Starting phenix.real_space_refine
on Wed May 14 03:54:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q63_18183/05_2025/8q63_18183.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q63_18183/05_2025/8q63_18183.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q63_18183/05_2025/8q63_18183.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q63_18183/05_2025/8q63_18183.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q63_18183/05_2025/8q63_18183.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q63_18183/05_2025/8q63_18183.cif"
  }
  resolution = 3.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      70      5.49       5
     S      35      5.16       5
     C    7041      2.51       5
     N    1971      2.21       5
     O    2229      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11346
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2698
          Classifications: {'peptide': 329}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 309}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "A"
      Number of atoms: 7200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 915, 7200
          Classifications: {'peptide': 915}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 44}
          Link IDs: {'PTRANS': 44, 'TRANS': 870}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 152
          Unresolved non-hydrogen angles: 185
          Unresolved non-hydrogen dihedrals: 119
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 73
    Chain: "N"
      Number of atoms: 642
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 642
          Classifications: {'DNA': 31}
          Link IDs: {'rna3p': 30}
    Chain: "T"
      Number of atoms: 630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 630
          Classifications: {'DNA': 31}
          Link IDs: {'rna3p': 30}
    Chain: "C"
      Number of atoms: 152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 152
          Classifications: {'RNA': 7}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 2}
          Link IDs: {'rna3p': 6}
    Chain: "C"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 6.96, per 1000 atoms: 0.61
  Number of scatterers: 11346
  At special positions: 0
  Unit cell: (103.79, 116.4, 118.34, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      35     16.00
     P      70     15.00
     O    2229      8.00
     N    1971      7.00
     C    7041      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.80
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2354

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 11 sheets defined
      59.8% alpha, 7.3% beta
      26 base pairs and 47 stacking pairs defined.
    Time for finding SS restraints: 3.92
  Creating SS restraints...
    Processing helix  chain 'B' and resid 7 through 14
      removed outlier: 3.890A  pdb=" N   LEU B  14 " --> pdb=" O   ASP B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 37
    Processing helix  chain 'B' and resid 38 through 41
    Processing helix  chain 'B' and resid 44 through 47
      removed outlier: 3.762A  pdb=" N   GLU B  47 " --> pdb=" O   HIS B  44 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 44 through 47'
    Processing helix  chain 'B' and resid 58 through 69
    Processing helix  chain 'B' and resid 79 through 90
    Processing helix  chain 'B' and resid 104 through 113
      removed outlier: 3.834A  pdb=" N   TYR B 108 " --> pdb=" O   ASP B 104 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   ASP B 113 " --> pdb=" O   SER B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 157
      removed outlier: 3.960A  pdb=" N   MET B 148 " --> pdb=" O   GLU B 144 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ILE B 154 " --> pdb=" O   TRP B 150 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   GLY B 155 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 164
      removed outlier: 3.729A  pdb=" N   GLY B 164 " --> pdb=" O   TYR B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 182
    Processing helix  chain 'B' and resid 190 through 199
    Processing helix  chain 'B' and resid 209 through 215
      removed outlier: 3.521A  pdb=" N   GLU B 212 " --> pdb=" O   ASP B 209 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LYS B 214 " --> pdb=" O   ASN B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 225
    Processing helix  chain 'B' and resid 230 through 234
      removed outlier: 4.297A  pdb=" N   ILE B 234 " --> pdb=" O   ALA B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 267
    Processing helix  chain 'B' and resid 268 through 270
      No H-bonds generated for 'chain 'B' and resid 268 through 270'
    Processing helix  chain 'B' and resid 273 through 278
      removed outlier: 4.141A  pdb=" N   MET B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 282
    Processing helix  chain 'B' and resid 284 through 293
    Processing helix  chain 'B' and resid 295 through 301
      removed outlier: 3.573A  pdb=" N   LEU B 299 " --> pdb=" O   ASP B 295 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LYS B 300 " --> pdb=" O   LYS B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 321
    Processing helix  chain 'A' and resid 387 through 395
    Processing helix  chain 'A' and resid 397 through 421
      removed outlier: 4.247A  pdb=" N   ASP A 414 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ARG A 415 " --> pdb=" O   PHE A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 442
