Starting phenix.real_space_refine
on Wed Feb  4 06:24:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pee_17630/02_2026/8pee_17630.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pee_17630/02_2026/8pee_17630.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pee_17630/02_2026/8pee_17630.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pee_17630/02_2026/8pee_17630.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pee_17630/02_2026/8pee_17630.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pee_17630/02_2026/8pee_17630.map"
  }
  resolution = 3.8
  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=   0.006 sd=   0.060
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      39      5.16       5
     C    5960      2.51       5
     N    1541      2.21       5
     O    1677      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9217
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 8967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1157, 8967
          Classifications: {'peptide': 1157}
          Link IDs: {'PTRANS': 29, 'TRANS': 1127}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'JJI': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 206
          Unusual residues: {'JIZ': 1, 'Y01': 5}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
  Time building chain proxies: 2.04, per 1000 atoms: 0.22
  Number of scatterers: 9217
  At special positions: 0
  Unit cell: (71.982, 114.669, 147.312, 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      39     16.00
     O    1677      8.00
     N    1541      7.00
     C    5960      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 305.1 milliseconds
  

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2122

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 6 sheets defined
      67.2% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 42
      removed outlier: 3.589A  pdb=" N   TYR A  41 " --> pdb=" O   MET A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 82
      removed outlier: 4.252A  pdb=" N   LEU A  64 " --> pdb=" O   HIS A  60 " (cutoff:3.500A)
      Proline residue:  A  65  - end of helix
    Processing helix  chain 'A' and resid 87 through 92
      removed outlier: 4.381A  pdb=" N   MET A  91 " --> pdb=" O   GLN A  87 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   SER A  92 " --> pdb=" O   SER A  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 87 through 92'
    Processing helix  chain 'A' and resid 99 through 152
      removed outlier: 3.890A  pdb=" N   TYR A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   PHE A 131 " --> pdb=" O   ILE A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 162
      removed outlier: 3.741A  pdb=" N   PHE A 159 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 207
      removed outlier: 4.176A  pdb=" N   VAL A 175 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   SER A 176 " --> pdb=" O   THR A 172 " (cutoff:3.500A)
      removed outlier: 5.521A  pdb=" N   ILE A 186 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   PHE A 190 " --> pdb=" O   ILE A 186 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   GLN A 191 " --> pdb=" O   GLY A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 256
      removed outlier: 3.720A  pdb=" N   LEU A 212 " --> pdb=" O   TRP A 208 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL A 213 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      Proline residue:  A 219  - end of helix
      removed outlier: 3.877A  pdb=" N   GLY A 222 " --> pdb=" O   SER A 218 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ALA A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   VAL A 249 " --> pdb=" O   LYS A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 264
    Processing helix  chain 'A' and resid 265 through 319
      removed outlier: 3.976A  pdb=" N   GLU A 269 " --> pdb=" O   GLY A 265 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   GLU A 279 " --> pdb=" O   ASN A 275 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ALA A 280 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ARG A 282 " --> pdb=" O   GLU A 278 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU A 316 " --> pdb=" O   TYR A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 344
      removed outlier: 3.518A  pdb=" N   SER A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 365
      removed outlier: 3.794A  pdb=" N   PHE A 351 " --> pdb=" O   ASN A 347 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   GLU A 360 " --> pdb=" O   GLY A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 401
      removed outlier: 4.053A  pdb=" N   LYS A 401 " --> pdb=" O   PRO A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 437
      removed outlier: 4.118A  pdb=" N   GLN A 437 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 465
    Processing helix  chain 'A' and resid 479 through 486
    Processing helix  chain 'A' and resid 492 through 501
    Processing helix  chain 'A' and resid 528 through 543
