Starting phenix.real_space_refine
on Thu Jul  2 18:23:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9wfg_65928/07_2026/9wfg_65928.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9wfg_65928/07_2026/9wfg_65928.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9wfg_65928/07_2026/9wfg_65928.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9wfg_65928/07_2026/9wfg_65928.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9wfg_65928/07_2026/9wfg_65928.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9wfg_65928/07_2026/9wfg_65928.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.043
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    5957      2.51       5
     N    1626      2.21       5
     O    1699      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9319
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9319
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1178, 9319
          Classifications: {'peptide': 1178}
          Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 1140}
          Chain breaks: 3
  Time building chain proxies: 2.12, per 1000 atoms: 0.23
  Number of scatterers: 9319
  At special positions: 0
  Unit cell: (83.46, 88.81, 144.45, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1699      8.00
     N    1626      7.00
     C    5957      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 332.4 milliseconds
  

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2184

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 4 sheets defined
      65.8% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 87 through 100
    Processing helix  chain 'A' and resid 102 through 140
    Processing helix  chain 'A' and resid 146 through 190
      removed outlier: 4.067A  pdb=" N   SER A 150 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   MET A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 198
      removed outlier: 3.724A  pdb=" N   LYS A 197 " --> pdb=" O   MET A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 214
    Processing helix  chain 'A' and resid 215 through 248
      removed outlier: 3.590A  pdb=" N   ALA A 233 " --> pdb=" O   ASP A 229 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   ALA A 241 " --> pdb=" O   GLY A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 270
      removed outlier: 3.977A  pdb=" N   ALA A 258 " --> pdb=" O   PHE A 254 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   PHE A 270 " --> pdb=" O   ALA A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 298
    Processing helix  chain 'A' and resid 298 through 306
    Processing helix  chain 'A' and resid 307 through 333
      removed outlier: 3.674A  pdb=" N   LYS A 318 " --> pdb=" O   HIS A 314 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ASN A 321 " --> pdb=" O   GLN A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 344
    Processing helix  chain 'A' and resid 348 through 362
      removed outlier: 3.567A  pdb=" N   ILE A 357 " --> pdb=" O   VAL A 353 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   GLU A 358 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      Proline residue:  A 359  - end of helix
      removed outlier: 4.379A  pdb=" N   SER A 362 " --> pdb=" O   GLU A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 426
      removed outlier: 4.175A  pdb=" N   SER A 402 " --> pdb=" O   LEU A 398 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   ARG A 403 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   GLY A 410 " --> pdb=" O   ASN A 406 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   TYR A 411 " --> pdb=" O   ARG A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 486 through 495
      removed outlier: 3.640A  pdb=" N   LEU A 490 " --> pdb=" O   GLY A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 538
    Processing helix  chain 'A' and resid 550 through 561
    Processing helix  chain 'A' and resid 564 through 570
      removed outlier: 3.787A  pdb=" N   ASP A 568 " --> pdb=" O   GLU A 564 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   TYR A 570 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 582
      removed outlier: 4.593A  pdb=" N   GLU A 581 " --> pdb=" O   ASN A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 583 through 599
    Processing helix  chain 'A' and resid 613 through 628
    Processing helix  chain 'A' and resid 739 through 752
    Processing helix  chain 'A' and resid 757 through 793
    Processing helix  chain 'A' and resid 799 through 844
      removed outlier: 3.506A  pdb=" N   ALA A 817 " --> pdb=" O   SER A 813 " (cutoff:3.500A)
      Proline residue:  A 818  - end of helix
      removed outlier: 4.091A  pdb=" N   ASN A 842 " --> pdb=" O   HIS A 838 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LEU A 844 " --> pdb=" O   LEU A 840 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 847 through 855
      removed outlier: 3.759A  pdb=" N   LYS A 851 " --> pdb=" O   ASN A 847 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL A 852 " --> pdb=" O   ALA A 848 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   PHE A 853 " --> pdb=" O   PHE A 849 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 867 through 902
      removed outlier: 3.588A  pdb=" N   LYS A 872 " --> pdb=" O   ARG A 868 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU A 873 " --> pdb=" O   ASP A 869 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   LYS A 886 " --> pdb=" O   THR A 882 " (cutoff:3.500A)
      Proline residue:  A 887  - end of helix
      removed outlier: 4.568A  pdb=" N   LEU A 900 " --> pdb=" O   TRP A 896 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   LEU A 901 " --> pdb=" O   ARG A 897 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 903 through 918
      removed outlier: 4.374A  pdb=" N   ILE A 909 " --> pdb=" O   ARG A 905 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   THR A 912 " --> pdb=" O   ALA A 908 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 927 through 952
    Processing helix  chain 'A' and resid 952 through 960
      removed outlier: 3.529A  pdb=" N   PHE A 958 " --> pdb=" O   GLU A 954 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 961 through 1000
      removed outlier: 3.626A  pdb=" N   LEU A 983 " --> pdb=" O   HIS A 979 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   LEU A 989 " --> pdb=" O   ARG A 985 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   TYR A 990 " --> pdb=" O   LYS A 986 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   PHE A 996 " --> pdb=" O   ILE A 992 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1000 through 1016