    Processing helix  chain 'A' and resid 448 through 476
      removed outlier: 4.518A  pdb=" N   VAL A 452 " --> pdb=" O   LYS A 448 " (cutoff:3.500A)
      Proline residue:  A 463  - end of helix
    Processing helix  chain 'A' and resid 490 through 497
      removed outlier: 3.764A  pdb=" N   GLY A 495 " --> pdb=" O   THR A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 515
      removed outlier: 4.529A  pdb=" N   GLY A 506 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 552
      removed outlier: 3.855A  pdb=" N   ILE A 536 " --> pdb=" O   ALA A 532 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLU A 549 " --> pdb=" O   GLU A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 611
      removed outlier: 3.747A  pdb=" N   VAL A 611 " --> pdb=" O   MET A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 663
      removed outlier: 3.628A  pdb=" N   GLU A 662 " --> pdb=" O   GLN A 658 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ARG A 663 " --> pdb=" O   LEU A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 717
      removed outlier: 3.884A  pdb=" N   VAL A 707 " --> pdb=" O   SER A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 731
    Processing helix  chain 'A' and resid 737 through 751
    Processing helix  chain 'A' and resid 777 through 813
    Processing helix  chain 'A' and resid 842 through 848
    Processing helix  chain 'A' and resid 857 through 873
    Processing helix  chain 'A' and resid 879 through 890
    Processing helix  chain 'A' and resid 890 through 900
    Processing helix  chain 'A' and resid 906 through 911
    Processing helix  chain 'A' and resid 913 through 930
    Processing helix  chain 'A' and resid 932 through 935
    Processing helix  chain 'A' and resid 948 through 959
      removed outlier: 3.703A  pdb=" N   ALA A 956 " --> pdb=" O   GLN A 952 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 960 through 967
    Processing helix  chain 'A' and resid 977 through 997
    Processing helix  chain 'A' and resid 998 through 1004
    Processing helix  chain 'A' and resid 1009 through 1021
      removed outlier: 3.729A  pdb=" N   VAL A1021 " --> pdb=" O   VAL A1017 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1025 through 1038
    Processing helix  chain 'A' and resid 1046 through 1066
      removed outlier: 4.435A  pdb=" N   PHE A1050 " --> pdb=" O   GLU A1046 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   TYR A1053 " --> pdb=" O   ASP A1049 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   HIS A1057 " --> pdb=" O   TYR A1053 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   SER A1060 " --> pdb=" O   LYS A1056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1067 through 1085
    Processing helix  chain 'A' and resid 1089 through 1094
      removed outlier: 4.066A  pdb=" N   LYS A1094 " --> pdb=" O   ASP A1090 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1149 through 1181
      Proline residue:  A1158  - end of helix
    Processing helix  chain 'A' and resid 1197 through 1213
    Processing helix  chain 'A' and resid 1216 through 1229
    Processing helix  chain 'A' and resid 1242 through 1244
      No H-bonds generated for 'chain 'A' and resid 1242 through 1244'
    Processing helix  chain 'A' and resid 1245 through 1260
    Processing helix  chain 'A' and resid 1264 through 1281
      removed outlier: 3.647A  pdb=" N   LEU A1279 " --> pdb=" O   ARG A1275 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   SER A1281 " --> pdb=" O   GLU A1277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1293
    Processing helix  chain 'A' and resid 1295 through 1301
      removed outlier: 3.774A  pdb=" N   LEU A1299 " --> pdb=" O   THR A1295 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   PHE A1300 " --> pdb=" O   THR A1296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1305 through 1310
    Processing helix  chain 'A' and resid 1339 through 1344
    Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 99
      removed outlier: 3.704A  pdb=" N   VAL B 135 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   MET B 247 " --> pdb=" O   MET B 168 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 206 through 207
      removed outlier: 3.953A  pdb=" N   ILE B 207 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 529 through 530
      removed outlier: 3.547A  pdb=" N   ALA A 635 " --> pdb=" O   LYS A 650 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 613 through 619
    Processing sheet with id=AA5, first strand: chain 'A' and resid 734 through 736
    Processing sheet with id=AA6, first strand: chain 'A' and resid 822 through 824
    Processing sheet with id=AA7, first strand: chain 'A' and resid 855 through 856
      removed outlier: 3.997A  pdb=" N   LYS A 855 " --> pdb=" O   SER A 938 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   SER A 938 " --> pdb=" O   LYS A 855 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 942 through 944
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1086 through 1087
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1109 through 1111
      removed outlier: 3.739A  pdb=" N   TRP A1110 " --> pdb=" O   ILE A1118 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1127 through 1131
      removed outlier: 3.610A  pdb=" N   ILE A1139 " --> pdb=" O   LYS A1128 " (cutoff:3.500A)

    527 hydrogen bonds defined for protein.