      removed outlier: 3.645A  pdb=" N   ARG A 534 " --> pdb=" O   GLY A 530 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ARG A 543 " --> pdb=" O   ARG A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 574
    Processing helix  chain 'A' and resid 584 through 591
      removed outlier: 3.993A  pdb=" N   VAL A 588 " --> pdb=" O   ARG A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 694 through 701
      removed outlier: 3.797A  pdb=" N   LYS A 698 " --> pdb=" O   TRP A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 707 through 737
      removed outlier: 3.932A  pdb=" N   GLN A 721 " --> pdb=" O   ASN A 717 " (cutoff:3.500A)
      Proline residue:  A 722  - end of helix
      removed outlier: 3.981A  pdb=" N   PHE A 735 " --> pdb=" O   VAL A 731 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 740 through 742
      No H-bonds generated for 'chain 'A' and resid 740 through 742'
    Processing helix  chain 'A' and resid 743 through 795
    Processing helix  chain 'A' and resid 796 through 802
    Processing helix  chain 'A' and resid 806 through 816
    Processing helix  chain 'A' and resid 821 through 826
      removed outlier: 3.579A  pdb=" N   THR A 825 " --> pdb=" O   VAL A 821 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 899
      removed outlier: 4.084A  pdb=" N   ILE A 832 " --> pdb=" O   ARG A 828 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   PHE A 833 " --> pdb=" O   LEU A 829 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   THR A 841 " --> pdb=" O   ALA A 837 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   TRP A 851 " --> pdb=" O   LEU A 847 " (cutoff:3.500A)
      removed outlier: 8.022A  pdb=" N   GLN A 852 " --> pdb=" O   ILE A 848 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   LEU A 853 " --> pdb=" O   TYR A 849 " (cutoff:3.500A)
      Proline residue:  A 862  - end of helix
      removed outlier: 4.043A  pdb=" N   ILE A 892 " --> pdb=" O   GLY A 888 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ASN A 899 " --> pdb=" O   GLU A 895 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 899 through 906
    Processing helix  chain 'A' and resid 909 through 962
      removed outlier: 3.716A  pdb=" N   GLU A 913 " --> pdb=" O   GLU A 909 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   ILE A 922 " --> pdb=" O   GLN A 918 " (cutoff:3.500A)
      Proline residue:  A 923  - end of helix
      removed outlier: 3.523A  pdb=" N   MET A 928 " --> pdb=" O   TYR A 924 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 966 through 990
      removed outlier: 3.874A  pdb=" N   PHE A 979 " --> pdb=" O   SER A 975 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   GLY A 980 " --> pdb=" O   ALA A 976 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 998 through 1010
    Processing helix  chain 'A' and resid 1068 through 1072
      removed outlier: 3.910A  pdb=" N   LYS A1072 " --> pdb=" O   GLY A1069 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1074 through 1080
      removed outlier: 4.142A  pdb=" N   GLU A1080 " --> pdb=" O   VAL A1076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1101 through 1107
    Processing helix  chain 'A' and resid 1122 through 1129
    Processing helix  chain 'A' and resid 1130 through 1132
      No H-bonds generated for 'chain 'A' and resid 1130 through 1132'
    Processing helix  chain 'A' and resid 1140 through 1149
    Processing helix  chain 'A' and resid 1150 through 1155
    Processing helix  chain 'A' and resid 1165 through 1169
    Processing helix  chain 'A' and resid 1173 through 1188
      removed outlier: 4.000A  pdb=" N   ARG A1188 " --> pdb=" O   ARG A1184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1199 through 1203
    Processing helix  chain 'A' and resid 1206 through 1221
    Processing helix  chain 'A' and resid 1229 through 1236
      removed outlier: 3.605A  pdb=" N   ILE A1233 " --> pdb=" O   ARG A1229 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 391
    Processing sheet with id=AA2, first strand: chain 'A' and resid 394 through 395
    Processing sheet with id=AA3, first strand: chain 'A' and resid 466 through 468
      removed outlier: 6.468A  pdb=" N   VAL A 419 " --> pdb=" O   VAL A 580 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1031 through 1032
      removed outlier: 3.717A  pdb=" N   PHE A1091 " --> pdb=" O   GLN A1032 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1034 through 1038
      removed outlier: 6.784A  pdb=" N   LEU A1052 " --> pdb=" O   GLY A1035 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   VAL A1037 " --> pdb=" O   GLN A1050 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   GLN A1050 " --> pdb=" O   VAL A1037 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1063 through 1064
      removed outlier: 6.219A  pdb=" N   LEU A1193 " --> pdb=" O   ILE A1224 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   ILE A1226 " --> pdb=" O   LEU A1193 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   LEU A1195 " --> pdb=" O   ILE A1226 " (cutoff:3.500A)

    564 hydrogen bonds defined for protein.
    1662 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: 1.05

