Starting phenix.real_space_refine
on Tue Jul 29 10:39:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8atw_15665/07_2025/8atw_15665.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8atw_15665/07_2025/8atw_15665.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8atw_15665/07_2025/8atw_15665.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8atw_15665/07_2025/8atw_15665.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8atw_15665/07_2025/8atw_15665.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8atw_15665/07_2025/8atw_15665.cif"
  }
  resolution = 3.62
  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=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      64      5.49       5
     S      36      5.16       5
     C    7024      2.51       5
     N    1957      2.21       5
     O    2202      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11283
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2758
          Classifications: {'peptide': 336}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 19, 'TRANS': 316}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 7235
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 922, 7235
          Classifications: {'peptide': 922}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 44, 'TRANS': 877}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 167
          Unresolved non-hydrogen angles: 202
          Unresolved non-hydrogen dihedrals: 132
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 80
    Chain: "N"
      Number of atoms: 582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 582
          Classifications: {'DNA': 28}
          Link IDs: {'rna3p': 27}
    Chain: "T"
      Number of atoms: 567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 567
          Classifications: {'DNA': 28}
          Link IDs: {'rna3p': 27}
    Chain: "C"
      Number of atoms: 109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 109
          Classifications: {'RNA': 5}
          Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 1}
          Link IDs: {'rna3p': 4}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.19, per 1000 atoms: 0.64
  Number of scatterers: 11283
  At special positions: 0
  Unit cell: (106.7, 114.46, 118.34, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      36     16.00
     P      64     15.00
     O    2202      8.00
     N    1957      7.00
     C    7024      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.70
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2380