    1524 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      59 hydrogen bonds
      118 hydrogen bond angles
      0 basepair planarities
      26 basepair parallelities
      47 stacking parallelities
  Total time for adding SS restraints: 4.94

  Time building geometry restraints manager: 3.30 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1999
        1.33 -     1.45: 3277
        1.45 -     1.57: 6274
        1.57 -     1.69: 146
        1.69 -     1.82: 60
  Bond restraints: 11756
  Sorted by residual:
  bond pdb=" O3'  DG N 136 "
       pdb=" P    DC N 137 "
    ideal  model  delta    sigma   weight residual
    1.607  1.449  0.158 1.50e-02 4.44e+03 1.11e+02
  bond pdb=" C3'  DC N 137 "
       pdb=" C2'  DC N 137 "
    ideal  model  delta    sigma   weight residual
    1.525  1.696 -0.171 2.00e-02 2.50e+03 7.27e+01
  bond pdb=" O3A GTP C 201 "
       pdb=" PA  GTP C 201 "
    ideal  model  delta    sigma   weight residual
    1.610  1.492  0.118 2.00e-02 2.50e+03 3.48e+01
  bond pdb=" C2'  DC N 137 "
       pdb=" C1'  DC N 137 "
    ideal  model  delta    sigma   weight residual
    1.525  1.409  0.116 2.00e-02 2.50e+03 3.35e+01
  bond pdb=" O3'  DC T  18 "
       pdb=" P    DA T  19 "
    ideal  model  delta    sigma   weight residual
    1.607  1.524  0.083 1.50e-02 4.44e+03 3.06e+01
  ... (remaining 11751 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.16: 16035
        4.16 -     8.32: 167
        8.32 -    12.48: 17
       12.48 -    16.64: 6
       16.64 -    20.80: 2
  Bond angle restraints: 16227
  Sorted by residual:
  angle pdb=" O3'  DG N 136 "
        pdb=" P    DC N 137 "
        pdb=" O5'  DC N 137 "
      ideal   model   delta    sigma   weight residual
     104.00  124.80  -20.80 1.50e+00 4.44e-01 1.92e+02
  angle pdb=" C3'  DC T  18 "
        pdb=" O3'  DC T  18 "
        pdb=" P    DA T  19 "
      ideal   model   delta    sigma   weight residual
     120.20  104.85   15.35 1.50e+00 4.44e-01 1.05e+02
  angle pdb=" C3'  DT T  20 "
        pdb=" O3'  DT T  20 "
        pdb=" P    DT T  21 "
      ideal   model   delta    sigma   weight residual
     120.20  105.74   14.46 1.50e+00 4.44e-01 9.29e+01
  angle pdb=" C2'  DC N 137 "
        pdb=" C1'  DC N 137 "
        pdb=" N1   DC N 137 "
      ideal   model   delta    sigma   weight residual
     113.50  100.28   13.22 1.50e+00 4.44e-01 7.76e+01
  angle pdb=" C3'  DA N 131 "
        pdb=" O3'  DA N 131 "
        pdb=" P    DA N 132 "
      ideal   model   delta    sigma   weight residual
     120.20  132.94  -12.74 1.50e+00 4.44e-01 7.22e+01
  ... (remaining 16222 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.16: 6546
       34.16 -    68.31: 366
       68.31 -   102.47: 16
      102.47 -   136.62: 1
      136.62 -   170.78: 2
  Dihedral angle restraints: 6931
    sinusoidal: 3300
      harmonic: 3631
  Sorted by residual:
  dihedral pdb=" C8  GTP C 201 "
           pdb=" C1' GTP C 201 "
           pdb=" N9  GTP C 201 "
           pdb=" O4' GTP C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -12.75  117.34     1      2.00e+01 2.50e-03 3.50e+01
  dihedral pdb=" C5'   G C 108 "
           pdb=" C4'   G C 108 "
           pdb=" C3'   G C 108 "
           pdb=" O3'   G C 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00  112.01   34.99     1      8.00e+00 1.56e-02 2.71e+01
  dihedral pdb=" O4'   G C 108 "
           pdb=" C4'   G C 108 "
           pdb=" C3'   G C 108 "
           pdb=" C2'   G C 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00   -7.29   31.29     1      8.00e+00 1.56e-02 2.18e+01
  ... (remaining 6928 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.127: 1716
       0.127 -    0.253: 36
       0.253 -    0.380: 4
       0.380 -    0.507: 17
       0.507 -    0.633: 27
  Chirality restraints: 1800
  Sorted by residual:
  chirality pdb=" P    DG T  10 "
            pdb=" OP1  DG T  10 "
            pdb=" OP2  DG T  10 "
            pdb=" O5'  DG T  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35    2.98   -0.63 2.00e-01 2.50e+01 1.00e+01
  chirality pdb=" P    DG N 108 "
            pdb=" OP1  DG N 108 "
            pdb=" OP2  DG N 108 "
            pdb=" O5'  DG N 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.94   -0.59 2.00e-01 2.50e+01 8.80e+00
  chirality pdb=" P    DC N 137 "
            pdb=" OP1  DC N 137 "
            pdb=" OP2  DC N 137 "
            pdb=" O5'  DC N 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.93   -0.59 2.00e-01 2.50e+01 8.57e+00
  ... (remaining 1797 not shown)

  Planarity restraints: 1825
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT N 135 "    0.034 2.00e-02 2.50e+03   1.68e-02 7.09e+00
        pdb=" N1   DT N 135 "   -0.037 2.00e-02 2.50e+03
        pdb=" C2   DT N 135 "   -0.006 2.00e-02 2.50e+03
        pdb=" O2   DT N 135 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3   DT N 135 "    0.008 2.00e-02 2.50e+03
        pdb=" C4   DT N 135 "    0.012 2.00e-02 2.50e+03
        pdb=" O4   DT N 135 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DT N 135 "   -0.000 2.00e-02 2.50e+03
        pdb=" C7   DT N 135 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DT N 135 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 159 "    0.017 2.00e-02 2.50e+03   1.60e-02 6.42e+00
        pdb=" CG  TRP B 159 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 159 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 159 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 159 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 159 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 159 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 159 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 159 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 159 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 320 "   -0.009 2.00e-02 2.50e+03   1.91e-02 3.63e+00