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.02 -     1.24: 764
        1.24 -     1.45: 3188
        1.45 -     1.66: 5379
        1.66 -     1.88: 71
        1.88 -     2.09: 1
  Bond restraints: 9403
  Sorted by residual:
  bond pdb=" CBD Y01 A1407 "
       pdb=" CBG Y01 A1407 "
    ideal  model  delta    sigma   weight residual
    1.520  1.023  0.497 2.00e-02 2.50e+03 6.18e+02
  bond pdb=" C03 JJI A1401 "
       pdb=" N02 JJI A1401 "
    ideal  model  delta    sigma   weight residual
    1.362  1.783 -0.421 2.00e-02 2.50e+03 4.42e+02
  bond pdb=" C08 JJI A1401 "
       pdb=" N04 JJI A1401 "
    ideal  model  delta    sigma   weight residual
    1.363  1.769 -0.406 2.00e-02 2.50e+03 4.13e+02
  bond pdb=" C13 JJI A1401 "
       pdb=" N06 JJI A1401 "
    ideal  model  delta    sigma   weight residual
    1.363  1.768 -0.405 2.00e-02 2.50e+03 4.11e+02
  bond pdb=" CAS Y01 A1407 "
       pdb=" CAU Y01 A1407 "
    ideal  model  delta    sigma   weight residual
    1.530  1.147  0.383 2.00e-02 2.50e+03 3.66e+02
  ... (remaining 9398 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.61: 12586
        3.61 -     7.22: 139
        7.22 -    10.83: 12
       10.83 -    14.44: 1
       14.44 -    18.04: 7
  Bond angle restraints: 12745
  Sorted by residual:
  angle pdb=" C02 JJI A1401 "
        pdb=" S01 JJI A1401 "
        pdb=" C04 JJI A1401 "
      ideal   model   delta    sigma   weight residual
      89.76  107.80  -18.04 3.00e+00 1.11e-01 3.62e+01
  angle pdb=" C12 JJI A1401 "
        pdb=" S03 JJI A1401 "
        pdb=" C14 JJI A1401 "
      ideal   model   delta    sigma   weight residual
      89.85  107.52  -17.67 3.00e+00 1.11e-01 3.47e+01
  angle pdb=" C07 JIZ A1402 "
        pdb=" S02 JIZ A1402 "
        pdb=" C09 JIZ A1402 "
      ideal   model   delta    sigma   weight residual
      89.67  107.31  -17.64 3.00e+00 1.11e-01 3.46e+01
  angle pdb=" C07 JJI A1401 "
        pdb=" S02 JJI A1401 "
        pdb=" C09 JJI A1401 "
      ideal   model   delta    sigma   weight residual
      89.54  107.09  -17.55 3.00e+00 1.11e-01 3.42e+01
  angle pdb=" C12 JIZ A1402 "
        pdb=" S03 JIZ A1402 "
        pdb=" C14 JIZ A1402 "
      ideal   model   delta    sigma   weight residual
      89.68  106.95  -17.27 3.00e+00 1.11e-01 3.31e+01
  ... (remaining 12740 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.96: 5577
       28.96 -    57.92: 229
       57.92 -    86.88: 25
       86.88 -   115.84: 10
      115.84 -   144.80: 5
  Dihedral angle restraints: 5846
    sinusoidal: 2535
      harmonic: 3311
  Sorted by residual:
  dihedral pdb=" CA  MET A  99 "
           pdb=" C   MET A  99 "
           pdb=" N   PHE A 100 "
           pdb=" CA  PHE A 100 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.12   22.88     0      5.00e+00 4.00e-02 2.09e+01
  dihedral pdb=" N04 JJI A1401 "
           pdb=" C08 JJI A1401 "
           pdb=" C10 JJI A1401 "
           pdb=" N05 JJI A1401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     132.37  -12.43  144.80     1      3.00e+01 1.11e-03 1.94e+01
  dihedral pdb=" N04 JJI A1401 "
           pdb=" C08 JJI A1401 "
           pdb=" C10 JJI A1401 "
           pdb=" O02 JJI A1401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     309.09  168.02  141.07     1      3.00e+01 1.11e-03 1.90e+01
  ... (remaining 5843 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.318: 1462
       0.318 -    0.636: 2
       0.636 -    0.954: 1
       0.954 -    1.272: 0
       1.272 -    1.590: 1
  Chirality restraints: 1466
  Sorted by residual:
  chirality pdb=" CBD Y01 A1407 "
            pdb=" CAK Y01 A1407 "
            pdb=" CBF Y01 A1407 "
            pdb=" CBG Y01 A1407 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.70    1.11    1.59 2.00e-01 2.50e+01 6.32e+01
  chirality pdb=" CBG Y01 A1407 "
            pdb=" CAQ Y01 A1407 "
            pdb=" CBD Y01 A1407 "
            pdb=" CBI Y01 A1407 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -1.68   -0.65 2.00e-01 2.50e+01 1.05e+01
  chirality pdb=" CBI Y01 A1407 "
            pdb=" CAU Y01 A1407 "
            pdb=" CBE Y01 A1407 "
            pdb=" CBG Y01 A1407 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.94    2.52    0.42 2.00e-01 2.50e+01 4.32e+00
  ... (remaining 1463 not shown)

