Starting phenix.real_space_refine
on Wed May 14 04:44:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c5u_16443/05_2025/8c5u_16443.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c5u_16443/05_2025/8c5u_16443.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c5u_16443/05_2025/8c5u_16443.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c5u_16443/05_2025/8c5u_16443.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c5u_16443/05_2025/8c5u_16443.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c5u_16443/05_2025/8c5u_16443.cif"
  }
  resolution = 3.62
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.011
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      74      5.49       5
     S      35      5.16       5
     C    7075      2.51       5
     N    1984      2.21       5
     O    2251      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11419
  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: 7224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 919, 7224
          Classifications: {'peptide': 919}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 46}
          Link IDs: {'PTRANS': 44, 'TRANS': 874}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 159
          Unresolved non-hydrogen angles: 194
          Unresolved non-hydrogen dihedrals: 124
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 80
    Chain: "N"
      Number of atoms: 663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 663
          Classifications: {'DNA': 32}
          Link IDs: {'rna3p': 31}
    Chain: "T"
      Number of atoms: 650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 650
          Classifications: {'DNA': 32}
          Link IDs: {'rna3p': 31}
    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: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.54, per 1000 atoms: 0.57
  Number of scatterers: 11419
  At special positions: 0
  Unit cell: (105.73, 117.37, 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      74     15.00
     O    2251      8.00
     N    1984      7.00
     C    7075      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: 2.96
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2362

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 10 sheets defined
      60.3% alpha, 7.5% beta
      26 base pairs and 49 stacking pairs defined.
    Time for finding SS restraints: 4.31
  Creating SS restraints...
    Processing helix  chain 'B' and resid 7 through 14
      removed outlier: 3.939A  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 58 through 69
    Processing helix  chain 'B' and resid 79 through 90
    Processing helix  chain 'B' and resid 105 through 113
      removed outlier: 3.867A  pdb=" N   SER B 109 " --> pdb=" O   TRP B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 143
      No H-bonds generated for 'chain 'B' and resid 141 through 143'
    Processing helix  chain 'B' and resid 144 through 157
      removed outlier: 3.785A  pdb=" N   MET B 148 " --> pdb=" O   GLU B 144 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLY B 155 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 164
    Processing helix  chain 'B' and resid 174 through 181
    Processing helix  chain 'B' and resid 190 through 199
    Processing helix  chain 'B' and resid 210 through 216
    Processing helix  chain 'B' and resid 217 through 225
      removed outlier: 3.623A  pdb=" N   GLU B 223 " --> pdb=" O   GLN B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 234
      removed outlier: 3.663A  pdb=" N   GLU B 233 " --> pdb=" O   SER B 230 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ILE B 234 " --> pdb=" O   ALA B 231 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 230 through 234'
    Processing helix  chain 'B' and resid 255 through 267
    Processing helix  chain 'B' and resid 273 through 278
      removed outlier: 4.230A  pdb=" N   MET B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 281
      No H-bonds generated for 'chain 'B' and resid 279 through 281'
    Processing helix  chain 'B' and resid 284 through 293
    Processing helix  chain 'B' and resid 295 through 301
    Processing helix  chain 'B' and resid 302 through 306
    Processing helix  chain 'B' and resid 307 through 321
    Processing helix  chain 'B' and resid 326 through 330
      removed outlier: 3.610A  pdb=" N   MET B 329 " --> pdb=" O   ASP B 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 395
    Processing helix  chain 'A' and resid 397 through 421
      removed outlier: 4.500A  pdb=" N   ASP A 414 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      removed outlier: 4.216A  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 449 through 478
      Proline residue:  A 463  - end of helix