    Processing helix  chain 'A' and resid 1025 through 1044
    Processing helix  chain 'A' and resid 1046 through 1069
      removed outlier: 4.154A  pdb=" N   GLY A1063 " --> pdb=" O   LEU A1059 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   GLY A1064 " --> pdb=" O   GLU A1060 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1071 through 1077
    Processing helix  chain 'A' and resid 1135 through 1144
      removed outlier: 3.545A  pdb=" N   VAL A1139 " --> pdb=" O   GLY A1135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1185 through 1190
    Processing helix  chain 'A' and resid 1193 through 1202
    Processing helix  chain 'A' and resid 1215 through 1229
      removed outlier: 4.102A  pdb=" N   ASP A1219 " --> pdb=" O   GLY A1215 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   HIS A1221 " --> pdb=" O   ILE A1217 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ASN A1228 " --> pdb=" O   THR A1224 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   VAL A1229 " --> pdb=" O   ILE A1225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1231 through 1238
      removed outlier: 4.130A  pdb=" N   LEU A1235 " --> pdb=" O   LEU A1231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1240 through 1244
      removed outlier: 4.288A  pdb=" N   ASP A1243 " --> pdb=" O   GLY A1240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1247 through 1252
      removed outlier: 3.724A  pdb=" N   LEU A1252 " --> pdb=" O   TRP A1248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1253 through 1269
    Processing helix  chain 'A' and resid 1283 through 1298
    Processing helix  chain 'A' and resid 1307 through 1311
    Processing sheet with id=AA1, first strand: chain 'A' and resid 470 through 471
      removed outlier: 4.345A  pdb=" N   VAL A 453 " --> pdb=" O   SER A 502 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   SER A 502 " --> pdb=" O   VAL A 453 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 521
      removed outlier: 6.581A  pdb=" N   PHE A 519 " --> pdb=" O   ILE A 604 " (cutoff:3.500A)
      removed outlier: 8.344A  pdb=" N   ASP A 606 " --> pdb=" O   PHE A 519 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   VAL A 521 " --> pdb=" O   ASP A 606 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   LEU A 477 " --> pdb=" O   THR A 633 " (cutoff:3.500A)
      removed outlier: 9.954A  pdb=" N   LEU A 478 " --> pdb=" O   SER A 649 " (cutoff:3.500A)
      removed outlier: 8.364A  pdb=" N   ASP A 651 " --> pdb=" O   LEU A 478 " (cutoff:3.500A)
      removed outlier: 8.678A  pdb=" N   THR A 480 " --> pdb=" O   ASP A 651 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1096 through 1105
      removed outlier: 4.881A  pdb=" N   SER A1098 " --> pdb=" O   ILE A1120 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   ILE A1120 " --> pdb=" O   SER A1098 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   SER A1100 " --> pdb=" O   CYS A1118 " (cutoff:3.500A)
      removed outlier: 4.964A  pdb=" N   CYS A1118 " --> pdb=" O   SER A1100 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   ILE A1104 " --> pdb=" O   SER A1114 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   SER A1114 " --> pdb=" O   ILE A1104 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1170 through 1173
      removed outlier: 3.706A  pdb=" N   PHE A1171 " --> pdb=" O   PHE A1272 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   LEU A1127 " --> pdb=" O   LEU A1318 " (cutoff:3.500A)

    568 hydrogen bonds defined for protein.
    1689 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.32

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3055
        1.34 -     1.46: 1991
        1.46 -     1.58: 4393
        1.58 -     1.70: 0
        1.70 -     1.82: 65
  Bond restraints: 9504
  Sorted by residual:
  bond pdb=" N   SER A 199 "
       pdb=" CA  SER A 199 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.00e-02 1.00e+04 8.23e+00
  bond pdb=" N   ILE A 198 "
       pdb=" CA  ILE A 198 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.24e-02 6.50e+03 8.14e+00
  bond pdb=" N   VAL A 194 "
       pdb=" CA  VAL A 194 "
    ideal  model  delta    sigma   weight residual
    1.462  1.494 -0.032 1.17e-02 7.31e+03 7.50e+00
  bond pdb=" N   GLU A 191 "
       pdb=" CA  GLU A 191 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.23e-02 6.61e+03 6.56e+00
  bond pdb=" N   LYS A 197 "
       pdb=" CA  LYS A 197 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.23e-02 6.61e+03 6.20e+00
  ... (remaining 9499 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.86: 12831
        6.86 -    13.72: 12
       13.72 -    20.58: 4
       20.58 -    27.44: 0
       27.44 -    34.30: 1
  Bond angle restraints: 12848
  Sorted by residual:
  angle pdb=" N   THR A 902 "
        pdb=" CA  THR A 902 "
        pdb=" C   THR A 902 "
      ideal   model   delta    sigma   weight residual
     110.14   75.84   34.30 1.55e+00 4.16e-01 4.90e+02
  angle pdb=" N   PHE A 920 "
        pdb=" CA  PHE A 920 "
        pdb=" C   PHE A 920 "
      ideal   model   delta    sigma   weight residual
     114.39   94.27   20.12 1.45e+00 4.76e-01 1.93e+02
  angle pdb=" C   THR A 902 "
        pdb=" CA  THR A 902 "
        pdb=" CB  THR A 902 "
      ideal   model   delta    sigma   weight residual
     109.71  129.64  -19.93 1.80e+00 3.09e-01 1.23e+02
  angle pdb=" N   GLY A 919 "
        pdb=" CA  GLY A 919 "
        pdb=" C   GLY A 919 "
      ideal   model   delta    sigma   weight residual
     113.18   95.05   18.13 2.37e+00 1.78e-01 5.85e+01
  angle pdb=" N   MET A 193 "
        pdb=" CA  MET A 193 "
        pdb=" CB  MET A 193 "
      ideal   model   delta    sigma   weight residual
     111.91  122.71  -10.80 1.52e+00 4.33e-01 5.04e+01
  ... (remaining 12843 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 4721
       17.87 -    35.73: 730
       35.73 -    53.60: 203
       53.60 -    71.47: 33
       71.47 -    89.33: 9
  Dihedral angle restraints: 5696
    sinusoidal: 2304
      harmonic: 3392
  Sorted by residual:
  dihedral pdb=" N   THR A 902 "
           pdb=" C   THR A 902 "
           pdb=" CA  THR A 902 "