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 10 sheets defined
      59.3% alpha, 8.8% beta
      23 base pairs and 42 stacking pairs defined.
    Time for finding SS restraints: 3.71
  Creating SS restraints...
    Processing helix  chain 'B' and resid 7 through 12
    Processing helix  chain 'B' and resid 25 through 37
    Processing helix  chain 'B' and resid 44 through 47
    Processing helix  chain 'B' and resid 58 through 69
    Processing helix  chain 'B' and resid 79 through 91
    Processing helix  chain 'B' and resid 104 through 114
      removed outlier: 4.228A  pdb=" N   TYR B 108 " --> pdb=" O   ASP B 104 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   SER B 109 " --> pdb=" O   TRP B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 157
      removed outlier: 3.670A  pdb=" N   ILE B 147 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 164
      removed outlier: 3.772A  pdb=" N   PHE B 163 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 181
    Processing helix  chain 'B' and resid 190 through 199
    Processing helix  chain 'B' and resid 210 through 215
    Processing helix  chain 'B' and resid 217 through 225
    Processing helix  chain 'B' and resid 230 through 234
      removed outlier: 4.028A  pdb=" N   GLU B 233 " --> pdb=" O   SER B 230 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   ILE B 234 " --> pdb=" O   ALA B 231 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 230 through 234'
    Processing helix  chain 'B' and resid 255 through 267
    Processing helix  chain 'B' and resid 273 through 278
      removed outlier: 3.602A  pdb=" N   VAL B 277 " --> pdb=" O   PRO B 273 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   MET B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 273 through 278'
    Processing helix  chain 'B' and resid 279 through 281
      No H-bonds generated for 'chain 'B' and resid 279 through 281'
    Processing helix  chain 'B' and resid 284 through 293
    Processing helix  chain 'B' and resid 295 through 301
      removed outlier: 3.793A  pdb=" N   LEU B 299 " --> pdb=" O   ASP B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 320
    Processing helix  chain 'B' and resid 326 through 330
      removed outlier: 3.659A  pdb=" N   MET B 329 " --> pdb=" O   ASP B 326 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ASP B 330 " --> pdb=" O   ILE B 327 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 326 through 330'
    Processing helix  chain 'A' and resid 387 through 395
    Processing helix  chain 'A' and resid 397 through 421
      removed outlier: 3.747A  pdb=" N   GLN A 413 " --> pdb=" O   ASN A 409 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   ASP A 414 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   ARG A 415 " --> pdb=" O   PHE A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 441
    Processing helix  chain 'A' and resid 446 through 477
      Proline residue:  A 463  - end of helix
    Processing helix  chain 'A' and resid 488 through 501
      removed outlier: 4.062A  pdb=" N   LEU A 494 " --> pdb=" O   ASP A 490 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   GLY A 495 " --> pdb=" O   THR A 491 " (cutoff:3.500A)
      Proline residue:  A 498  - end of helix
    Processing helix  chain 'A' and resid 504 through 519
    Processing helix  chain 'A' and resid 531 through 553
      removed outlier: 3.646A  pdb=" N   ILE A 536 " --> pdb=" O   ALA A 532 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU A 552 " --> pdb=" O   SER A 548 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LYS A 553 " --> pdb=" O   GLU A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 612
    Processing helix  chain 'A' and resid 652 through 661
      removed outlier: 4.427A  pdb=" N   GLY A 661 " --> pdb=" O   ARG A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 717
    Processing helix  chain 'A' and resid 719 through 732
      removed outlier: 3.975A  pdb=" N   THR A 732 " --> pdb=" O   VAL A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 737 through 751
      removed outlier: 3.537A  pdb=" N   GLY A 751 " --> pdb=" O   VAL A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 775 through 813
    Processing helix  chain 'A' and resid 842 through 848
    Processing helix  chain 'A' and resid 860 through 873
    Processing helix  chain 'A' and resid 879 through 890
    Processing helix  chain 'A' and resid 890 through 900
    Processing helix  chain 'A' and resid 907 through 911
    Processing helix  chain 'A' and resid 913 through 930
    Processing helix  chain 'A' and resid 932 through 935
      removed outlier: 3.560A  pdb=" N   GLU A 935 " --> pdb=" O   ASN A 932 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 932 through 935'
    Processing helix  chain 'A' and resid 948 through 959
    Processing helix  chain 'A' and resid 960 through 967
    Processing helix  chain 'A' and resid 977 through 994
    Processing helix  chain 'A' and resid 998 through 1005
    Processing helix  chain 'A' and resid 1009 through 1021
      removed outlier: 4.285A  pdb=" N   VAL A1021 " --> pdb=" O   VAL A1017 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1025 through 1038
    Processing helix  chain 'A' and resid 1047 through 1066
    Processing helix  chain 'A' and resid 1068 through 1085
    Processing helix  chain 'A' and resid 1090 through 1094
      removed outlier: 3.656A  pdb=" N   LYS A1094 " --> pdb=" O   VAL A1091 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1149 through 1181
      Proline residue:  A1158  - end of helix
    Processing helix  chain 'A' and resid 1197 through 1214
    Processing helix  chain 'A' and resid 1216 through 1229
    Processing helix  chain 'A' and resid 1242 through 1260
      removed outlier: 3.642A  pdb=" N   GLN A1246 " --> pdb=" O   THR A1242 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   LYS A1247 " --> pdb=" O   ASP A1243 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU A1259 " --> pdb=" O   LEU A1255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1264 through 1280
    Processing helix  chain 'A' and resid 1283 through 1293
    Processing helix  chain 'A' and resid 1295 through 1302
      removed outlier: 3.984A  pdb=" N   ASP A1302 " --> pdb=" O   SER A1298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1305 through 1310
      removed outlier: 4.212A  pdb=" N   LEU A1309 " --> pdb=" O   ASP A1305 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLU A1310 " --> pdb=" O   LEU A1306 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1305 through 1310'
    Processing helix  chain 'A' and resid 1340 through 1346
      removed outlier: 4.003A  pdb=" N   ASN A1345 " --> pdb=" O   VAL A1342 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.277A  pdb=" N   TYR B  73 " --> pdb=" O   GLN B  96 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   LEU B  98 " --> pdb=" O   TYR B  73 " (cutoff:3.500A)
      removed outlier: 5.634A  pdb=" N   LEU B  75 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   SER B  74 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU B  76 " --> pdb=" O   ASP B  52 " (cutoff:3.500A)
      removed outlier: 5.251A  pdb=" N   LYS B 167 " --> pdb=" O   ASN B 129 " (cutoff:3.500A)
      removed outlier: 9.372A  pdb=" N   LYS B 131 " --> pdb=" O   LYS B 167 " (cutoff:3.500A)
      removed outlier: 13.135A  pdb=" N   LEU B 169 " --> pdb=" O   LYS B 131 " (cutoff:3.500A)
      removed outlier: 10.105A  pdb=" N   LEU B 133 " --> pdb=" O   LEU B 169 " (cutoff:3.500A)
      removed outlier: 12.528A  pdb=" N   TRP B 171 " --> pdb=" O   LEU B 133 " (cutoff:3.500A)
      removed outlier: 9.968A  pdb=" N   VAL B 135 " --> pdb=" O   TRP B 171 " (cutoff:3.500A)
      removed outlier: 11.572A  pdb=" N   ASN B 137 " --> pdb=" O   PRO B 173 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   VAL B 166 " --> pdb=" O   PRO B 249 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   ALA B 206 " --> pdb=" O   LEU B 244 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   GLU B 246 " --> pdb=" O   LEU B 204 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   LEU B 204 " --> pdb=" O   GLU B 246 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   ASP B 248 " --> pdb=" O   THR B 202 " (cutoff:3.500A)
      removed outlier: 5.527A  pdb=" N   THR B 202 " --> pdb=" O   ASP B 248 " (cutoff:3.500A)
      removed outlier: 9.616A  pdb=" N   ILE B 227 " --> pdb=" O   LYS B 203 " (cutoff:3.500A)
      removed outlier: 7.271A  pdb=" N   ILE B 205 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 528 through 530
    Processing sheet with id=AA3, first strand: chain 'A' and resid 613 through 619
      removed outlier: 3.641A  pdb=" N   GLY A 629 " --> pdb=" O   VAL A 616 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 734 through 736
    Processing sheet with id=AA5, first strand: chain 'A' and resid 822 through 824
    Processing sheet with id=AA6, first strand: chain 'A' and resid 855 through 856
    Processing sheet with id=AA7, first strand: chain 'A' and resid 942 through 944
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1087 through 1088
      removed outlier: 3.530A  pdb=" N   VAL A1323 " --> pdb=" O   GLY A1236 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1109 through 1111
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1127 through 1131
      removed outlier: 3.517A  pdb=" N   ILE A1139 " --> pdb=" O   LYS A1128 " (cutoff:3.500A)

