   HIS A1072 
 PHE   0.020   0.002   PHE A 900 
 TYR   0.026   0.002   TYR A 371 
 ARG   0.007   0.000   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03505 (  298)
  hydrogen bonds       : angle       4.60498 (  816)
  SS BOND              : bond        0.00705 (    1)
  SS BOND              : angle       2.10476 (    2)
  covalent geometry    : bond        0.00391 ( 8779)
  covalent geometry    : angle       0.65239 (11849)

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

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

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 175
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLN cc_start: 0.7643 (tp40) cc_final: 0.7375 (tm-30)
REVERT: A   20 ARG cc_start: 0.7963 (tpp-160) cc_final: 0.7229 (tmm-80)
REVERT: A  144 SER cc_start: 0.8671 (p) cc_final: 0.8384 (t)
REVERT: A  154 ASP cc_start: 0.7331 (t0) cc_final: 0.7033 (t0)
REVERT: A  160 SER cc_start: 0.8276 (m) cc_final: 0.7887 (p)
REVERT: A  210 MET cc_start: 0.8062 (mmm) cc_final: 0.7368 (mmm)
REVERT: A  320 HIS cc_start: 0.7855 (m90) cc_final: 0.7453 (m90)
REVERT: A  359 ASP cc_start: 0.6201 (m-30) cc_final: 0.5931 (m-30)
REVERT: A  417 MET cc_start: 0.8013 (ttm) cc_final: 0.7796 (ttm)
REVERT: A  477 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7888 (tp-100)
REVERT: A  487 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8225 (mt)
REVERT: A  548 GLN cc_start: 0.9117 (pt0) cc_final: 0.8667 (pm20)
REVERT: A  658 ASP cc_start: 0.8913 (m-30) cc_final: 0.8417 (m-30)
REVERT: A  689 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7778 (pttt)
REVERT: A  700 ARG cc_start: 0.9050 (ttp80) cc_final: 0.8800 (ttp80)
REVERT: A  843 ASN cc_start: 0.8223 (m110) cc_final: 0.7769 (m110)
REVERT: A  886 VAL cc_start: 0.7915 (t) cc_final: 0.7581 (m)
REVERT: A  901 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8490 (mm110)
REVERT: A  978 ASN cc_start: 0.8113 (m-40) cc_final: 0.7581 (t0)
REVERT: A  997 TYR cc_start: 0.8188 (p90) cc_final: 0.7688 (p90)
REVERT: A 1009 MET cc_start: 0.7026 (mtt) cc_final: 0.6754 (mtt)
REVERT: A 1045 THR cc_start: 0.8122 (p) cc_final: 0.7867 (p)
REVERT: A 1051 MET cc_start: 0.8953 (mmm) cc_final: 0.8717 (mmm)
  outliers start: 34
  outliers final: 23
  residues processed: 197
  average time/residue: 0.1777
  time to fit residues: 50.3514
Evaluate side-chains
  192 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 166
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   44 GLN
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  477 GLN
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  689 LYS
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1096 ASN
Chi-restraints excluded: chain A residue 1142 PHE
Chi-restraints excluded: chain A residue 1177 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 77 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0030
   chunk 22 optimal weight:    0.2980
   chunk 29 optimal weight:    0.6980
   chunk 65 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.5590

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

Flipped N/Q/H residues before XYZ refinement:
** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 880 GLN ** 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 = 0.3984 r_free = 0.3984 target = 0.141935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.109126 restraints weight = 13753.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.113418 restraints weight = 6026.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.116223 restraints weight = 3515.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.5956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8780  Z= 0.125
  Angle     :  0.655  12.097  11851  Z= 0.332
  Chirality :  0.042   0.215   1273
  Planarity :  0.004   0.046   1521
  Dihedral  :  6.276  53.552   1161
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  8.02 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 25.37 %
    Favored  : 71.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.26), residues: 1035
  helix:  1.79 (0.30), residues: 307
  sheet: -0.44 (0.37), residues: 202
  loop : -1.55 (0.26), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP A 145 
 HIS   0.005   0.001   HIS A1072 
 PHE   0.023   0.002   PHE A1099 
 TYR   0.026   0.001   TYR A 371 
 ARG   0.007   0.000   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03211 (  298)
  hydrogen bonds       : angle       4.55237 (  816)
  SS BOND              : bond        0.00095 (    1)
  SS BOND              : angle       2.19069 (    2)
  covalent geometry    : bond        0.00288 ( 8779)
  covalent geometry    : angle       0.65411 (11849)