  Planarity restraints: 1596
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 822 "   -0.020 2.00e-02 2.50e+03   4.00e-02 1.60e+01
        pdb=" C   LYS A 822 "    0.069 2.00e-02 2.50e+03
        pdb=" O   LYS A 822 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   GLY A 823 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 997 "   -0.013 2.00e-02 2.50e+03   2.62e-02 6.87e+00
        pdb=" C   ALA A 997 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ALA A 997 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   THR A 998 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A1240 "    0.012 2.00e-02 2.50e+03   2.41e-02 5.82e+00
        pdb=" C   VAL A1240 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   VAL A1240 "    0.015 2.00e-02 2.50e+03
        pdb=" N   VAL A1241 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1593 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1582
        2.77 -     3.30: 9748
        3.30 -     3.83: 15092
        3.83 -     4.37: 17092
        4.37 -     4.90: 28586
  Nonbonded interactions: 72100
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 153 "
            pdb=" OD1 ASN A 153 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   ARG A1164 "
            pdb=" OG1 THR A1170 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   PRO A 381 "
            pdb=" OH  TYR A 461 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   TYR A 706 "
            pdb=" OG1 THR A 772 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OG  SER A1089 "
            pdb=" OE1 GLU A1096 "
     model   vdw
     2.300 3.040
  ... (remaining 72095 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.180
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
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      :  0.016   0.497   9404  Z= 0.830
  Angle     :  1.007  18.045  12745  Z= 0.546
  Chirality :  0.071   1.590   1466
  Planarity :  0.004   0.040   1596
  Dihedral  : 16.305 144.797   3724
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  1.48 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.26), residues: 1153
  helix:  1.10 (0.20), residues: 759
  sheet: -0.60 (0.79), residues: 39
  loop : -1.60 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 485 
 TYR   0.016   0.001   TYR A 461 
 PHE   0.025   0.002   PHE A 766 
 TRP   0.027   0.001   TRP A 694 
 HIS   0.004   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.01576 ( 9403)
  covalent geometry    : angle       1.00734 (12745)
  hydrogen bonds       : bond        0.08503 (  564)
  hydrogen bonds       : angle       4.54337 ( 1662)
  Misc. bond           : bond        0.17062 (    1)

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 160
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A  461 TYR cc_start: 0.7903 (t80) cc_final: 0.7606 (t80)
REVERT: A 1026 MET cc_start: 0.7424 (pmm) cc_final: 0.7222 (pmm)
  outliers start: 3
  outliers final: 1
  residues processed: 162
  average time/residue: 0.0664
  time to fit residues: 15.5367
Evaluate side-chains
  115 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:   20.0000
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    7.9990
   chunk 53 optimal weight:    0.0970
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    7.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 153 ASN
A 162 HIS
A 276 ASN
A1020 GLN
A1099 GLN
** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.215128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.172931 restraints weight = 14002.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.172568 restraints weight = 11869.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.175217 restraints weight = 9045.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.175365 restraints weight = 6007.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.175536 restraints weight = 5603.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.4245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.1226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9404  Z= 0.140
  Angle     :  0.654   8.939  12745  Z= 0.319
  Chirality :  0.042   0.248   1466
  Planarity :  0.004   0.060   1596
  Dihedral  : 12.086 125.777   1645
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 10.56 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.25), residues: 1153
  helix:  1.32 (0.20), residues: 751
  sheet: -0.29 (0.82), residues: 39
  loop : -1.62 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 488 
 TYR   0.017   0.001   TYR A 243 
 PHE   0.020   0.001   PHE A 516 
 TRP   0.020   0.002   TRP A1104 
 HIS   0.003   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9403)
  covalent geometry    : angle       0.65372 (12745)
  hydrogen bonds       : bond        0.04562 (  564)
  hydrogen bonds       : angle       4.12082 ( 1662)
  Misc. bond           : bond        0.00058 (    1)

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A   41 TYR cc_start: 0.6898 (m-80) cc_final: 0.6673 (m-80)
REVERT: A 1062 LEU cc_start: 0.8416 (tp) cc_final: 0.8075 (mt)
  outliers start: 13
  outliers final: 10
  residues processed: 132
  average time/residue: 0.0641
  time to fit residues: 12.5075
Evaluate side-chains
  119 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  704 TRP
Chi-restraints excluded: chain A residue  936 ILE
Chi-restraints excluded: chain A residue 1165 VAL
Chi-restraints excluded: chain A residue 1257 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 114 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9980
   chunk 46 optimal weight:   10.0000
   chunk 82 optimal weight:    5.9990
   chunk 78 optimal weight:    4.9990
   chunk 54 optimal weight:    9.9990
   chunk 84 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 37 optimal weight:   20.0000
   chunk 26 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   overall best weight:    2.7986