           pdb=" CB  THR A 902 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  105.40   18.00     0      2.50e+00 1.60e-01 5.18e+01
  dihedral pdb=" C   ASN A 192 "
           pdb=" N   ASN A 192 "
           pdb=" CA  ASN A 192 "
           pdb=" CB  ASN A 192 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.12   15.52     0      2.50e+00 1.60e-01 3.85e+01
  dihedral pdb=" N   ASN A 192 "
           pdb=" C   ASN A 192 "
           pdb=" CA  ASN A 192 "
           pdb=" CB  ASN A 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.59  -12.79     0      2.50e+00 1.60e-01 2.62e+01
  ... (remaining 5693 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 1433
       0.106 -    0.211: 27
       0.211 -    0.317: 4
       0.317 -    0.423: 1
       0.423 -    0.529: 1
  Chirality restraints: 1466
  Sorted by residual:
  chirality pdb=" CA  ASN A 192 "
            pdb=" N   ASN A 192 "
            pdb=" C   ASN A 192 "
            pdb=" CB  ASN A 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.98    0.53 2.00e-01 2.50e+01 6.99e+00
  chirality pdb=" CA  LEU A 355 "
            pdb=" N   LEU A 355 "
            pdb=" C   LEU A 355 "
            pdb=" CB  LEU A 355 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.77e+00
  chirality pdb=" CA  MET A 193 "
            pdb=" N   MET A 193 "
            pdb=" C   MET A 193 "
            pdb=" CB  MET A 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.22e+00
  ... (remaining 1463 not shown)

  Planarity restraints: 1627
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 886 "   -0.078 5.00e-02 4.00e+02   1.14e-01 2.07e+01
        pdb=" N   PRO A 887 "    0.197 5.00e-02 4.00e+02
        pdb=" CA  PRO A 887 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO A 887 "   -0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 192 "    0.017 2.00e-02 2.50e+03   3.44e-02 1.18e+01
        pdb=" C   ASN A 192 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   ASN A 192 "    0.022 2.00e-02 2.50e+03
        pdb=" N   MET A 193 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 189 "    0.009 2.00e-02 2.50e+03   1.74e-02 3.04e+00
        pdb=" C   TYR A 189 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   TYR A 189 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PHE A 190 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1624 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.48: 48
        2.48 -     3.08: 6455
        3.08 -     3.69: 14734
        3.69 -     4.29: 20301
        4.29 -     4.90: 34111
  Nonbonded interactions: 75649
  Sorted by model distance:
  nonbonded pdb=" N   THR A 902 "
            pdb=" O   THR A 902 "
     model   vdw
     1.875 2.496
  nonbonded pdb=" O   ILE A 891 "
            pdb=" OG1 THR A 895 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OG1 THR A1183 "
            pdb=" OD2 ASP A1186 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   LEU A 783 "
            pdb=" OG1 THR A 787 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" N   PHE A 920 "
            pdb=" N   LEU A 921 "
     model   vdw
     2.262 2.560
  ... (remaining 75644 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.340
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
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      :  0.003   0.051   9504  Z= 0.154
  Angle     :  0.782  34.299  12848  Z= 0.434
  Chirality :  0.044   0.529   1466
  Planarity :  0.004   0.114   1627
  Dihedral  : 18.227  89.334   3512
  Min Nonbonded Distance : 1.875

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 31.30 %
    Favored  : 67.81 %
  Cbeta Deviations :  0.37 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.26), residues: 1170
  helix:  1.86 (0.20), residues: 713
  sheet:  0.29 (0.83), residues: 45
  loop : -2.18 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 743 
 TYR   0.020   0.001   TYR A 911 
 PHE   0.028   0.001   PHE A 620 
 TRP   0.009   0.001   TRP A 896 
 HIS   0.003   0.001   HIS A 207 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.15 ( 9504)
  covalent geometry    : angle       0.78229 /  0.43 (12848)
  hydrogen bonds       : bond        0.16187 / 11.26 (  568)
  hydrogen bonds       : angle       6.10792 /  4.50 ( 1689)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 126
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
REVERT: A  355 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.6142 (mp)
  outliers start: 9
  outliers final: 3
  residues processed: 130
  average time/residue: 0.0965
  time to fit residues: 17.5409
Evaluate side-chains
  125 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 121
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue 1034 LEU
Chi-restraints excluded: chain A residue 1055 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    0.4980
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    0.7980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:    0.0770
   overall best weight:    0.5940

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 200 HIS
A 837 GLN
A1326 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.206134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.155506 restraints weight = 10295.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3891 rms_B_bonded: 2.93
r_work: 0.3583 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.0795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9504  Z= 0.128
  Angle     :  0.589  12.329  12848  Z= 0.296
  Chirality :  0.039   0.218   1466
  Planarity :  0.004   0.070   1627
  Dihedral  :  5.176  53.089   1297
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 29.92 %
    Favored  : 66.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.26), residues: 1170
  helix:  2.10 (0.19), residues: 712
  sheet: -0.09 (0.83), residues: 45
  loop : -2.07 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 743 
 TYR   0.013   0.001   TYR A 911 
 PHE   0.019   0.001   PHE A 620 
 TRP   0.009   0.001   TRP A 896 
 HIS   0.004   0.001   HIS A1268 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.13 ( 9504)
  covalent geometry    : angle       0.58945 /  0.30 (12848)
  hydrogen bonds       : bond        0.04188 /  2.89 (  568)
  hydrogen bonds       : angle       4.41491 /  3.29 ( 1689)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 131
  time to evaluate  : 0.207 
Fit side-chains
REVERT: A  355 LEU cc_start: 0.6092 (OUTLIER) cc_final: 0.5652 (mp)
REVERT: A  869 ASP cc_start: 0.7707 (t0) cc_final: 0.7140 (t0)