      removed outlier: 3.831A  pdb=" N   GLU A 478 " --> pdb=" O   SER A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 497
      removed outlier: 3.905A  pdb=" N   GLY A 495 " --> pdb=" O   THR A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 515
      removed outlier: 3.664A  pdb=" N   LYS A 507 " --> pdb=" O   ILE A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 552
      removed outlier: 3.831A  pdb=" N   ILE A 536 " --> pdb=" O   ALA A 532 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LEU A 552 " --> pdb=" O   SER A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 612
      removed outlier: 3.654A  pdb=" N   VAL A 611 " --> pdb=" O   MET A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 663
    Processing helix  chain 'A' and resid 703 through 717
    Processing helix  chain 'A' and resid 719 through 731
    Processing helix  chain 'A' and resid 737 through 751
      removed outlier: 3.568A  pdb=" N   VAL A 743 " --> pdb=" O   LYS A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 775 through 814
    Processing helix  chain 'A' and resid 842 through 848
    Processing helix  chain 'A' and resid 857 through 873
      removed outlier: 4.443A  pdb=" N   LEU A 862 " --> pdb=" O   GLY A 858 " (cutoff:3.500A)
      removed outlier: 4.928A  pdb=" N   LYS A 863 " --> pdb=" O   PRO A 859 " (cutoff:3.500A)
    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
    Processing helix  chain 'A' and resid 960 through 967
      removed outlier: 3.615A  pdb=" N   GLN A 966 " --> pdb=" O   GLU A 962 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 977 through 997
    Processing helix  chain 'A' and resid 998 through 1005
    Processing helix  chain 'A' and resid 1009 through 1021
      removed outlier: 4.055A  pdb=" N   VAL A1013 " --> pdb=" O   THR A1009 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   GLN A1015 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 5.220A  pdb=" N   THR A1016 " --> pdb=" O   VAL A1012 " (cutoff:3.500A)
      removed outlier: 4.368A  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 1039 through 1041
      No H-bonds generated for 'chain 'A' and resid 1039 through 1041'
    Processing helix  chain 'A' and resid 1047 through 1066
    Processing helix  chain 'A' and resid 1067 through 1085
      removed outlier: 3.539A  pdb=" N   ILE A1072 " --> pdb=" O   SER A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1090 through 1094
    Processing helix  chain 'A' and resid 1149 through 1181
      Proline residue:  A1158  - end of helix
    Processing helix  chain 'A' and resid 1194 through 1196
      No H-bonds generated for 'chain 'A' and resid 1194 through 1196'
    Processing helix  chain 'A' and resid 1197 through 1214
    Processing helix  chain 'A' and resid 1216 through 1229
    Processing helix  chain 'A' and resid 1242 through 1260
    Processing helix  chain 'A' and resid 1264 through 1281
    Processing helix  chain 'A' and resid 1283 through 1293
      removed outlier: 3.501A  pdb=" N   ARG A1287 " --> pdb=" O   LEU A1283 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ASN A1288 " --> pdb=" O   ILE A1284 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   VAL A1289 " --> pdb=" O   GLU A1285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1295 through 1300
      removed outlier: 3.584A  pdb=" N   LEU A1299 " --> pdb=" O   THR A1295 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   PHE A1300 " --> pdb=" O   THR A1296 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1295 through 1300'
    Processing helix  chain 'A' and resid 1305 through 1310
      removed outlier: 3.558A  pdb=" N   LEU A1309 " --> pdb=" O   ASP A1305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1339 through 1346
    Processing sheet with id=AA1, first strand: chain 'B' and resid 98 through 99
      removed outlier: 6.949A  pdb=" N   LEU B  98 " --> pdb=" O   TYR B  73 " (cutoff:3.500A)
      removed outlier: 5.645A  pdb=" N   LEU B  75 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   VAL B  50 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 8.129A  pdb=" N   LEU B  76 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   ASP B  52 " --> pdb=" O   LEU B  76 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA B 206 " --> pdb=" O   LEU B 244 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   GLU B 246 " --> pdb=" O   LEU B 204 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   LEU B 204 " --> pdb=" O   GLU B 246 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   ASP B 248 " --> pdb=" O   THR B 202 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   THR B 202 " --> pdb=" O   ASP B 248 " (cutoff:3.500A)
      removed outlier: 8.741A  pdb=" N   ILE B 227 " --> pdb=" O   LYS B 203 " (cutoff:3.500A)