    540 hydrogen bonds defined for protein.
    1563 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      52 hydrogen bonds
      104 hydrogen bond angles
      0 basepair planarities
      23 basepair parallelities
      42 stacking parallelities
  Total time for adding SS restraints: 4.87

  Time building geometry restraints manager: 3.22 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2617
        1.33 -     1.45: 2671
        1.45 -     1.57: 6212
        1.57 -     1.69: 116
        1.69 -     1.81: 61
  Bond restraints: 11677
  Sorted by residual:
  bond pdb=" O3'  DT N 109 "
       pdb=" P    DA N 110 "
    ideal  model  delta    sigma   weight residual
    1.607  1.436  0.171 1.50e-02 4.44e+03 1.30e+02
  bond pdb=" C4'  DT T  20 "
       pdb=" O4'  DT T  20 "
    ideal  model  delta    sigma   weight residual
    1.450  1.621 -0.171 2.00e-02 2.50e+03 7.32e+01
  bond pdb=" C4'  DT T  21 "
       pdb=" O4'  DT T  21 "
    ideal  model  delta    sigma   weight residual
    1.450  1.568 -0.118 2.00e-02 2.50e+03 3.47e+01
  bond pdb=" O3'  DT T  12 "
       pdb=" P    DT T  13 "
    ideal  model  delta    sigma   weight residual
    1.607  1.690 -0.083 1.50e-02 4.44e+03 3.03e+01
  bond pdb=" O3'  DA T  27 "
       pdb=" P    DA T  28 "
    ideal  model  delta    sigma   weight residual
    1.607  1.539  0.068 1.50e-02 4.44e+03 2.03e+01
  ... (remaining 11672 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.78: 15885
        2.78 -     5.56: 178
        5.56 -     8.34: 19
        8.34 -    11.12: 6
       11.12 -    13.90: 6
  Bond angle restraints: 16094
  Sorted by residual:
  angle pdb=" C5'  DA T  34 "
        pdb=" C4'  DA T  34 "
        pdb=" O4'  DA T  34 "
      ideal   model   delta    sigma   weight residual
     109.40  123.30  -13.90 1.50e+00 4.44e-01 8.59e+01
  angle pdb=" O3'  DA T  28 "
        pdb=" C3'  DA T  28 "
        pdb=" C2'  DA T  28 "
      ideal   model   delta    sigma   weight residual
     111.50   98.72   12.78 1.50e+00 4.44e-01 7.25e+01
  angle pdb=" C5'  DT N 112 "
        pdb=" C4'  DT N 112 "
        pdb=" O4'  DT N 112 "
      ideal   model   delta    sigma   weight residual
     109.40  121.24  -11.84 1.50e+00 4.44e-01 6.23e+01
  angle pdb=" C5'  DT T  29 "
        pdb=" C4'  DT T  29 "
        pdb=" O4'  DT T  29 "
      ideal   model   delta    sigma   weight residual
     109.40  119.88  -10.48 1.50e+00 4.44e-01 4.88e+01
  angle pdb=" O4'  DT T  20 "
        pdb=" C4'  DT T  20 "
        pdb=" C3'  DT T  20 "
      ideal   model   delta    sigma   weight residual
     105.40   95.72    9.68 1.50e+00 4.44e-01 4.16e+01
  ... (remaining 16089 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.65: 6053
       21.65 -    43.30: 641
       43.30 -    64.95: 169
       64.95 -    86.60: 20
       86.60 -   108.26: 5
  Dihedral angle restraints: 6888
    sinusoidal: 3214
      harmonic: 3674
  Sorted by residual:
  dihedral pdb=" O5' GTP C 201 "
           pdb=" O3A GTP C 201 "
           pdb=" PA  GTP C 201 "
           pdb=" PB  GTP C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     274.12  165.87  108.26     1      2.00e+01 2.50e-03 3.15e+01
  dihedral pdb=" C8  GTP C 201 "
           pdb=" C1' GTP C 201 "
           pdb=" N9  GTP C 201 "
           pdb=" O4' GTP C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59    2.87  101.72     1      2.00e+01 2.50e-03 2.89e+01
  dihedral pdb=" CA  MET B 267 "
           pdb=" C   MET B 267 "
           pdb=" N   ILE B 268 "
           pdb=" CA  ILE B 268 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.14   18.86     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 6885 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.131: 1756
       0.131 -    0.262: 16
       0.262 -    0.393: 6
       0.393 -    0.524: 2
       0.524 -    0.655: 2
  Chirality restraints: 1782
  Sorted by residual:
  chirality pdb=" C4'  DT T  20 "
            pdb=" C5'  DT T  20 "
            pdb=" O4'  DT T  20 "
            pdb=" C3'  DT T  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -3.18    0.66 2.00e-01 2.50e+01 1.07e+01
  chirality pdb=" P    DG N 108 "
            pdb=" OP1  DG N 108 "
            pdb=" OP2  DG N 108 "
            pdb=" O5'  DG N 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.99   -0.65 2.00e-01 2.50e+01 1.04e+01
  chirality pdb=" C4'  DT T  29 "
            pdb=" C5'  DT T  29 "
            pdb=" O4'  DT T  29 "
            pdb=" C3'  DT T  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.02   -0.51 2.00e-01 2.50e+01 6.41e+00
  ... (remaining 1779 not shown)