REVERT: A 1256 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7811 (mm-30)
  outliers start: 34
  outliers final: 20
  residues processed: 154
  average time/residue: 0.0858
  time to fit residues: 18.4341
Evaluate side-chains
  145 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  245 CYS
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain A residue  766 VAL
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  783 LEU
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  911 TYR
Chi-restraints excluded: chain A residue  924 VAL
Chi-restraints excluded: chain A residue  981 LEU
Chi-restraints excluded: chain A residue 1034 LEU
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1065 ILE
Chi-restraints excluded: chain A residue 1120 ILE
Chi-restraints excluded: chain A residue 1256 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 100 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 99 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 837 GLN
A1055 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.202236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.140465 restraints weight = 10454.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 2.90
r_work: 0.3537 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.1096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   9504  Z= 0.177
  Angle     :  0.613  12.909  12848  Z= 0.304
  Chirality :  0.041   0.234   1466
  Planarity :  0.004   0.056   1627
  Dihedral  :  5.082  51.494   1295
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 29.13 %
    Favored  : 65.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.25), residues: 1170
  helix:  1.94 (0.19), residues: 709
  sheet: -0.32 (0.81), residues: 45
  loop : -2.10 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 743 
 TYR   0.015   0.002   TYR A 911 
 PHE   0.023   0.001   PHE A 620 
 TRP   0.011   0.001   TRP A 335 
 HIS   0.005   0.001   HIS A 333 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00418 /  0.18 ( 9504)
  covalent geometry    : angle       0.61297 /  0.30 (12848)
  hydrogen bonds       : bond        0.04327 /  2.99 (  568)
  hydrogen bonds       : angle       4.25002 /  3.17 ( 1689)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 125
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A  140 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7280 (mtt-85)
REVERT: A  355 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5591 (mp)
REVERT: A  377 MET cc_start: 0.6176 (tpt) cc_final: 0.2731 (pmm)
REVERT: A  586 GLU cc_start: 0.8163 (mp0) cc_final: 0.7643 (mp0)
REVERT: A  869 ASP cc_start: 0.7827 (t0) cc_final: 0.7120 (t0)
REVERT: A  977 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7203 (mp)
REVERT: A 1053 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7320 (pt0)
REVERT: A 1256 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7995 (mm-30)
  outliers start: 53
  outliers final: 35
  residues processed: 170
  average time/residue: 0.0788
  time to fit residues: 19.4132
Evaluate side-chains
  156 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 116
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ARG
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  245 CYS
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  598 HIS
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  766 VAL
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  783 LEU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue  806 SER
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  911 TYR
Chi-restraints excluded: chain A residue  924 VAL
Chi-restraints excluded: chain A residue  977 LEU
Chi-restraints excluded: chain A residue  981 LEU
Chi-restraints excluded: chain A residue 1015 LEU
Chi-restraints excluded: chain A residue 1034 LEU
Chi-restraints excluded: chain A residue 1053 GLU
Chi-restraints excluded: chain A residue 1055 HIS
Chi-restraints excluded: chain A residue 1065 ILE
Chi-restraints excluded: chain A residue 1120 ILE
Chi-restraints excluded: chain A residue 1151 CYS
Chi-restraints excluded: chain A residue 1256 GLU
Chi-restraints excluded: chain A residue 1300 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 7 optimal weight:    8.9990
   chunk 79 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0020
   chunk 41 optimal weight:    0.0000
   chunk 93 optimal weight:    8.9990
   chunk 116 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.5996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 HIS
A 837 GLN
A1055 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.204549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.142445 restraints weight = 10521.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 2.55
r_work: 0.3595 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.1214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   9504  Z= 0.123
  Angle     :  0.576  13.909  12848  Z= 0.283
  Chirality :  0.039   0.222   1466
  Planarity :  0.003   0.049   1627
  Dihedral  :  5.012  53.201   1295
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 30.31 %
    Favored  : 64.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.26), residues: 1170
  helix:  2.13 (0.19), residues: 710
  sheet: -0.30 (0.82), residues: 45
  loop : -2.05 (0.31), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 743 
 TYR   0.013   0.001   TYR A 597 
 PHE   0.025   0.001   PHE A 620 
 TRP   0.010   0.001   TRP A 896 
 HIS   0.003   0.001   HIS A1055 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.12 ( 9504)
  covalent geometry    : angle       0.57579 /  0.28 (12848)
  hydrogen bonds       : bond        0.03848 /  2.66 (  568)
  hydrogen bonds       : angle       4.12127 /  3.08 ( 1689)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 127
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A  289 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7084 (mmm-85)
REVERT: A  377 MET cc_start: 0.5991 (tpt) cc_final: 0.2611 (pmm)
REVERT: A  740 LEU cc_start: 0.4822 (tt) cc_final: 0.4247 (tt)
REVERT: A  869 ASP cc_start: 0.7768 (t0) cc_final: 0.6974 (t0)
REVERT: A  954 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7762 (tp30)
REVERT: A 1053 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7084 (pt0)
REVERT: A 1189 ILE cc_start: 0.8326 (pt) cc_final: 0.8071 (pt)
REVERT: A 1221 HIS cc_start: 0.7926 (t-170) cc_final: 0.7717 (t-170)
REVERT: A 1256 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7939 (mm-30)