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 276 ASN
A 749 ASN
A1020 GLN
** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.191203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.148682 restraints weight = 12889.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.147195 restraints weight = 19565.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.149336 restraints weight = 15178.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.151261 restraints weight = 9423.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.151660 restraints weight = 8581.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   9404  Z= 0.269
  Angle     :  0.751   9.952  12745  Z= 0.369
  Chirality :  0.045   0.198   1466
  Planarity :  0.004   0.067   1596
  Dihedral  : 10.696 114.800   1644
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.94 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.25), residues: 1153
  helix:  1.01 (0.19), residues: 750
  sheet: -0.29 (0.85), residues: 39
  loop : -1.52 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 485 
 TYR   0.021   0.002   TYR A  41 
 PHE   0.027   0.002   PHE A 339 
 TRP   0.019   0.002   TRP A1104 
 HIS   0.008   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00640 ( 9403)
  covalent geometry    : angle       0.75125 (12745)
  hydrogen bonds       : bond        0.05453 (  564)
  hydrogen bonds       : angle       4.45089 ( 1662)
  Misc. bond           : bond        0.00027 (    1)

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A   41 TYR cc_start: 0.7284 (m-80) cc_final: 0.7084 (m-80)
  outliers start: 23
  outliers final: 17
  residues processed: 140
  average time/residue: 0.0618
  time to fit residues: 12.8426
Evaluate side-chains
  130 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain A residue  704 TRP
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain A residue  825 THR
Chi-restraints excluded: chain A residue  844 ILE
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  936 ILE
Chi-restraints excluded: chain A residue 1049 LEU
Chi-restraints excluded: chain A residue 1165 VAL
Chi-restraints excluded: chain A residue 1257 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 93 optimal weight:    8.9990
   chunk 41 optimal weight:    0.0270
   chunk 75 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9990
   chunk 37 optimal weight:    7.9990
   chunk 84 optimal weight:    0.8980
   chunk 99 optimal weight:    0.0770
   chunk 26 optimal weight:    1.9990
   chunk 108 optimal weight:    9.9990
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
A 153 ASN
** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1020 GLN
** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.198451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.160226 restraints weight = 12766.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.159750 restraints weight = 17602.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.161265 restraints weight = 14749.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.162423 restraints weight = 9902.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.162743 restraints weight = 9721.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9404  Z= 0.127
  Angle     :  0.625  10.731  12745  Z= 0.300
  Chirality :  0.041   0.337   1466
  Planarity :  0.004   0.062   1596
  Dihedral  :  9.667  99.947   1644
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.26 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.25), residues: 1153
  helix:  1.34 (0.19), residues: 748
  sheet:  0.00 (0.88), residues: 39
  loop : -1.45 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1229 
 TYR   0.019   0.001   TYR A 243 
 PHE   0.013   0.001   PHE A 200 
 TRP   0.017   0.001   TRP A1104 
 HIS   0.004   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9403)
  covalent geometry    : angle       0.62513 (12745)
  hydrogen bonds       : bond        0.04517 (  564)
  hydrogen bonds       : angle       4.08332 ( 1662)
  Misc. bond           : bond        0.00001 (    1)