  Planarity restraints: 1838
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA T  28 "   -0.022 2.00e-02 2.50e+03   1.21e-02 4.02e+00
        pdb=" N9   DA T  28 "    0.027 2.00e-02 2.50e+03
        pdb=" C8   DA T  28 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7   DA T  28 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5   DA T  28 "    0.004 2.00e-02 2.50e+03
        pdb=" C6   DA T  28 "   -0.001 2.00e-02 2.50e+03
        pdb=" N6   DA T  28 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1   DA T  28 "    0.004 2.00e-02 2.50e+03
        pdb=" C2   DA T  28 "   -0.010 2.00e-02 2.50e+03
        pdb=" N3   DA T  28 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DA T  28 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 272 "   -0.033 5.00e-02 4.00e+02   4.85e-02 3.77e+00
        pdb=" N   PRO B 273 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 273 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 273 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 119 "    0.024 5.00e-02 4.00e+02   3.70e-02 2.19e+00
        pdb=" N   PRO B 120 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B 120 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 120 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1835 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 828
        2.74 -     3.28: 11157
        3.28 -     3.82: 19479
        3.82 -     4.36: 22248
        4.36 -     4.90: 37648
  Nonbonded interactions: 91360
  Sorted by model distance:
  nonbonded pdb=" O   LEU B  23 "
            pdb=" OH  TYR B  29 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OG1 THR A1132 "
            pdb=" O   GLN A1135 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" NH2 ARG A1206 "
            pdb=" O   SER A1346 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" OD2 ASP A 775 "
            pdb=" OG  SER A 777 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   PRO B 102 "
            pdb=" OH  TYR B 108 "
     model   vdw
     2.283 3.040
  ... (remaining 91355 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.210
  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:             0.010
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     32.040
  Find NCS groups from input model:        0.110
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.171  11678  Z= 0.275
  Angle     :  0.737  13.899  16094  Z= 0.407
  Chirality :  0.054   0.655   1782
  Planarity :  0.004   0.049   1838
  Dihedral  : 18.135 108.255   4508
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.06 (0.24), residues: 1250
  helix:  1.59 (0.20), residues: 708
  sheet:  0.27 (0.56), residues: 85
  loop : -0.58 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 159 
 HIS   0.004   0.001   HIS A1169 
 PHE   0.020   0.001   PHE A1300 
 TYR   0.021   0.002   TYR A 979 
 ARG   0.007   0.000   ARG A 984 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14427 (  592)
  hydrogen bonds       : angle       5.76474 ( 1667)
  covalent geometry    : bond        0.00481 (11677)
  covalent geometry    : angle       0.73670 (16094)
  Misc. bond           : bond        0.09025 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 1.030 
Fit side-chains
REVERT: B   52 ASP cc_start: 0.6643 (t70) cc_final: 0.6442 (t70)
REVERT: B   71 ARG cc_start: 0.7645 (ptp-110) cc_final: 0.7430 (ptt180)
REVERT: B  247 MET cc_start: 0.8059 (mmt) cc_final: 0.7852 (mmp)
REVERT: A  398 LEU cc_start: 0.8355 (mt) cc_final: 0.8045 (mt)
REVERT: A  402 LYS cc_start: 0.8556 (mptt) cc_final: 0.8352 (mptt)
REVERT: A  514 LEU cc_start: 0.8787 (mt) cc_final: 0.7974 (tp)
REVERT: A 1057 HIS cc_start: 0.6975 (m90) cc_final: 0.6355 (m90)
REVERT: A 1325 LEU cc_start: 0.8353 (mm) cc_final: 0.8106 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.2219
  time to fit residues: 65.9300
Evaluate side-chains
  153 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 1.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 97 optimal weight:    0.8980
   chunk 54 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 52 optimal weight:    8.9990
   chunk 101 optimal weight:    5.9990
   chunk 39 optimal weight:   20.0000
   chunk 61 optimal weight:    1.9990
   chunk 75 optimal weight:    9.9990
   chunk 117 optimal weight:   20.0000
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1129 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.145335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.115195 restraints weight = 17698.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.118745 restraints weight = 9715.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.121136 restraints weight = 6740.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.1035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085  11678  Z= 0.148
  Angle     :  0.571   9.384  16094  Z= 0.302
  Chirality :  0.040   0.185   1782
  Planarity :  0.004   0.040   1838
  Dihedral  : 18.418  97.986   2081
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.04 %
    Favored  : 90.03 %
  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:  0.99 (0.24), residues: 1250
  helix:  1.59 (0.20), residues: 710
  sheet:  0.35 (0.45), residues: 124
  loop : -0.84 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 159 
 HIS   0.004   0.001   HIS B 265 
 PHE   0.018   0.001   PHE A 886 
 TYR   0.015   0.001   TYR A1229 
 ARG   0.008   0.000   ARG A 827 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04501 (  592)
  hydrogen bonds       : angle       4.46702 ( 1667)
  covalent geometry    : bond        0.00337 (11677)
  covalent geometry    : angle       0.57088 (16094)
  Misc. bond           : bond        0.00085 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 171
  time to evaluate  : 1.223 
Fit side-chains
REVERT: A  514 LEU cc_start: 0.8794 (mt) cc_final: 0.8027 (tp)
REVERT: A 1057 HIS cc_start: 0.7017 (m90) cc_final: 0.6589 (m90)
REVERT: A 1096 PHE cc_start: 0.7642 (p90) cc_final: 0.7400 (p90)
  outliers start: 10
  outliers final: 7
  residues processed: 176
  average time/residue: 0.2108
  time to fit residues: 55.4819
Evaluate side-chains
  157 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 150
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1233 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 12 optimal weight:    8.9990
   chunk 53 optimal weight:    0.4980
   chunk 103 optimal weight:   10.0000
   chunk 74 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 107 optimal weight:    1.9990
   chunk 18 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 95 optimal weight:    7.9990
   chunk 93 optimal weight:    2.9990
   chunk 115 optimal weight:   20.0000
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
B 265 HIS
A 492 ASN
** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.145584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.115374 restraints weight = 17970.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.119014 restraints weight = 9739.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.121388 restraints weight = 6688.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.1413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11678  Z= 0.127
  Angle     :  0.535   8.105  16094  Z= 0.282
  Chirality :  0.038   0.181   1782
  Planarity :  0.004   0.041   1838
  Dihedral  : 18.376  99.834   2081
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 12.02 %
    Favored  : 86.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.24), residues: 1250
  helix:  1.68 (0.20), residues: 702
  sheet:  0.32 (0.45), residues: 126
  loop : -0.68 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  24 
 HIS   0.005   0.001   HIS B 265 
 PHE   0.014   0.001   PHE A 886 
 TYR   0.022   0.001   TYR B 161 
 ARG   0.007   0.000   ARG A 827 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03943 (  592)
  hydrogen bonds       : angle       4.15632 ( 1667)
  covalent geometry    : bond        0.00278 (11677)
  covalent geometry    : angle       0.53529 (16094)
  Misc. bond           : bond        0.00073 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 176
  time to evaluate  : 1.210 
Fit side-chains
REVERT: A  471 HIS cc_start: 0.7571 (t-170) cc_final: 0.7282 (t-170)
REVERT: A  922 PHE cc_start: 0.8449 (m-10) cc_final: 0.8065 (m-10)
REVERT: A 1057 HIS cc_start: 0.7094 (m90) cc_final: 0.6611 (m90)
REVERT: A 1096 PHE cc_start: 0.7654 (p90) cc_final: 0.7317 (p90)
  outliers start: 15
  outliers final: 12
  residues processed: 186
  average time/residue: 0.2101
  time to fit residues: 58.0379
Evaluate side-chains
  159 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 147
  time to evaluate  : 1.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1233 VAL
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1325 LEU
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 37 optimal weight:   10.0000
   chunk 28 optimal weight:   20.0000
   chunk 60 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 84 optimal weight:    0.0980
   chunk 73 optimal weight:    0.9990
   chunk 46 optimal weight:    5.9990
   chunk 74 optimal weight:    6.9990
   chunk 92 optimal weight:   10.0000
   chunk 52 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    3.6188