  outliers start: 49
  outliers final: 33
  residues processed: 166
  average time/residue: 0.0827
  time to fit residues: 19.5397
Evaluate side-chains
  160 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 123
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ARG
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  245 CYS
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  289 ARG
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  333 HIS
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  598 HIS
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  783 LEU
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  911 TYR
Chi-restraints excluded: chain A residue  954 GLU
Chi-restraints excluded: chain A residue  981 LEU
Chi-restraints excluded: chain A residue 1034 LEU
Chi-restraints excluded: chain A residue 1053 GLU
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1065 ILE
Chi-restraints excluded: chain A residue 1120 ILE
Chi-restraints excluded: chain A residue 1256 GLU
Chi-restraints excluded: chain A residue 1300 THR
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0060
   chunk 67 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.7800

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 HIS
A 837 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.204248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.141918 restraints weight = 10465.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 2.56
r_work: 0.3592 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.1282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   9504  Z= 0.130
  Angle     :  0.579  14.745  12848  Z= 0.283
  Chirality :  0.039   0.228   1466
  Planarity :  0.003   0.028   1627
  Dihedral  :  4.742  54.596   1293
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  5.61 %
    Allowed  : 29.63 %
    Favored  : 64.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.26), residues: 1170
  helix:  2.16 (0.19), residues: 711
  sheet: -0.38 (0.82), residues: 45
  loop : -2.07 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 743 
 TYR   0.015   0.001   TYR A 597 
 PHE   0.026   0.001   PHE A 620 
 TRP   0.009   0.001   TRP A 896 
 HIS   0.011   0.001   HIS A 333 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.13 ( 9504)
  covalent geometry    : angle       0.57926 /  0.28 (12848)
  hydrogen bonds       : bond        0.03776 /  2.60 (  568)
  hydrogen bonds       : angle       4.07652 /  3.04 ( 1689)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 126
  time to evaluate  : 0.345 
Fit side-chains
REVERT: A  289 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7013 (mmm-85)
REVERT: A  355 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5487 (mp)
REVERT: A  377 MET cc_start: 0.5797 (tpt) cc_final: 0.2422 (pmm)
REVERT: A  491 PHE cc_start: 0.7204 (t80) cc_final: 0.7001 (t80)
REVERT: A  586 GLU cc_start: 0.8055 (mp0) cc_final: 0.7582 (mp0)
REVERT: A  809 GLN cc_start: 0.6047 (OUTLIER) cc_final: 0.5598 (tt0)
REVERT: A  869 ASP cc_start: 0.7769 (t0) cc_final: 0.6975 (t0)
REVERT: A  914 MET cc_start: 0.3546 (OUTLIER) cc_final: 0.2387 (tpp)
REVERT: A  954 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7804 (tp30)
REVERT: A 1053 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7262 (pt0)
REVERT: A 1163 GLU cc_start: 0.6127 (OUTLIER) cc_final: 0.5873 (pt0)
REVERT: A 1221 HIS cc_start: 0.7915 (t-170) cc_final: 0.7684 (t-170)
REVERT: A 1230 ARG cc_start: 0.7199 (mtt-85) cc_final: 0.6844 (mmt90)
REVERT: A 1238 ASP cc_start: 0.6253 (OUTLIER) cc_final: 0.5816 (m-30)
  outliers start: 57
  outliers final: 41
  residues processed: 173
  average time/residue: 0.0952
  time to fit residues: 23.2692
Evaluate side-chains
  171 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 122
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ARG
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  245 CYS
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  289 ARG
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  333 HIS
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  598 HIS
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  783 LEU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue  806 SER
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  809 GLN
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  901 LEU
Chi-restraints excluded: chain A residue  914 MET
Chi-restraints excluded: chain A residue  924 VAL
Chi-restraints excluded: chain A residue  954 GLU
Chi-restraints excluded: chain A residue  981 LEU
Chi-restraints excluded: chain A residue 1034 LEU
Chi-restraints excluded: chain A residue 1053 GLU
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1065 ILE
Chi-restraints excluded: chain A residue 1120 ILE
Chi-restraints excluded: chain A residue 1151 CYS
Chi-restraints excluded: chain A residue 1163 GLU
Chi-restraints excluded: chain A residue 1238 ASP
Chi-restraints excluded: chain A residue 1300 THR
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 103 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 29 optimal weight:    5.9990
   chunk 95 optimal weight:    9.9990
   chunk 15 optimal weight:    0.6980
   chunk 13 optimal weight:    0.4980
   chunk 16 optimal weight:    0.0050
   chunk 80 optimal weight:    0.0970
   chunk 72 optimal weight:    2.9990
   overall best weight:    0.4192

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 130 GLN
A 292 HIS
A 333 HIS
A 837 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.205623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.144049 restraints weight = 10452.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3838 rms_B_bonded: 2.53
r_work: 0.3668 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.1383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.055   9504  Z= 0.112
  Angle     :  0.571  15.035  12848  Z= 0.278
  Chirality :  0.038   0.221   1466
  Planarity :  0.003   0.030   1627
  Dihedral  :  4.668  55.656   1293
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 30.12 %
    Favored  : 64.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.26), residues: 1170
  helix:  2.28 (0.19), residues: 711
  sheet: -0.35 (0.83), residues: 45
  loop : -2.06 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 743 
 TYR   0.010   0.001   TYR A 911 
 PHE   0.027   0.001   PHE A 620 
 TRP   0.009   0.001   TRP A 896 
 HIS   0.010   0.001   HIS A 333 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 ( 9504)