        pdb=" C   GLU B 320 "    0.033 2.00e-02 2.50e+03
        pdb=" O   GLU B 320 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   TRP B 321 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1822 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 285
        2.68 -     3.23: 11044
        3.23 -     3.79: 18562
        3.79 -     4.34: 24480
        4.34 -     4.90: 38376
  Nonbonded interactions: 92747
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A1132 "
            pdb=" O   GLN A1135 "
     model   vdw
     2.121 3.040
  nonbonded pdb=" OD1 ASP A 843 "
            pdb=" NE2 GLN A 916 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" O   SER B 190 "
            pdb=" OG  SER B 193 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" N   LYS B  49 "
            pdb=" O   LYS B 131 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" OD1 ASP A 876 "
            pdb=" NH1 ARG A 883 "
     model   vdw
     2.264 3.120
  ... (remaining 92742 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     31.460
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.171  11757  Z= 0.356
  Angle     :  1.034  20.795  16227  Z= 0.537
  Chirality :  0.094   0.633   1800
  Planarity :  0.004   0.042   1825
  Dihedral  : 18.500 170.778   4577
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.66 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.25), residues: 1232
  helix:  1.59 (0.21), residues: 666
  sheet: -1.19 (0.56), residues: 80
  loop : -1.01 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP B 159 
 HIS   0.013   0.001   HIS A 943 
 PHE   0.028   0.002   PHE A 936 
 TYR   0.020   0.002   TYR A 954 
 ARG   0.003   0.000   ARG A 989 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15627 (  586)
  hydrogen bonds       : angle       6.37006 ( 1642)
  covalent geometry    : bond        0.00689 (11756)
  covalent geometry    : angle       1.03364 (16227)
  Misc. bond           : bond        0.01190 (    1)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 176
  time to evaluate  : 1.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  727 ASN cc_start: 0.7988 (m-40) cc_final: 0.7538 (m110)
REVERT: A  796 ASP cc_start: 0.8051 (m-30) cc_final: 0.7790 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 177
  average time/residue: 0.2286
  time to fit residues: 59.8156
Evaluate side-chains
  129 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 1.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 97 optimal weight:    3.9990
   chunk 54 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:   20.0000
   chunk 52 optimal weight:   30.0000
   chunk 101 optimal weight:    9.9990
   chunk 39 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 75 optimal weight:    5.9990
   chunk 117 optimal weight:   40.0000
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN
A 628 HIS
A 642 ASN
** A 925 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 = 0.4117 r_free = 0.4117 target = 0.152053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.120488 restraints weight = 20462.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.124467 restraints weight = 11057.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.126936 restraints weight = 7576.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.1222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  11757  Z= 0.188
  Angle     :  0.654   8.376  16227  Z= 0.346
  Chirality :  0.042   0.151   1800
  Planarity :  0.004   0.042   1825
  Dihedral  : 19.476 174.143   2162
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  9.48 %
    Favored  : 89.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.25), residues: 1232
  helix:  1.55 (0.20), residues: 673
  sheet: -0.95 (0.58), residues: 74
  loop : -1.02 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 159 
 HIS   0.006   0.001   HIS A1188 
 PHE   0.034   0.002   PHE A 754 
 TYR   0.031   0.002   TYR A 496 
 ARG   0.003   0.000   ARG A 829 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05390 (  586)
  hydrogen bonds       : angle       4.73525 ( 1642)
  covalent geometry    : bond        0.00427 (11756)
  covalent geometry    : angle       0.65406 (16227)
  Misc. bond           : bond        0.00122 (    1)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 157
  time to evaluate  : 1.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  159 TRP cc_start: 0.7753 (t60) cc_final: 0.6814 (t60)
REVERT: A  656 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.9024 (tt)
REVERT: A  796 ASP cc_start: 0.8050 (m-30) cc_final: 0.7798 (m-30)
REVERT: A  856 LYS cc_start: 0.7210 (mmmt) cc_final: 0.6926 (mmmt)
REVERT: A 1157 LEU cc_start: 0.6592 (tp) cc_final: 0.6242 (tp)
  outliers start: 14
  outliers final: 8
  residues processed: 164
  average time/residue: 0.2340
  time to fit residues: 55.6651
Evaluate side-chains
  151 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 142
  time to evaluate  : 1.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 18 optimal weight:   40.0000
   chunk 115 optimal weight:    5.9990
   chunk 76 optimal weight:    5.9990
   chunk 29 optimal weight:    0.5980
   chunk 60 optimal weight:    7.9990
   chunk 70 optimal weight:    0.8980
   chunk 127 optimal weight:   10.0000
   chunk 58 optimal weight:   20.0000
   chunk 36 optimal weight:   10.0000
   chunk 47 optimal weight:    1.9990
   chunk 99 optimal weight:    9.9990
   overall best weight:    3.0986

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

Flipped N/Q/H residues before XYZ refinement:
A 628 HIS