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

Flipped N/Q/H residues before XYZ refinement:
B 265 HIS
A1057 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.143703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.113484 restraints weight = 17885.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.116986 restraints weight = 9802.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.119314 restraints weight = 6797.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11678  Z= 0.158
  Angle     :  0.552   8.574  16094  Z= 0.291
  Chirality :  0.039   0.164   1782
  Planarity :  0.004   0.037   1838
  Dihedral  : 18.412 102.143   2081
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.73 %
    Favored  : 83.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.24), residues: 1250
  helix:  1.72 (0.20), residues: 692
  sheet:  0.24 (0.45), residues: 126
  loop : -0.71 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  24 
 HIS   0.006   0.001   HIS B 265 
 PHE   0.015   0.001   PHE A1300 
 TYR   0.018   0.001   TYR B 161 
 ARG   0.005   0.000   ARG A 827 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04118 (  592)
  hydrogen bonds       : angle       4.14312 ( 1667)
  covalent geometry    : bond        0.00360 (11677)
  covalent geometry    : angle       0.55159 (16094)
  Misc. bond           : bond        0.00047 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 150
  time to evaluate  : 0.984 
Fit side-chains
REVERT: B   60 GLN cc_start: 0.7230 (tm-30) cc_final: 0.6649 (tm-30)
REVERT: A 1057 HIS cc_start: 0.7227 (m-70) cc_final: 0.6893 (m90)
REVERT: A 1096 PHE cc_start: 0.7602 (p90) cc_final: 0.7208 (p90)
  outliers start: 23
  outliers final: 16
  residues processed: 165
  average time/residue: 0.2813
  time to fit residues: 71.0887
Evaluate side-chains
  157 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 141
  time to evaluate  : 1.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  867 ILE
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1233 VAL
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1325 LEU
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 82 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 80 optimal weight:    6.9990
   chunk 12 optimal weight:   30.0000
   chunk 81 optimal weight:    0.5980
   chunk 106 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 51 optimal weight:    8.9990
   chunk 22 optimal weight:    0.0060
   overall best weight:    0.8598