  covalent geometry    : angle       0.57064 /  0.28 (12848)
  hydrogen bonds       : bond        0.03564 /  2.45 (  568)
  hydrogen bonds       : angle       4.02001 /  3.00 ( 1689)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 124
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  289 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.6885 (mmm-85)
REVERT: A  377 MET cc_start: 0.5442 (tpt) cc_final: 0.2289 (pmm)
REVERT: A  491 PHE cc_start: 0.7298 (t80) cc_final: 0.7070 (t80)
REVERT: A  809 GLN cc_start: 0.6108 (OUTLIER) cc_final: 0.5680 (tt0)
REVERT: A  869 ASP cc_start: 0.7563 (t0) cc_final: 0.6796 (t0)
REVERT: A  914 MET cc_start: 0.3688 (OUTLIER) cc_final: 0.2470 (tpp)
REVERT: A  944 PHE cc_start: 0.8391 (t80) cc_final: 0.8069 (t80)
REVERT: A  954 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7793 (tp30)
REVERT: A 1053 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7249 (pt0)
REVERT: A 1230 ARG cc_start: 0.7199 (mtt-85) cc_final: 0.6958 (mtt90)
REVERT: A 1238 ASP cc_start: 0.6144 (OUTLIER) cc_final: 0.5743 (m-30)
  outliers start: 53
  outliers final: 39
  residues processed: 167
  average time/residue: 0.0950
  time to fit residues: 22.4444
Evaluate side-chains
  162 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 117
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ARG
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  245 CYS
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  289 ARG
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  333 HIS
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain A residue  598 HIS
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  783 LEU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  809 GLN
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  914 MET
Chi-restraints excluded: chain A residue  924 VAL
Chi-restraints excluded: chain A residue  954 GLU
Chi-restraints excluded: chain A residue  981 LEU
Chi-restraints excluded: chain A residue  992 ILE
Chi-restraints excluded: chain A residue 1015 LEU
Chi-restraints excluded: chain A residue 1034 LEU
Chi-restraints excluded: chain A residue 1053 GLU
Chi-restraints excluded: chain A residue 1065 ILE
Chi-restraints excluded: chain A residue 1120 ILE
Chi-restraints excluded: chain A residue 1151 CYS
Chi-restraints excluded: chain A residue 1238 ASP
Chi-restraints excluded: chain A residue 1300 THR
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0470
   chunk 102 optimal weight:    0.4980
   chunk 23 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0270
   chunk 69 optimal weight:    0.6980
   chunk 115 optimal weight:    2.9990
   chunk 91 optimal weight:    0.6980
   overall best weight:    0.3736

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 292 HIS
A 333 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.206203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.144848 restraints weight = 10442.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3787 rms_B_bonded: 2.52
r_work: 0.3626 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7232
moved from start:          0.1464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.062   9504  Z= 0.110
  Angle     :  0.568  15.482  12848  Z= 0.277
  Chirality :  0.038   0.213   1466
  Planarity :  0.003   0.030   1627
  Dihedral  :  4.587  56.800   1293
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 31.00 %
    Favored  : 64.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.26), residues: 1170
  helix:  2.35 (0.19), residues: 711
  sheet: -0.41 (0.83), residues: 45
  loop : -2.04 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 743 
 TYR   0.009   0.001   TYR A 447 
 PHE   0.029   0.001   PHE A 620 
 TRP   0.009   0.001   TRP A 896 
 HIS   0.008   0.001   HIS A1221 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00243 /  0.11 ( 9504)
  covalent geometry    : angle       0.56849 /  0.28 (12848)
  hydrogen bonds       : bond        0.03470 /  2.39 (  568)
  hydrogen bonds       : angle       3.96408 /  2.96 ( 1689)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 121
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A  193 MET cc_start: 0.7046 (OUTLIER) cc_final: 0.6835 (ptt)
REVERT: A  377 MET cc_start: 0.5413 (tpt) cc_final: 0.2256 (pmm)
REVERT: A  491 PHE cc_start: 0.7190 (t80) cc_final: 0.6982 (t80)
REVERT: A  809 GLN cc_start: 0.5946 (OUTLIER) cc_final: 0.4868 (tm-30)
REVERT: A  914 MET cc_start: 0.3357 (OUTLIER) cc_final: 0.2256 (tpp)
REVERT: A  944 PHE cc_start: 0.8259 (t80) cc_final: 0.8011 (t80)
REVERT: A  954 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7820 (tp30)
REVERT: A 1053 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7138 (pt0)
REVERT: A 1230 ARG cc_start: 0.7116 (mtt-85) cc_final: 0.6898 (mtt90)
REVERT: A 1238 ASP cc_start: 0.6200 (OUTLIER) cc_final: 0.5772 (m-30)
  outliers start: 47
  outliers final: 36
  residues processed: 159
  average time/residue: 0.0830
  time to fit residues: 19.2397
Evaluate side-chains
  153 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 111
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  245 CYS
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  333 HIS
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain A residue  598 HIS
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  783 LEU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue  806 SER
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  809 GLN
Chi-restraints excluded: chain A residue  914 MET
Chi-restraints excluded: chain A residue  924 VAL
Chi-restraints excluded: chain A residue  954 GLU
Chi-restraints excluded: chain A residue  981 LEU
Chi-restraints excluded: chain A residue 1034 LEU
Chi-restraints excluded: chain A residue 1053 GLU
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1065 ILE
Chi-restraints excluded: chain A residue 1120 ILE
Chi-restraints excluded: chain A residue 1238 ASP
Chi-restraints excluded: chain A residue 1299 VAL
Chi-restraints excluded: chain A residue 1300 THR
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 37 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 103 optimal weight:    0.6980
   chunk 47 optimal weight:    6.9990
   chunk 56 optimal weight:    0.3980
   chunk 70 optimal weight:    0.9990
   chunk 54 optimal weight:    7.9990