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

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

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2070 Ramachandran restraints generated.
    1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 169
  time to evaluate  : 1.045 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.7925 (tpp-160) cc_final: 0.7150 (tmm-80)
REVERT: A   64 PHE cc_start: 0.7655 (p90) cc_final: 0.7355 (p90)
REVERT: A  127 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7878 (ttmt)
REVERT: A  144 SER cc_start: 0.8678 (p) cc_final: 0.8323 (t)
REVERT: A  154 ASP cc_start: 0.7320 (t0) cc_final: 0.7027 (t0)
REVERT: A  160 SER cc_start: 0.8174 (m) cc_final: 0.7825 (p)
REVERT: A  210 MET cc_start: 0.8050 (mmm) cc_final: 0.7452 (mmm)
REVERT: A  417 MET cc_start: 0.7931 (ttm) cc_final: 0.7691 (ttm)
REVERT: A  419 LYS cc_start: 0.8564 (ttmm) cc_final: 0.8238 (ttpt)
REVERT: A  487 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8217 (mt)
REVERT: A  548 GLN cc_start: 0.9135 (pt0) cc_final: 0.8685 (pm20)
REVERT: A  557 LYS cc_start: 0.6295 (mmtm) cc_final: 0.5306 (ptpp)
REVERT: A  658 ASP cc_start: 0.8891 (m-30) cc_final: 0.8379 (m-30)
REVERT: A  700 ARG cc_start: 0.9045 (ttp80) cc_final: 0.8829 (ttp80)
REVERT: A  843 ASN cc_start: 0.8203 (m110) cc_final: 0.7754 (m110)
REVERT: A  886 VAL cc_start: 0.7861 (t) cc_final: 0.7514 (m)
REVERT: A  901 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8533 (mm-40)
REVERT: A  978 ASN cc_start: 0.8073 (m-40) cc_final: 0.7595 (t0)
REVERT: A  997 TYR cc_start: 0.8155 (p90) cc_final: 0.7634 (p90)
REVERT: A 1039 GLN cc_start: 0.8386 (mt0) cc_final: 0.8160 (mt0)
REVERT: A 1045 THR cc_start: 0.8101 (p) cc_final: 0.7838 (p)
REVERT: A 1051 MET cc_start: 0.8977 (mmm) cc_final: 0.8672 (mmt)
  outliers start: 28
  outliers final: 22
  residues processed: 188
  average time/residue: 0.1819
  time to fit residues: 48.8952
Evaluate side-chains
  186 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   44 GLN
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  127 LYS
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  728 LYS
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1096 ASN
Chi-restraints excluded: chain A residue 1142 PHE
Chi-restraints excluded: chain A residue 1177 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 52 optimal weight:   10.0000
   chunk 85 optimal weight:    0.9980
   chunk 102 optimal weight:    0.4980
   chunk 93 optimal weight:    0.0270
   chunk 45 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    6.9990
   chunk 65 optimal weight:    6.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.8440

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

Flipped N/Q/H residues before XYZ refinement:
** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1025 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.141720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.108926 restraints weight = 13829.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.113191 restraints weight = 6066.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.115993 restraints weight = 3541.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.6052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8780  Z= 0.141
  Angle     :  0.644   9.831  11851  Z= 0.330
  Chirality :  0.041   0.204   1273
  Planarity :  0.004   0.046   1521
  Dihedral  :  5.876  51.293   1157
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  7.83 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 25.89 %
    Favored  : 71.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.26), residues: 1035
  helix:  1.79 (0.30), residues: 307
  sheet: -0.53 (0.37), residues: 206
  loop : -1.55 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP A 145 
 HIS   0.005   0.001   HIS A 641 
 PHE   0.019   0.001   PHE A 900 
 TYR   0.027   0.001   TYR A 371 
 ARG   0.007   0.000   ARG A 742 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03260 (  298)
  hydrogen bonds       : angle       4.51756 (  816)
  SS BOND              : bond        0.00017 (    1)
  SS BOND              : angle       1.77565 (    2)
  covalent geometry    : bond        0.00331 ( 8779)
  covalent geometry    : angle       0.64387 (11849)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3944.57 seconds
wall clock time: 69 minutes 7.02 seconds (4147.02 seconds total)