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

Flipped N/Q/H residues before XYZ refinement:
B  72 GLN
B 265 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.148570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.117153 restraints weight = 17812.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.120912 restraints weight = 9835.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.123411 restraints weight = 6852.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.1798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  11678  Z= 0.112
  Angle     :  0.519   8.548  16094  Z= 0.273
  Chirality :  0.037   0.170   1782
  Planarity :  0.004   0.045   1838
  Dihedral  : 18.267 101.588   2081
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 16.31 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.24), residues: 1250
  helix:  1.83 (0.20), residues: 688
  sheet:  0.55 (0.46), residues: 118
  loop : -0.67 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  24 
 HIS   0.004   0.001   HIS B 265 
 PHE   0.012   0.001   PHE B  85 
 TYR   0.023   0.001   TYR A1229 
 ARG   0.004   0.000   ARG A1275 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03583 (  592)
  hydrogen bonds       : angle       4.01417 ( 1667)
  covalent geometry    : bond        0.00241 (11677)
  covalent geometry    : angle       0.51863 (16094)
  Misc. bond           : bond        0.00065 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 172
  time to evaluate  : 1.309 
Fit side-chains
REVERT: B   60 GLN cc_start: 0.7126 (tm-30) cc_final: 0.6618 (tm-30)
REVERT: B   85 PHE cc_start: 0.7747 (t80) cc_final: 0.7533 (t80)
REVERT: A  471 HIS cc_start: 0.7487 (t-170) cc_final: 0.7267 (t-170)
REVERT: A  514 LEU cc_start: 0.8742 (mt) cc_final: 0.7980 (tp)
REVERT: A  922 PHE cc_start: 0.8352 (m-10) cc_final: 0.7982 (m-10)
REVERT: A 1057 HIS cc_start: 0.7199 (m-70) cc_final: 0.6831 (m90)
REVERT: A 1096 PHE cc_start: 0.7504 (p90) cc_final: 0.7142 (p90)
REVERT: A 1229 TYR cc_start: 0.7644 (m-10) cc_final: 0.7010 (m-80)
  outliers start: 17
  outliers final: 14
  residues processed: 184
  average time/residue: 0.2322
  time to fit residues: 63.8329
Evaluate side-chains
  163 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 1.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  867 ILE
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1233 VAL
Chi-restraints excluded: chain A residue 1325 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 54 optimal weight:    9.9990
   chunk 15 optimal weight:    9.9990
   chunk 70 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 80 optimal weight:   20.0000
   chunk 106 optimal weight:    6.9990
   chunk 103 optimal weight:    3.9990
   chunk 101 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 67 optimal weight:   30.0000
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
B  72 GLN
B 265 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.142641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.110380 restraints weight = 18297.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.113886 restraints weight = 10376.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.116239 restraints weight = 7380.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076  11678  Z= 0.235
  Angle     :  0.617   8.328  16094  Z= 0.325
  Chirality :  0.042   0.156   1782
  Planarity :  0.004   0.046   1838
  Dihedral  : 18.578 107.127   2081
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.24 %
    Favored  : 80.43 %
  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:  0.84 (0.24), residues: 1250
  helix:  1.51 (0.20), residues: 699
  sheet: -0.05 (0.45), residues: 121
  loop : -0.79 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  24 
 HIS   0.008   0.001   HIS B 265 
 PHE   0.021   0.002   PHE A1138 
 TYR   0.016   0.002   TYR B 335 
 ARG   0.010   0.000   ARG A 827 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04862 (  592)
  hydrogen bonds       : angle       4.34326 ( 1667)
  covalent geometry    : bond        0.00547 (11677)
  covalent geometry    : angle       0.61692 (16094)
  Misc. bond           : bond        0.00036 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 140
  time to evaluate  : 1.116 
Fit side-chains
REVERT: B   60 GLN cc_start: 0.7318 (tm-30) cc_final: 0.7072 (tm-30)
REVERT: A  709 TYR cc_start: 0.8289 (m-80) cc_final: 0.8070 (m-80)
REVERT: A  926 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7435 (mm-30)
REVERT: A 1057 HIS cc_start: 0.7016 (m-70) cc_final: 0.6632 (m90)
REVERT: A 1096 PHE cc_start: 0.7536 (p90) cc_final: 0.7099 (p90)
REVERT: A 1170 MET cc_start: 0.8278 (tmm) cc_final: 0.8041 (tmm)
  outliers start: 25
  outliers final: 18
  residues processed: 158
  average time/residue: 0.2004
  time to fit residues: 48.1501
Evaluate side-chains
  151 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 ASP
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  844 MET
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1233 VAL
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1325 LEU
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 99 optimal weight:    9.9990
   chunk 76 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 79 optimal weight:   20.0000
   chunk 59 optimal weight:    9.9990
   chunk 51 optimal weight:    1.9990
   chunk 92 optimal weight:   10.0000
   chunk 56 optimal weight:    8.9990
   chunk 90 optimal weight:    0.2980
   chunk 32 optimal weight:    6.9990
   overall best weight:    3.8588