   chunk 67 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 837 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.204221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.154838 restraints weight = 10608.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 3.31
r_work: 0.3540 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   9504  Z= 0.145
  Angle     :  0.593  15.651  12848  Z= 0.290
  Chirality :  0.039   0.201   1466
  Planarity :  0.003   0.032   1627
  Dihedral  :  4.636  58.131   1293
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 30.31 %
    Favored  : 64.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.26), residues: 1170
  helix:  2.23 (0.19), residues: 714
  sheet: -0.51 (0.83), residues: 45
  loop : -2.14 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 743 
 TYR   0.027   0.001   TYR A 526 
 PHE   0.031   0.001   PHE A 620 
 TRP   0.008   0.001   TRP A 335 
 HIS   0.011   0.001   HIS A 333 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00338 /  0.14 ( 9504)
  covalent geometry    : angle       0.59270 /  0.29 (12848)
  hydrogen bonds       : bond        0.03730 /  2.56 (  568)
  hydrogen bonds       : angle       4.00181 /  2.99 ( 1689)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 123
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  122 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6759 (tt)
REVERT: A  289 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.6931 (mmm-85)
REVERT: A  491 PHE cc_start: 0.7321 (t80) cc_final: 0.7091 (t80)
REVERT: A  524 ARG cc_start: 0.8062 (mtt180) cc_final: 0.7774 (ttm170)
REVERT: A  586 GLU cc_start: 0.8164 (mp0) cc_final: 0.7736 (mp0)
REVERT: A  740 LEU cc_start: 0.5005 (tt) cc_final: 0.4561 (tt)
REVERT: A  809 GLN cc_start: 0.6160 (OUTLIER) cc_final: 0.5729 (tt0)
REVERT: A  869 ASP cc_start: 0.7743 (t0) cc_final: 0.7145 (t0)
REVERT: A  914 MET cc_start: 0.3098 (OUTLIER) cc_final: 0.2218 (tpp)
REVERT: A  954 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7972 (tp30)
REVERT: A 1053 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7273 (pt0)
REVERT: A 1230 ARG cc_start: 0.7189 (mtt-85) cc_final: 0.6956 (mtt90)
REVERT: A 1238 ASP cc_start: 0.6211 (OUTLIER) cc_final: 0.5734 (m-30)
  outliers start: 52
  outliers final: 41
  residues processed: 168
  average time/residue: 0.0777
  time to fit residues: 18.9695
Evaluate side-chains
  164 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 116
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 ASP
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  245 CYS
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  289 ARG
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain A residue  598 HIS
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  783 LEU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue  806 SER
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  809 GLN
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  914 MET
Chi-restraints excluded: chain A residue  924 VAL
Chi-restraints excluded: chain A residue  954 GLU
Chi-restraints excluded: chain A residue  981 LEU
Chi-restraints excluded: chain A residue 1034 LEU
Chi-restraints excluded: chain A residue 1053 GLU
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1065 ILE
Chi-restraints excluded: chain A residue 1120 ILE
Chi-restraints excluded: chain A residue 1151 CYS
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain A residue 1238 ASP
Chi-restraints excluded: chain A residue 1299 VAL
Chi-restraints excluded: chain A residue 1300 THR
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 109 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 52 optimal weight:    7.9990
   chunk 4 optimal weight:    4.9990
   chunk 111 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 102 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   overall best weight:    0.7580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.205174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.142458 restraints weight = 10593.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3817 rms_B_bonded: 2.64
r_work: 0.3651 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.1620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9504  Z= 0.129
  Angle     :  0.592  15.372  12848  Z= 0.290
  Chirality :  0.039   0.175   1466
  Planarity :  0.003   0.033   1627
  Dihedral  :  4.436  59.870   1290
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 30.41 %
    Favored  : 64.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.26), residues: 1170
  helix:  2.26 (0.19), residues: 713
  sheet: -0.39 (0.83), residues: 45
  loop : -2.10 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A1292 
 TYR   0.013   0.001   TYR A 526 
 PHE   0.027   0.001   PHE A 620 
 TRP   0.009   0.001   TRP A 896 
 HIS   0.006   0.001   HIS A1221 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.13 ( 9504)
  covalent geometry    : angle       0.59243 /  0.29 (12848)
  hydrogen bonds       : bond        0.03616 /  2.48 (  568)
  hydrogen bonds       : angle       3.99178 /  2.98 ( 1689)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 112
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A  122 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6697 (tt)
REVERT: A  355 LEU cc_start: 0.5871 (OUTLIER) cc_final: 0.5535 (mp)
REVERT: A  491 PHE cc_start: 0.7335 (t80) cc_final: 0.7109 (t80)
REVERT: A  524 ARG cc_start: 0.8096 (mtt180) cc_final: 0.7834 (ttm170)
REVERT: A  809 GLN cc_start: 0.6084 (OUTLIER) cc_final: 0.4994 (tm-30)
REVERT: A  869 ASP cc_start: 0.7605 (t0) cc_final: 0.7033 (t0)
REVERT: A  914 MET cc_start: 0.3160 (OUTLIER) cc_final: 0.2472 (tpp)
REVERT: A  954 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7887 (tp30)
REVERT: A  982 MET cc_start: 0.8186 (tmm) cc_final: 0.7957 (tmm)
REVERT: A 1053 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7206 (pt0)
REVERT: A 1230 ARG cc_start: 0.7188 (mtt-85) cc_final: 0.6979 (mtt90)
REVERT: A 1238 ASP cc_start: 0.6152 (OUTLIER) cc_final: 0.5700 (m-30)
  outliers start: 53
  outliers final: 42
  residues processed: 157
  average time/residue: 0.0851
  time to fit residues: 19.4275
Evaluate side-chains
  161 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 112
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  245 CYS
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain A residue  598 HIS
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  783 LEU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue  806 SER