** A 925 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 = 0.4143 r_free = 0.4143 target = 0.153574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.120488 restraints weight = 20590.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.124732 restraints weight = 10814.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.127514 restraints weight = 7331.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11757  Z= 0.147
  Angle     :  0.599   7.739  16227  Z= 0.314
  Chirality :  0.040   0.148   1800
  Planarity :  0.004   0.040   1825
  Dihedral  : 19.220 168.472   2162
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 12.86 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.25), residues: 1232
  helix:  1.63 (0.20), residues: 680
  sheet: -1.26 (0.52), residues: 90
  loop : -1.01 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B 159 
 HIS   0.005   0.001   HIS A 943 
 PHE   0.022   0.002   PHE A 936 
 TYR   0.029   0.001   TYR A 496 
 ARG   0.002   0.000   ARG A 829 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04612 (  586)
  hydrogen bonds       : angle       4.40136 ( 1642)
  covalent geometry    : bond        0.00327 (11756)
  covalent geometry    : angle       0.59912 (16227)
  Misc. bond           : bond        0.00083 (    1)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 158
  time to evaluate  : 1.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  150 TRP cc_start: 0.7206 (m-10) cc_final: 0.6962 (m-10)
REVERT: B  228 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7861 (tt)
REVERT: B  321 TRP cc_start: 0.8053 (t60) cc_final: 0.7483 (t60)
REVERT: A  607 MET cc_start: 0.8056 (ttp) cc_final: 0.7828 (ttp)
REVERT: A  796 ASP cc_start: 0.8021 (m-30) cc_final: 0.7788 (m-30)
REVERT: A  856 LYS cc_start: 0.7359 (mmmt) cc_final: 0.6813 (mmmt)
REVERT: A 1157 LEU cc_start: 0.6646 (tp) cc_final: 0.6376 (tp)
  outliers start: 23
  outliers final: 14
  residues processed: 170
  average time/residue: 0.2098
  time to fit residues: 52.9131
Evaluate side-chains
  157 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 1.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  628 HIS
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 101 optimal weight:   10.0000
   chunk 118 optimal weight:   30.0000
   chunk 18 optimal weight:   50.0000
   chunk 113 optimal weight:    8.9990
   chunk 112 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 36 optimal weight:    9.9990
   chunk 52 optimal weight:    2.9990
   chunk 77 optimal weight:   20.0000
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 628 HIS
** A 925 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 = 0.4117 r_free = 0.4117 target = 0.151098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.117265 restraints weight = 20467.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.121299 restraints weight = 11038.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.123960 restraints weight = 7619.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  11757  Z= 0.159
  Angle     :  0.593   7.848  16227  Z= 0.312
  Chirality :  0.040   0.201   1800
  Planarity :  0.004   0.045   1825
  Dihedral  : 19.135 165.209   2162
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 14.37 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.25), residues: 1232
  helix:  1.68 (0.21), residues: 674
  sheet: -1.18 (0.55), residues: 80
  loop : -0.99 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 159 
 HIS   0.005   0.001   HIS A 628 
 PHE   0.022   0.001   PHE B 132 
 TYR   0.025   0.002   TYR A 496 
 ARG   0.002   0.000   ARG A 829 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04515 (  586)
  hydrogen bonds       : angle       4.39846 ( 1642)
  covalent geometry    : bond        0.00365 (11756)
  covalent geometry    : angle       0.59298 (16227)
  Misc. bond           : bond        0.00064 (    1)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 151
  time to evaluate  : 1.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  159 TRP cc_start: 0.7994 (t60) cc_final: 0.7648 (t60)
REVERT: B  228 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7892 (tt)
REVERT: A  796 ASP cc_start: 0.8109 (m-30) cc_final: 0.7866 (m-30)
REVERT: A  865 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8907 (tt)
REVERT: A 1157 LEU cc_start: 0.6627 (tp) cc_final: 0.6422 (tp)
REVERT: A 1201 MET cc_start: 0.7735 (ttp) cc_final: 0.7402 (ttp)
  outliers start: 28
  outliers final: 16
  residues processed: 169
  average time/residue: 0.2155
  time to fit residues: 53.9284
Evaluate side-chains
  158 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  865 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 7 optimal weight:   20.0000
   chunk 8 optimal weight:    5.9990
   chunk 124 optimal weight:   10.0000
   chunk 113 optimal weight:   10.0000
   chunk 20 optimal weight:    6.9990
   chunk 45 optimal weight:    8.9990
   chunk 35 optimal weight:   20.0000
   chunk 104 optimal weight:    8.9990
   chunk 83 optimal weight:   20.0000
   chunk 46 optimal weight:   10.0000
   chunk 105 optimal weight:    0.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 459 ASN
A1160 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.147886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.113932 restraints weight = 20433.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.117810 restraints weight = 11137.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.120355 restraints weight = 7766.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  11757  Z= 0.217
  Angle     :  0.651   9.460  16227  Z= 0.340
  Chirality :  0.042   0.236   1800
  Planarity :  0.004   0.041   1825
  Dihedral  : 19.210 161.941   2162
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 16.24 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.25), residues: 1232
  helix:  1.45 (0.20), residues: 675
  sheet: -1.38 (0.51), residues: 90
  loop : -1.03 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 159 
 HIS   0.006   0.001   HIS B  44 