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

Flipped N/Q/H residues before XYZ refinement:
B 265 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.143611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.113097 restraints weight = 18027.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.116549 restraints weight = 9970.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.118872 restraints weight = 7004.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  11678  Z= 0.165
  Angle     :  0.572   9.392  16094  Z= 0.302
  Chirality :  0.039   0.165   1782
  Planarity :  0.004   0.049   1838
  Dihedral  : 18.496 107.888   2081
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 17.43 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.24), residues: 1250
  helix:  1.61 (0.20), residues: 692
  sheet:  0.04 (0.45), residues: 118
  loop : -0.82 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  24 
 HIS   0.006   0.001   HIS B 265 
 PHE   0.016   0.001   PHE A1300 
 TYR   0.020   0.002   TYR B 335 
 ARG   0.009   0.000   ARG A 827 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04350 (  592)
  hydrogen bonds       : angle       4.25107 ( 1667)
  covalent geometry    : bond        0.00382 (11677)
  covalent geometry    : angle       0.57189 (16094)
  Misc. bond           : bond        0.00037 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 1.191 
Fit side-chains
REVERT: B  329 MET cc_start: 0.6858 (mtm) cc_final: 0.6329 (mmm)
REVERT: A  529 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.7819 (ppp)
REVERT: A  694 GLN cc_start: 0.7630 (mp10) cc_final: 0.7429 (mp10)
REVERT: A  926 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7352 (mm-30)
REVERT: A 1057 HIS cc_start: 0.7066 (m-70) cc_final: 0.6746 (m-70)
REVERT: A 1096 PHE cc_start: 0.7499 (p90) cc_final: 0.7079 (p90)
  outliers start: 27
  outliers final: 19
  residues processed: 161
  average time/residue: 0.2041
  time to fit residues: 49.8916
Evaluate side-chains
  155 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  529 MET
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  844 MET
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1233 VAL
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1325 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 108 optimal weight:    6.9990
   chunk 54 optimal weight:    7.9990
   chunk 15 optimal weight:    9.9990
   chunk 121 optimal weight:   10.0000
   chunk 112 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 71 optimal weight:    0.3980
   overall best weight:    3.0586

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

Flipped N/Q/H residues before XYZ refinement:
B 265 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.143873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.113182 restraints weight = 17984.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.116804 restraints weight = 9721.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.119210 restraints weight = 6704.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  11678  Z= 0.147
  Angle     :  0.573  10.620  16094  Z= 0.299
  Chirality :  0.039   0.164   1782
  Planarity :  0.004   0.046   1838
  Dihedral  : 18.428 108.286   2081
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.71 %
    Favored  : 79.96 %
  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:  0.94 (0.24), residues: 1250
  helix:  1.60 (0.20), residues: 697
  sheet:  0.08 (0.45), residues: 118
  loop : -0.79 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B  24 
 HIS   0.005   0.001   HIS B 265 
 PHE   0.013   0.001   PHE A1300 
 TYR   0.018   0.002   TYR B 108 
 ARG   0.007   0.000   ARG A 827 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04161 (  592)
  hydrogen bonds       : angle       4.19669 ( 1667)
  covalent geometry    : bond        0.00335 (11677)
  covalent geometry    : angle       0.57346 (16094)
  Misc. bond           : bond        0.00043 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 146
  time to evaluate  : 1.218 
Fit side-chains
REVERT: B  319 MET cc_start: 0.8103 (mmp) cc_final: 0.7850 (mtm)
REVERT: B  329 MET cc_start: 0.6859 (mtm) cc_final: 0.6294 (mmm)
REVERT: A  529 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.7731 (ppp)
REVERT: A  694 GLN cc_start: 0.7680 (mp10) cc_final: 0.7440 (mp10)
REVERT: A  926 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7390 (mm-30)
REVERT: A 1057 HIS cc_start: 0.6966 (m-70) cc_final: 0.6667 (m-70)
REVERT: A 1096 PHE cc_start: 0.7444 (p90) cc_final: 0.7042 (p90)
  outliers start: 25
  outliers final: 21
  residues processed: 163
  average time/residue: 0.1981
  time to fit residues: 49.0720
Evaluate side-chains
  162 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 1.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue  116 ARG
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  529 MET
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1233 VAL
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1325 LEU
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 110 optimal weight:   10.0000
   chunk 64 optimal weight:    6.9990
   chunk 87 optimal weight:    5.9990
   chunk 69 optimal weight:    4.9990
   chunk 19 optimal weight:    9.9990
   chunk 92 optimal weight:    9.9990
   chunk 109 optimal weight:    6.9990
   chunk 66 optimal weight:    6.9990
   chunk 58 optimal weight:    0.7980
   chunk 91 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   overall best weight:    5.1588