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A   41 TYR cc_start: 0.7016 (m-80) cc_final: 0.6785 (m-80)
REVERT: A   64 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7809 (tt)
REVERT: A  436 MET cc_start: 0.8532 (mmm) cc_final: 0.8269 (tpp)
  outliers start: 26
  outliers final: 17
  residues processed: 140
  average time/residue: 0.0689
  time to fit residues: 14.2242
Evaluate side-chains
  131 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 MET
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain A residue  704 TRP
Chi-restraints excluded: chain A residue  766 PHE
Chi-restraints excluded: chain A residue  825 THR
Chi-restraints excluded: chain A residue  936 ILE
Chi-restraints excluded: chain A residue 1111 ILE
Chi-restraints excluded: chain A residue 1165 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 93 optimal weight:    4.9990
   chunk 89 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   chunk 78 optimal weight:    4.9990
   chunk 100 optimal weight:    8.9990
   chunk 97 optimal weight:    0.9990
   chunk 99 optimal weight:    1.9990
   chunk 49 optimal weight:   30.0000
   chunk 39 optimal weight:   10.0000
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1020 GLN
A1126 ASN
** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.195615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.154815 restraints weight = 12857.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.152738 restraints weight = 20046.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.154282 restraints weight = 18595.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.156885 restraints weight = 11684.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.157034 restraints weight = 9178.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9404  Z= 0.152
  Angle     :  0.627  12.287  12745  Z= 0.305
  Chirality :  0.042   0.361   1466
  Planarity :  0.004   0.059   1596
  Dihedral  :  9.482  95.897   1644
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 16.79 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.25), residues: 1153
  helix:  1.34 (0.19), residues: 748
  sheet: -0.07 (0.87), residues: 39
  loop : -1.42 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 488 
 TYR   0.017   0.001   TYR A 243 
 PHE   0.018   0.001   PHE A 953 
 TRP   0.010   0.001   TRP A 158 
 HIS   0.005   0.001   HIS A1250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9403)
  covalent geometry    : angle       0.62731 (12745)
  hydrogen bonds       : bond        0.04608 (  564)
  hydrogen bonds       : angle       4.11262 ( 1662)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 120
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.7040 (m-80) cc_final: 0.6778 (m-80)
REVERT: A   64 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8282 (tt)
REVERT: A  693 PHE cc_start: 0.6187 (OUTLIER) cc_final: 0.5059 (m-80)
REVERT: A 1026 MET cc_start: 0.7127 (pmm) cc_final: 0.6639 (pmm)
REVERT: A 1118 LEU cc_start: 0.5764 (OUTLIER) cc_final: 0.5491 (mt)
  outliers start: 28
  outliers final: 21
  residues processed: 137
  average time/residue: 0.0649
  time to fit residues: 13.4271
Evaluate side-chains
  141 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 MET
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  704 TRP
Chi-restraints excluded: chain A residue  755 PHE
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  766 PHE
Chi-restraints excluded: chain A residue  825 THR
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  936 ILE
Chi-restraints excluded: chain A residue 1111 ILE
Chi-restraints excluded: chain A residue 1118 LEU
Chi-restraints excluded: chain A residue 1165 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 59 optimal weight:    0.0770
   chunk 110 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 57 optimal weight:    6.9990
   chunk 40 optimal weight:    0.5980
   chunk 86 optimal weight:    0.8980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.197744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.157535 restraints weight = 12850.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.154952 restraints weight = 19149.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.156626 restraints weight = 17063.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.158516 restraints weight = 11283.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.158768 restraints weight = 9882.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9404  Z= 0.125
  Angle     :  0.620  13.148  12745  Z= 0.298
  Chirality :  0.041   0.362   1466
  Planarity :  0.003   0.056   1596
  Dihedral  :  9.156  92.321   1644
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.85 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.26), residues: 1153
  helix:  1.46 (0.20), residues: 749
  sheet: -0.10 (0.86), residues: 39
  loop : -1.35 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1229 
 TYR   0.019   0.001   TYR A 461 
 PHE   0.014   0.001   PHE A 200 
 TRP   0.012   0.001   TRP A 158 
 HIS   0.007   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 9403)
  covalent geometry    : angle       0.61962 (12745)
  hydrogen bonds       : bond        0.04354 (  564)
  hydrogen bonds       : angle       4.03985 ( 1662)
  Misc. bond           : bond        0.00001 (    1)

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 125
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.6952 (m-80) cc_final: 0.6656 (m-80)
REVERT: A  436 MET cc_start: 0.8590 (mmm) cc_final: 0.8376 (tpp)
REVERT: A  693 PHE cc_start: 0.6127 (OUTLIER) cc_final: 0.5032 (m-80)
REVERT: A  766 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7478 (t80)
REVERT: A 1026 MET cc_start: 0.7126 (pmm) cc_final: 0.6630 (pmm)
REVERT: A 1086 MET cc_start: 0.5386 (pmm) cc_final: 0.4953 (pmm)
REVERT: A 1118 LEU cc_start: 0.5819 (tp) cc_final: 0.5574 (mt)
  outliers start: 30
  outliers final: 21
  residues processed: 145
  average time/residue: 0.0774
  time to fit residues: 16.5692
Evaluate side-chains
  136 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 MET
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain A residue  565 VAL
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  704 TRP
Chi-restraints excluded: chain A residue  766 PHE
Chi-restraints excluded: chain A residue  825 THR
Chi-restraints excluded: chain A residue  833 PHE
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  936 ILE
Chi-restraints excluded: chain A residue 1111 ILE
Chi-restraints excluded: chain A residue 1165 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 94 optimal weight:    7.9990
   chunk 19 optimal weight:    7.9990
   chunk 65 optimal weight:    0.8980
   chunk 80 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 99 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 45 optimal weight:    9.9990
   chunk 98 optimal weight:    0.0670
   overall best weight:    0.7322

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1020 GLN
** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.197738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.157256 restraints weight = 12781.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.154916 restraints weight = 19283.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.156643 restraints weight = 17133.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.158362 restraints weight = 11241.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.158707 restraints weight = 10289.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9404  Z= 0.130
  Angle     :  0.627  14.552  12745  Z= 0.302
  Chirality :  0.042   0.409   1466
  Planarity :  0.003   0.053   1596
  Dihedral  :  9.290  90.527   1644
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 17.74 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.26), residues: 1153
  helix:  1.50 (0.20), residues: 749
  sheet: -0.32 (0.81), residues: 48
  loop : -1.29 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1229 
 TYR   0.019   0.001   TYR A 461 
 PHE   0.023   0.001   PHE A 395 
 TRP   0.012   0.001   TRP A 158 
 HIS   0.007   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 9403)
  covalent geometry    : angle       0.62695 (12745)
  hydrogen bonds       : bond        0.04332 (  564)
  hydrogen bonds       : angle       4.03687 ( 1662)
  Misc. bond           : bond        0.00001 (    1)