 PHE   0.038   0.002   PHE A 936 
 TYR   0.024   0.002   TYR A 496 
 ARG   0.003   0.000   ARG A 829 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05054 (  586)
  hydrogen bonds       : angle       4.63693 ( 1642)
  covalent geometry    : bond        0.00497 (11756)
  covalent geometry    : angle       0.65071 (16227)
  Misc. bond           : bond        0.00053 (    1)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 143
  time to evaluate  : 1.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  150 TRP cc_start: 0.7289 (m-10) cc_final: 0.7001 (m-10)
REVERT: B  228 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7920 (tt)
REVERT: B  292 ARG cc_start: 0.7617 (mmm-85) cc_final: 0.7403 (mmm-85)
REVERT: A  796 ASP cc_start: 0.8118 (m-30) cc_final: 0.7877 (m-30)
REVERT: A  865 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8947 (tt)
REVERT: A 1160 ASN cc_start: 0.8942 (m110) cc_final: 0.8555 (m-40)
  outliers start: 31
  outliers final: 22
  residues processed: 160
  average time/residue: 0.2207
  time to fit residues: 52.0201
Evaluate side-chains
  162 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue   44 HIS
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  628 HIS
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  865 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue  912 ASP
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1193 THR
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 91 optimal weight:    8.9990
   chunk 92 optimal weight:    5.9990
   chunk 90 optimal weight:   20.0000
   chunk 70 optimal weight:    5.9990
   chunk 104 optimal weight:    7.9990
   chunk 78 optimal weight:    7.9990
   chunk 105 optimal weight:    0.9990
   chunk 93 optimal weight:    9.9990
   chunk 9 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 36 optimal weight:   10.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.148584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.114682 restraints weight = 20646.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.118627 restraints weight = 11199.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.121206 restraints weight = 7770.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  11757  Z= 0.192
  Angle     :  0.633   8.764  16227  Z= 0.330
  Chirality :  0.041   0.204   1800
  Planarity :  0.004   0.040   1825
  Dihedral  : 19.182 161.175   2162
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 17.18 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.25), residues: 1232
  helix:  1.47 (0.20), residues: 674
  sheet: -1.38 (0.51), residues: 90
  loop : -0.97 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP B 159 
 HIS   0.004   0.001   HIS A 943 
 PHE   0.030   0.002   PHE B 132 
 TYR   0.022   0.002   TYR A 496 
 ARG   0.004   0.000   ARG A 533 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04814 (  586)
  hydrogen bonds       : angle       4.57920 ( 1642)
  covalent geometry    : bond        0.00440 (11756)
  covalent geometry    : angle       0.63307 (16227)
  Misc. bond           : bond        0.00050 (    1)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 145
  time to evaluate  : 1.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  150 TRP cc_start: 0.7323 (m-10) cc_final: 0.7093 (m-10)
REVERT: B  159 TRP cc_start: 0.8056 (t60) cc_final: 0.7628 (t60)
REVERT: B  292 ARG cc_start: 0.7660 (mmm-85) cc_final: 0.7410 (mmm-85)
REVERT: A  727 ASN cc_start: 0.7992 (m-40) cc_final: 0.7540 (m110)
REVERT: A  796 ASP cc_start: 0.8038 (m-30) cc_final: 0.7807 (m-30)
REVERT: A  865 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8954 (tt)
REVERT: A 1157 LEU cc_start: 0.6710 (tp) cc_final: 0.6397 (tp)
REVERT: A 1160 ASN cc_start: 0.8901 (m110) cc_final: 0.8652 (m-40)
  outliers start: 33
  outliers final: 23
  residues processed: 161
  average time/residue: 0.2110
  time to fit residues: 50.4901
Evaluate side-chains
  163 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 139
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  628 HIS
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  736 VAL
Chi-restraints excluded: chain A residue  865 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1193 THR
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 124 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 96 optimal weight:    1.9990
   chunk 88 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   chunk 102 optimal weight:    6.9990
   chunk 18 optimal weight:   20.0000
   chunk 100 optimal weight:    0.9990
   chunk 53 optimal weight:    6.9990
   chunk 59 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
B  44 HIS
A 691 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.153191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.119591 restraints weight = 20504.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.123663 restraints weight = 10916.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.126403 restraints weight = 7502.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7219
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  11757  Z= 0.126
  Angle     :  0.610  10.625  16227  Z= 0.313
  Chirality :  0.040   0.206   1800
  Planarity :  0.004   0.045   1825
  Dihedral  : 18.971 160.420   2162
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 18.40 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.25), residues: 1232
  helix:  1.66 (0.20), residues: 681
  sheet: -0.81 (0.54), residues: 84
  loop : -0.89 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 159 
 HIS   0.012   0.001   HIS B  44 
 PHE   0.026   0.001   PHE B 132 
 TYR   0.023   0.002   TYR A 496 
 ARG   0.002   0.000   ARG A 883 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04119 (  586)
  hydrogen bonds       : angle       4.27736 ( 1642)