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

Flipped N/Q/H residues before XYZ refinement:
B 265 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.142622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.112091 restraints weight = 18129.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.115570 restraints weight = 10053.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.117875 restraints weight = 7024.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  11678  Z= 0.197
  Angle     :  0.600   9.775  16094  Z= 0.314
  Chirality :  0.040   0.152   1782
  Planarity :  0.004   0.046   1838
  Dihedral  : 18.554 110.907   2081
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 17.99 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.24), residues: 1250
  helix:  1.52 (0.20), residues: 690
  sheet:  0.07 (0.45), residues: 118
  loop : -0.86 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B  24 
 HIS   0.007   0.001   HIS B 265 
 PHE   0.019   0.002   PHE A1300 
 TYR   0.018   0.002   TYR B 108 
 ARG   0.008   0.000   ARG A 827 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04582 (  592)
  hydrogen bonds       : angle       4.31305 ( 1667)
  covalent geometry    : bond        0.00458 (11677)
  covalent geometry    : angle       0.60031 (16094)
  Misc. bond           : bond        0.00040 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 1.148 
Fit side-chains
REVERT: B  329 MET cc_start: 0.6823 (mtm) cc_final: 0.6359 (mmm)
REVERT: A  529 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.7872 (ppp)
REVERT: A  709 TYR cc_start: 0.8199 (m-80) cc_final: 0.7952 (m-80)
REVERT: A  926 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7374 (mm-30)
REVERT: A 1057 HIS cc_start: 0.6954 (m-70) cc_final: 0.6663 (m-70)
REVERT: A 1096 PHE cc_start: 0.7486 (p90) cc_final: 0.7001 (p90)
  outliers start: 24
  outliers final: 21
  residues processed: 156
  average time/residue: 0.2037
  time to fit residues: 47.9911
Evaluate side-chains
  159 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 137
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue  116 ARG
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  529 MET
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1233 VAL
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1325 LEU
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 111 optimal weight:    0.9990
   chunk 74 optimal weight:    7.9990
   chunk 97 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0070
   chunk 75 optimal weight:    0.9980
   chunk 92 optimal weight:    8.9990
   chunk 113 optimal weight:    8.9990
   chunk 35 optimal weight:   10.0000
   chunk 91 optimal weight:    6.9990
   chunk 50 optimal weight:    0.2980
   chunk 103 optimal weight:    4.9990
   overall best weight:    1.4602

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

Flipped N/Q/H residues before XYZ refinement:
A 952 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.146768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.116489 restraints weight = 17770.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.120130 restraints weight = 9638.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.122523 restraints weight = 6665.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  11678  Z= 0.126
  Angle     :  0.565   9.994  16094  Z= 0.294
  Chirality :  0.038   0.162   1782
  Planarity :  0.004   0.050   1838
  Dihedral  : 18.323 110.040   2081
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 18.45 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.24), residues: 1250
  helix:  1.72 (0.20), residues: 692
  sheet:  0.22 (0.46), residues: 118
  loop : -0.84 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.001   TRP B 235 
 HIS   0.004   0.001   HIS B 127 
 PHE   0.010   0.001   PHE A 886 
 TYR   0.017   0.002   TYR B 108 
 ARG   0.004   0.000   ARG A 883 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03872 (  592)
  hydrogen bonds       : angle       4.11701 ( 1667)
  covalent geometry    : bond        0.00286 (11677)
  covalent geometry    : angle       0.56484 (16094)
  Misc. bond           : bond        0.00053 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 161
  time to evaluate  : 1.111 
Fit side-chains
REVERT: B  329 MET cc_start: 0.6849 (mtm) cc_final: 0.6313 (mmm)
REVERT: A  926 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7303 (mm-30)
REVERT: A 1057 HIS cc_start: 0.7091 (m-70) cc_final: 0.6702 (m-70)
REVERT: A 1096 PHE cc_start: 0.7421 (p90) cc_final: 0.7022 (p90)
REVERT: A 1229 TYR cc_start: 0.7758 (m-10) cc_final: 0.7065 (m-80)
  outliers start: 19
  outliers final: 18
  residues processed: 176
  average time/residue: 0.2080
  time to fit residues: 54.3876
Evaluate side-chains
  163 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 145
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue  116 ARG
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1233 VAL
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1325 LEU
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 4 optimal weight:   30.0000
   chunk 127 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9990
   chunk 40 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   chunk 63 optimal weight:    5.9990
   chunk 88 optimal weight:    0.2980
   chunk 86 optimal weight:    9.9990
   chunk 20 optimal weight:    7.9990
   chunk 87 optimal weight:    8.9990
   overall best weight:    2.8186

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

Flipped N/Q/H residues before XYZ refinement:
** A 471 HIS ** 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 = 0.3793 r_free = 0.3793 target = 0.145937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.114263 restraints weight = 18030.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.117823 restraints weight = 10165.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.120189 restraints weight = 7197.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  11678  Z= 0.145
  Angle     :  0.577   9.619  16094  Z= 0.300
  Chirality :  0.039   0.205   1782
  Planarity :  0.004   0.051   1838
  Dihedral  : 18.375 110.327   2081
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 19.48 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.24), residues: 1250
  helix:  1.68 (0.20), residues: 692
  sheet:  0.22 (0.46), residues: 118
  loop : -0.85 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B  24 
 HIS   0.004   0.001   HIS B 127 
 PHE   0.011   0.001   PHE A 873 
 TYR   0.014   0.002   TYR B  73 
 ARG   0.007   0.000   ARG A1275 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04033 (  592)
  hydrogen bonds       : angle       4.12574 ( 1667)
  covalent geometry    : bond        0.00339 (11677)
  covalent geometry    : angle       0.57656 (16094)
  Misc. bond           : bond        0.00053 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3442.66 seconds
wall clock time: 61 minutes 4.80 seconds (3664.80 seconds total)