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 122
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.6892 (m-80) cc_final: 0.6588 (m-80)
REVERT: A  693 PHE cc_start: 0.6053 (OUTLIER) cc_final: 0.4962 (m-80)
REVERT: A  766 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7525 (t80)
REVERT: A 1026 MET cc_start: 0.7024 (pmm) cc_final: 0.6586 (pmm)
REVERT: A 1086 MET cc_start: 0.5452 (pmm) cc_final: 0.5062 (pmm)
REVERT: A 1118 LEU cc_start: 0.5985 (OUTLIER) cc_final: 0.5782 (mt)
  outliers start: 37
  outliers final: 24
  residues processed: 147
  average time/residue: 0.0618
  time to fit residues: 13.5448
Evaluate side-chains
  144 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 117
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 MET
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  197 PHE
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain A residue  565 VAL
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  704 TRP
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  766 PHE
Chi-restraints excluded: chain A residue  833 PHE
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  936 ILE
Chi-restraints excluded: chain A residue  940 PHE
Chi-restraints excluded: chain A residue 1042 THR
Chi-restraints excluded: chain A residue 1111 ILE
Chi-restraints excluded: chain A residue 1118 LEU
Chi-restraints excluded: chain A residue 1165 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 95 optimal weight:    9.9990
   chunk 76 optimal weight:    0.6980
   chunk 69 optimal weight:    3.9990
   chunk 59 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.197277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.157391 restraints weight = 12655.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.155111 restraints weight = 18852.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.156846 restraints weight = 17382.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.159176 restraints weight = 11289.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.159431 restraints weight = 9051.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9404  Z= 0.134
  Angle     :  0.638  14.349  12745  Z= 0.307
  Chirality :  0.042   0.415   1466
  Planarity :  0.003   0.052   1596
  Dihedral  :  9.261  89.299   1644
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.22 %
    Favored  : 77.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.26), residues: 1153
  helix:  1.50 (0.20), residues: 751
  sheet: -0.37 (0.80), residues: 48
  loop : -1.28 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1229 
 TYR   0.016   0.001   TYR A 243 
 PHE   0.040   0.002   PHE A 395 
 TRP   0.012   0.001   TRP A 158 
 HIS   0.007   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9403)
  covalent geometry    : angle       0.63830 (12745)
  hydrogen bonds       : bond        0.04347 (  564)
  hydrogen bonds       : angle       4.04581 ( 1662)
  Misc. bond           : bond        0.00005 (    1)

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 120
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.6919 (m-80) cc_final: 0.6636 (m-80)
REVERT: A  693 PHE cc_start: 0.6028 (OUTLIER) cc_final: 0.4945 (m-80)
REVERT: A  766 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7583 (t80)
REVERT: A 1086 MET cc_start: 0.5378 (pmm) cc_final: 0.5043 (pmm)
REVERT: A 1118 LEU cc_start: 0.5969 (OUTLIER) cc_final: 0.5743 (mt)
  outliers start: 30
  outliers final: 24
  residues processed: 138
  average time/residue: 0.0748
  time to fit residues: 15.4049
Evaluate side-chains
  144 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 117
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 MET
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  197 PHE
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain A residue  565 VAL
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  704 TRP
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  766 PHE
Chi-restraints excluded: chain A residue  787 MET
Chi-restraints excluded: chain A residue  833 PHE
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  936 ILE
Chi-restraints excluded: chain A residue  940 PHE
Chi-restraints excluded: chain A residue 1042 THR
Chi-restraints excluded: chain A residue 1111 ILE
Chi-restraints excluded: chain A residue 1118 LEU
Chi-restraints excluded: chain A residue 1165 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 104 optimal weight:    9.9990
   chunk 12 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 19 optimal weight:    7.9990
   chunk 99 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1020 GLN
** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.195167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.155375 restraints weight = 12688.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.154230 restraints weight = 17973.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.156134 restraints weight = 16290.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.156166 restraints weight = 10619.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.156897 restraints weight = 9632.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.2529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9404  Z= 0.158
  Angle     :  0.654  14.497  12745  Z= 0.317
  Chirality :  0.043   0.433   1466
  Planarity :  0.003   0.052   1596
  Dihedral  :  9.322  88.836   1644
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.22 %
    Favored  : 77.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.26), residues: 1153
  helix:  1.42 (0.20), residues: 750
  sheet: -0.44 (0.80), residues: 48
  loop : -1.22 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 463 
 TYR   0.017   0.001   TYR A 243 
 PHE   0.028   0.002   PHE A 339 
 TRP   0.011   0.001   TRP A 158 
 HIS   0.007   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 9403)
  covalent geometry    : angle       0.65362 (12745)
  hydrogen bonds       : bond        0.04558 (  564)
  hydrogen bonds       : angle       4.13487 ( 1662)
  Misc. bond           : bond        0.00028 (    1)