  covalent geometry    : bond        0.00281 (11756)
  covalent geometry    : angle       0.60963 (16227)
  Misc. bond           : bond        0.00054 (    1)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 160
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
REVERT: B  150 TRP cc_start: 0.7118 (m-10) cc_final: 0.6877 (m-10)
REVERT: B  159 TRP cc_start: 0.7997 (t60) cc_final: 0.7785 (t60)
REVERT: B  292 ARG cc_start: 0.7591 (mmm-85) cc_final: 0.7317 (mmm-85)
REVERT: B  296 LYS cc_start: 0.8034 (mmtm) cc_final: 0.7750 (mmmt)
REVERT: B  321 TRP cc_start: 0.7917 (t60) cc_final: 0.7277 (t60)
REVERT: A  461 MET cc_start: 0.6953 (mtp) cc_final: 0.6685 (mmm)
REVERT: A  796 ASP cc_start: 0.8012 (m-30) cc_final: 0.7791 (m-30)
REVERT: A  926 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7331 (tm-30)
REVERT: A  936 PHE cc_start: 0.7451 (t80) cc_final: 0.6090 (t80)
REVERT: A 1157 LEU cc_start: 0.6473 (tp) cc_final: 0.6236 (tp)
REVERT: A 1201 MET cc_start: 0.7726 (ttp) cc_final: 0.7477 (ttp)
  outliers start: 22
  outliers final: 17
  residues processed: 173
  average time/residue: 0.2088
  time to fit residues: 53.4346
Evaluate side-chains
  160 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 143
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue  172 MET
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  628 HIS
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 116 optimal weight:    8.9990
   chunk 28 optimal weight:   20.0000
   chunk 106 optimal weight:    8.9990
   chunk 30 optimal weight:    3.9990
   chunk 93 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 64 optimal weight:   10.0000
   chunk 7 optimal weight:   20.0000
   chunk 40 optimal weight:    4.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    6.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.147635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.113851 restraints weight = 20499.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.117691 restraints weight = 11202.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.120196 restraints weight = 7810.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  11757  Z= 0.227
  Angle     :  0.682   9.926  16227  Z= 0.351
  Chirality :  0.043   0.191   1800
  Planarity :  0.005   0.042   1825
  Dihedral  : 19.187 162.179   2162
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 19.25 %
    Favored  : 78.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.25), residues: 1232
  helix:  1.40 (0.20), residues: 674
  sheet: -1.05 (0.51), residues: 94
  loop : -0.97 (0.31), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP B 259 
 HIS   0.006   0.001   HIS B  44 
 PHE   0.033   0.002   PHE B 132 
 TYR   0.033   0.002   TYR A 954 
 ARG   0.004   0.000   ARG A 533 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05054 (  586)
  hydrogen bonds       : angle       4.63357 ( 1642)
  covalent geometry    : bond        0.00522 (11756)
  covalent geometry    : angle       0.68222 (16227)
  Misc. bond           : bond        0.00040 (    1)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 144
  time to evaluate  : 1.268 
Fit side-chains
REVERT: B  150 TRP cc_start: 0.7262 (m-10) cc_final: 0.6912 (m-10)
REVERT: B  159 TRP cc_start: 0.8037 (t60) cc_final: 0.7777 (t60)
REVERT: B  292 ARG cc_start: 0.7651 (mmm-85) cc_final: 0.7384 (mmm-85)
REVERT: B  296 LYS cc_start: 0.8079 (mmtm) cc_final: 0.7750 (mmmt)
REVERT: B  321 TRP cc_start: 0.7994 (t60) cc_final: 0.7452 (t60)
REVERT: A  727 ASN cc_start: 0.7979 (m-40) cc_final: 0.7538 (m110)
REVERT: A  796 ASP cc_start: 0.8053 (m-30) cc_final: 0.7829 (m-30)
REVERT: A  926 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7528 (tm-30)
REVERT: A  936 PHE cc_start: 0.7566 (t80) cc_final: 0.6916 (t80)
REVERT: A 1160 ASN cc_start: 0.8872 (m110) cc_final: 0.8583 (m-40)
REVERT: A 1201 MET cc_start: 0.7458 (ttp) cc_final: 0.7120 (ttp)
  outliers start: 24
  outliers final: 20
  residues processed: 154
  average time/residue: 0.2195
  time to fit residues: 50.1185
Evaluate side-chains
  158 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  736 VAL
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue  954 TYR
Chi-restraints excluded: chain A residue 1036 GLN
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 22 optimal weight:    7.9990
   chunk 115 optimal weight:   30.0000
   chunk 113 optimal weight:   40.0000
   chunk 69 optimal weight:    9.9990
   chunk 123 optimal weight:   10.0000
   chunk 90 optimal weight:    8.9990
   chunk 42 optimal weight:   20.0000
   chunk 14 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   chunk 61 optimal weight:    9.9990
   overall best weight:    7.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.145953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.112126 restraints weight = 20739.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.115943 restraints weight = 11323.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.118447 restraints weight = 7871.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.2496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  11757  Z= 0.258
  Angle     :  0.723  10.189  16227  Z= 0.373
  Chirality :  0.045   0.225   1800
  Planarity :  0.005   0.041   1825
  Dihedral  : 19.323 161.755   2162
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.62 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.25), residues: 1232
  helix:  1.08 (0.20), residues: 674
  sheet: -1.11 (0.52), residues: 94
  loop : -0.94 (0.31), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 259 
 HIS   0.005   0.001   HIS A 822 
 PHE   0.037   0.002   PHE B 132 
 TYR   0.036   0.003   TYR A 954 
 ARG   0.002   0.000   ARG A 811 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05382 (  586)
  hydrogen bonds       : angle       4.88489 ( 1642)