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  809 GLN
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  911 TYR
Chi-restraints excluded: chain A residue  914 MET
Chi-restraints excluded: chain A residue  924 VAL
Chi-restraints excluded: chain A residue  954 GLU
Chi-restraints excluded: chain A residue  981 LEU
Chi-restraints excluded: chain A residue 1034 LEU
Chi-restraints excluded: chain A residue 1053 GLU
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1065 ILE
Chi-restraints excluded: chain A residue 1111 LEU
Chi-restraints excluded: chain A residue 1120 ILE
Chi-restraints excluded: chain A residue 1155 THR
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain A residue 1238 ASP
Chi-restraints excluded: chain A residue 1299 VAL
Chi-restraints excluded: chain A residue 1300 THR
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0370
   chunk 65 optimal weight:    3.9990
   chunk 112 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 77 optimal weight:    0.3980
   chunk 115 optimal weight:    0.7980
   chunk 7 optimal weight:    8.9990
   overall best weight:    0.4858

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.206312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.144766 restraints weight = 10424.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3845 rms_B_bonded: 2.54
r_work: 0.3677 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7340
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   9504  Z= 0.115
  Angle     :  0.578  15.119  12848  Z= 0.282
  Chirality :  0.038   0.152   1466
  Planarity :  0.003   0.029   1627
  Dihedral  :  4.357  58.251   1290
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 30.51 %
    Favored  : 64.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.26), residues: 1170
  helix:  2.37 (0.19), residues: 713
  sheet: -0.37 (0.83), residues: 45
  loop : -2.07 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 743 
 TYR   0.009   0.001   TYR A 447 
 PHE   0.026   0.001   PHE A 620 
 TRP   0.010   0.001   TRP A 896 
 HIS   0.006   0.001   HIS A1221 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.11 ( 9504)
  covalent geometry    : angle       0.57800 /  0.28 (12848)
  hydrogen bonds       : bond        0.03415 /  2.34 (  568)
  hydrogen bonds       : angle       3.94526 /  2.95 ( 1689)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 112
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A  122 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6633 (tt)
REVERT: A  524 ARG cc_start: 0.8081 (mtt180) cc_final: 0.7786 (ttm170)
REVERT: A  809 GLN cc_start: 0.6026 (OUTLIER) cc_final: 0.5120 (tm-30)
REVERT: A  869 ASP cc_start: 0.7612 (t0) cc_final: 0.7042 (t0)
REVERT: A  914 MET cc_start: 0.2853 (OUTLIER) cc_final: 0.2329 (tpp)
REVERT: A  954 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7826 (tp30)
REVERT: A  982 MET cc_start: 0.8121 (tmm) cc_final: 0.7909 (tmm)
REVERT: A 1053 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7160 (pt0)
REVERT: A 1230 ARG cc_start: 0.7145 (mtt-85) cc_final: 0.6938 (mtt90)
REVERT: A 1238 ASP cc_start: 0.6159 (OUTLIER) cc_final: 0.5693 (m-30)
  outliers start: 49
  outliers final: 42
  residues processed: 153
  average time/residue: 0.0756
  time to fit residues: 16.9129
Evaluate side-chains
  156 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 108
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 ASP
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  245 CYS
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain A residue  598 HIS
Chi-restraints excluded: chain A residue  612 VAL
Chi-restraints excluded: chain A residue  764 LEU
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  783 LEU
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue  806 SER
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  809 GLN
Chi-restraints excluded: chain A residue  881 LEU
Chi-restraints excluded: chain A residue  911 TYR
Chi-restraints excluded: chain A residue  914 MET
Chi-restraints excluded: chain A residue  924 VAL
Chi-restraints excluded: chain A residue  954 GLU
Chi-restraints excluded: chain A residue  981 LEU
Chi-restraints excluded: chain A residue 1034 LEU
Chi-restraints excluded: chain A residue 1053 GLU
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1065 ILE
Chi-restraints excluded: chain A residue 1111 LEU
Chi-restraints excluded: chain A residue 1120 ILE
Chi-restraints excluded: chain A residue 1155 THR
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain A residue 1238 ASP
Chi-restraints excluded: chain A residue 1299 VAL
Chi-restraints excluded: chain A residue 1300 THR
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 115 optimal weight:    5.9990
   chunk 94 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0050
   chunk 73 optimal weight:    0.9990
   chunk 57 optimal weight:   20.0000
   chunk 95 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 104 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0970
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.4992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 544 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.206778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.144960 restraints weight = 10380.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3847 rms_B_bonded: 2.56
r_work: 0.3678 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.1767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9504  Z= 0.114
  Angle     :  0.581  14.842  12848  Z= 0.282
  Chirality :  0.038   0.146   1466
  Planarity :  0.003   0.030   1627
  Dihedral  :  4.328  57.193   1290
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 30.81 %
    Favored  : 64.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.26), residues: 1170
  helix:  2.35 (0.19), residues: 720
  sheet: -0.38 (0.83), residues: 45
  loop : -2.07 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 743 
 TYR   0.009   0.001   TYR A 447 
 PHE   0.027   0.001   PHE A 620 
 TRP   0.012   0.001   TRP A 896 
 HIS   0.006   0.001   HIS A1221 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.11 ( 9504)
  covalent geometry    : angle       0.58073 /  0.28 (12848)
  hydrogen bonds       : bond        0.03378 /  2.31 (  568)
  hydrogen bonds       : angle       3.92153 /  2.93 ( 1689)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2118.39 seconds
wall clock time: 36 minutes 58.25 seconds (2218.25 seconds total)