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 117
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.6956 (m-80) cc_final: 0.6650 (m-80)
REVERT: A  693 PHE cc_start: 0.6047 (OUTLIER) cc_final: 0.4981 (m-80)
REVERT: A  766 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7592 (t80)
REVERT: A 1086 MET cc_start: 0.5411 (pmm) cc_final: 0.5075 (pmm)
REVERT: A 1118 LEU cc_start: 0.6029 (OUTLIER) cc_final: 0.5764 (mt)
  outliers start: 30
  outliers final: 25
  residues processed: 137
  average time/residue: 0.0777
  time to fit residues: 15.8560
Evaluate side-chains
  144 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 116
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 MET
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  197 PHE
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  565 VAL
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  704 TRP
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  766 PHE
Chi-restraints excluded: chain A residue  833 PHE
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  936 ILE
Chi-restraints excluded: chain A residue  940 PHE
Chi-restraints excluded: chain A residue 1042 THR
Chi-restraints excluded: chain A residue 1111 ILE
Chi-restraints excluded: chain A residue 1118 LEU
Chi-restraints excluded: chain A residue 1165 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 84 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.193874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.153753 restraints weight = 12759.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.151575 restraints weight = 19233.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.152930 restraints weight = 18292.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.155502 restraints weight = 11529.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.155429 restraints weight = 9346.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.2659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9404  Z= 0.177
  Angle     :  0.683  14.686  12745  Z= 0.330
  Chirality :  0.043   0.432   1466
  Planarity :  0.004   0.053   1596
  Dihedral  :  9.389  88.094   1644
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 19.85 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.26), residues: 1153
  helix:  1.34 (0.19), residues: 750
  sheet: -0.01 (0.87), residues: 40
  loop : -1.31 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 485 
 TYR   0.017   0.001   TYR A 243 
 PHE   0.025   0.002   PHE A 339 
 TRP   0.010   0.001   TRP A 158 
 HIS   0.007   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 9403)
  covalent geometry    : angle       0.68344 (12745)
  hydrogen bonds       : bond        0.04754 (  564)
  hydrogen bonds       : angle       4.18884 ( 1662)
  Misc. bond           : bond        0.00051 (    1)

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 117
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.7074 (m-80) cc_final: 0.6762 (m-80)
REVERT: A  693 PHE cc_start: 0.6130 (OUTLIER) cc_final: 0.5087 (m-80)
REVERT: A 1086 MET cc_start: 0.5475 (pmm) cc_final: 0.5135 (pmm)
  outliers start: 29
  outliers final: 25
  residues processed: 136
  average time/residue: 0.0733
  time to fit residues: 14.9665
Evaluate side-chains
  140 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 MET
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  197 PHE
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  565 VAL
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  704 TRP
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  766 PHE
Chi-restraints excluded: chain A residue  833 PHE
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  936 ILE
Chi-restraints excluded: chain A residue  940 PHE
Chi-restraints excluded: chain A residue 1042 THR
Chi-restraints excluded: chain A residue 1111 ILE
Chi-restraints excluded: chain A residue 1165 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 52 optimal weight:    0.4980
   chunk 103 optimal weight:    7.9990
   chunk 70 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 107 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1020 GLN
** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.196465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.156544 restraints weight = 12480.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.153300 restraints weight = 19049.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.155077 restraints weight = 16451.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.157062 restraints weight = 10568.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.157087 restraints weight = 9141.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9404  Z= 0.134
  Angle     :  0.657  15.368  12745  Z= 0.314
  Chirality :  0.042   0.433   1466
  Planarity :  0.003   0.052   1596
  Dihedral  :  9.177  85.494   1644
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 20.91 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.82 (0.26), residues: 1153
  helix:  1.44 (0.20), residues: 751
  sheet: -0.52 (0.80), residues: 48
  loop : -1.22 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 485 
 TYR   0.017   0.001   TYR A 243 
 PHE   0.042   0.002   PHE A 395 
 TRP   0.011   0.001   TRP A 158 
 HIS   0.006   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 9403)
  covalent geometry    : angle       0.65748 (12745)
  hydrogen bonds       : bond        0.04443 (  564)
  hydrogen bonds       : angle       4.08608 ( 1662)
  Misc. bond           : bond        0.00013 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1233.41 seconds
wall clock time: 22 minutes 1.39 seconds (1321.39 seconds total)