  covalent geometry    : bond        0.00594 (11756)
  covalent geometry    : angle       0.72294 (16227)
  Misc. bond           : bond        0.00040 (    1)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 142
  time to evaluate  : 1.098 
Fit side-chains
REVERT: B  159 TRP cc_start: 0.8060 (t60) cc_final: 0.7848 (t60)
REVERT: B  288 TYR cc_start: 0.8212 (t80) cc_final: 0.7856 (t80)
REVERT: B  296 LYS cc_start: 0.8125 (mmtm) cc_final: 0.7768 (mmmt)
REVERT: B  321 TRP cc_start: 0.8005 (t60) cc_final: 0.7428 (t60)
REVERT: A  796 ASP cc_start: 0.8076 (m-30) cc_final: 0.7857 (m-30)
REVERT: A  883 ARG cc_start: 0.7626 (mtm-85) cc_final: 0.7342 (mtm-85)
REVERT: A  926 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7506 (tm-30)
REVERT: A  936 PHE cc_start: 0.7579 (t80) cc_final: 0.6847 (t80)
REVERT: A 1128 LYS cc_start: 0.7920 (ptpt) cc_final: 0.7564 (ptmm)
REVERT: A 1160 ASN cc_start: 0.8871 (m110) cc_final: 0.8577 (m-40)
  outliers start: 25
  outliers final: 20
  residues processed: 156
  average time/residue: 0.2157
  time to fit residues: 49.5937
Evaluate side-chains
  157 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  736 VAL
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue  954 TYR
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 63 optimal weight:   10.0000
   chunk 88 optimal weight:    5.9990
   chunk 8 optimal weight:    9.9990
   chunk 124 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 17 optimal weight:    6.9990
   chunk 32 optimal weight:   10.0000
   chunk 97 optimal weight:    3.9990
   chunk 37 optimal weight:    7.9990
   chunk 120 optimal weight:    0.3980
   overall best weight:    4.0788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.148562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.114796 restraints weight = 20515.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.118675 restraints weight = 11133.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.121231 restraints weight = 7740.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  11757  Z= 0.174
  Angle     :  0.683  10.748  16227  Z= 0.349
  Chirality :  0.043   0.275   1800
  Planarity :  0.004   0.046   1825
  Dihedral  : 19.189 161.083   2162
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 20.47 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.25), residues: 1232
  helix:  1.20 (0.20), residues: 680
  sheet: -1.08 (0.54), residues: 90
  loop : -0.99 (0.31), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 159 
 HIS   0.004   0.001   HIS A 943 
 PHE   0.034   0.002   PHE B 132 
 TYR   0.031   0.002   TYR A 496 
 ARG   0.002   0.000   ARG A 800 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04855 (  586)
  hydrogen bonds       : angle       4.65999 ( 1642)
  covalent geometry    : bond        0.00402 (11756)
  covalent geometry    : angle       0.68319 (16227)
  Misc. bond           : bond        0.00047 (    1)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
REVERT: B  137 ASN cc_start: 0.8205 (t0) cc_final: 0.7883 (t0)
REVERT: B  296 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7788 (mmmt)
REVERT: B  321 TRP cc_start: 0.7967 (t60) cc_final: 0.7429 (t60)
REVERT: A  727 ASN cc_start: 0.7950 (m-40) cc_final: 0.7481 (m110)
REVERT: A  796 ASP cc_start: 0.8042 (m-30) cc_final: 0.7832 (m-30)
REVERT: A  926 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7492 (tm-30)
REVERT: A  936 PHE cc_start: 0.7563 (t80) cc_final: 0.6837 (t80)
REVERT: A 1160 ASN cc_start: 0.8857 (m110) cc_final: 0.8571 (m-40)
  outliers start: 22
  outliers final: 20
  residues processed: 155
  average time/residue: 0.2011
  time to fit residues: 46.8984
Evaluate side-chains
  162 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 2.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  736 VAL
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue  954 TYR
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 117 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   chunk 89 optimal weight:   10.0000
   chunk 114 optimal weight:   20.0000
   chunk 25 optimal weight:    6.9990
   chunk 50 optimal weight:    5.9990
   chunk 67 optimal weight:   40.0000
   chunk 42 optimal weight:   20.0000
   chunk 68 optimal weight:    9.9990
   chunk 90 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 628 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.146464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.112787 restraints weight = 20591.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.116613 restraints weight = 11233.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.119079 restraints weight = 7813.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.2588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070  11757  Z= 0.239
  Angle     :  0.722  11.288  16227  Z= 0.369
  Chirality :  0.045   0.335   1800
  Planarity :  0.005   0.043   1825
  Dihedral  : 19.307 162.535   2162
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 15.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 20.00 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.25), residues: 1232
  helix:  1.02 (0.20), residues: 680
  sheet: -1.35 (0.50), residues: 100
  loop : -1.08 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.073   0.003   TRP B 159 
 HIS   0.005   0.001   HIS A1163 
 PHE   0.036   0.002   PHE B 132 
 TYR   0.034   0.002   TYR A 954 
 ARG   0.002   0.000   ARG A 533 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05236 (  586)
  hydrogen bonds       : angle       4.84574 ( 1642)
  covalent geometry    : bond        0.00554 (11756)
  covalent geometry    : angle       0.72173 (16227)
  Misc. bond           : bond        0.00040 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3498.14 seconds
wall clock time: 62 minutes 12.39 seconds (3732.39 seconds total)