      removed outlier: 7.753A  pdb=" N   ILE B 205 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 529 through 530
    Processing sheet with id=AA3, first strand: chain 'A' and resid 613 through 619
    Processing sheet with id=AA4, first strand: chain 'A' and resid 734 through 736
    Processing sheet with id=AA5, first strand: chain 'A' and resid 822 through 824
    Processing sheet with id=AA6, first strand: chain 'A' and resid 855 through 856
    Processing sheet with id=AA7, first strand: chain 'A' and resid 942 through 944
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1086 through 1088
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1109 through 1111
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1128 through 1131
      removed outlier: 3.679A  pdb=" N   ILE A1139 " --> pdb=" O   LYS A1128 " (cutoff:3.500A)

    536 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
      49 stacking parallelities
  Total time for adding SS restraints: 5.35

  Time building geometry restraints manager: 3.45 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2672
        1.33 -     1.45: 2719
        1.45 -     1.57: 6243
        1.57 -     1.69: 141
        1.69 -     1.81: 60
  Bond restraints: 11835
  Sorted by residual:
  bond pdb=" O3'  DT T  20 "
       pdb=" P    DT T  21 "
    ideal  model  delta    sigma   weight residual
    1.607  1.704 -0.097 1.50e-02 4.44e+03 4.21e+01
  bond pdb=" C1'  DA N 132 "
       pdb=" N9   DA N 132 "
    ideal  model  delta    sigma   weight residual
    1.460  1.374  0.086 2.00e-02 2.50e+03 1.87e+01
  bond pdb=" O3'  DC T  11 "
       pdb=" P    DA T  12 "
    ideal  model  delta    sigma   weight residual
    1.607  1.663 -0.056 1.50e-02 4.44e+03 1.38e+01
  bond pdb=" N   VAL A 627 "
       pdb=" CA  VAL A 627 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.18e-02 7.18e+03 9.42e+00
  bond pdb=" N   LYS A1007 "
       pdb=" CA  LYS A1007 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.10e-02 8.26e+03 8.53e+00
  ... (remaining 11830 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.01: 16166
        3.01 -     6.01: 162
        6.01 -     9.02: 14
        9.02 -    12.02: 4
       12.02 -    15.03: 2
  Bond angle restraints: 16348
  Sorted by residual:
  angle pdb=" C5'  DC T  25 "
        pdb=" C4'  DC T  25 "
        pdb=" O4'  DC T  25 "
      ideal   model   delta    sigma   weight residual
     109.40  118.99   -9.59 1.50e+00 4.44e-01 4.09e+01
  angle pdb=" C   TYR A 499 "
        pdb=" CA  TYR A 499 "
        pdb=" CB  TYR A 499 "
      ideal   model   delta    sigma   weight residual
     110.44  101.95    8.49 1.68e+00 3.54e-01 2.55e+01
  angle pdb=" PA  GTP C 201 "
        pdb=" O3A GTP C 201 "
        pdb=" PB  GTP C 201 "
      ideal   model   delta    sigma   weight residual
     120.50  135.53  -15.03 3.00e+00 1.11e-01 2.51e+01
  angle pdb=" C3'  DT T  20 "
        pdb=" O3'  DT T  20 "
        pdb=" P    DT T  21 "
      ideal   model   delta    sigma   weight residual
     120.20  112.88    7.32 1.50e+00 4.44e-01 2.38e+01
  angle pdb=" O3'  DA N 131 "
        pdb=" C3'  DA N 131 "
        pdb=" C2'  DA N 131 "
      ideal   model   delta    sigma   weight residual
     111.50  104.99    6.51 1.50e+00 4.44e-01 1.89e+01
  ... (remaining 16343 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.60: 6485
       29.60 -    59.19: 447
       59.19 -    88.78: 37
       88.78 -   118.38: 3
      118.38 -   147.97: 4
  Dihedral angle restraints: 6976
    sinusoidal: 3332
      harmonic: 3644
  Sorted by residual:
  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  -30.76   54.76     1      8.00e+00 1.56e-02 6.35e+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   93.88   53.12     1      8.00e+00 1.56e-02 6.00e+01
  dihedral pdb=" C4'   G C 108 "
           pdb=" C3'   G C 108 "
           pdb=" C2'   G C 108 "
           pdb=" C1'   G C 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   13.18  -48.18     1      8.00e+00 1.56e-02 5.00e+01
  ... (remaining 6973 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.105: 1731
       0.105 -    0.209: 70
       0.209 -    0.314: 8
       0.314 -    0.418: 1
       0.418 -    0.523: 2
  Chirality restraints: 1812
  Sorted by residual:
  chirality pdb=" P    DT T  41 "
            pdb=" OP1  DT T  41 "
            pdb=" OP2  DT T  41 "
            pdb=" O5'  DT T  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.87   -0.52 2.00e-01 2.50e+01 6.83e+00
  chirality pdb=" P    DT N 111 "
            pdb=" OP1  DT N 111 "
            pdb=" OP2  DT N 111 "
            pdb=" O5'  DT N 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.84   -0.50 2.00e-01 2.50e+01 6.24e+00
  chirality pdb=" P     G C 102 "
            pdb=" OP1   G C 102 "
            pdb=" OP2   G C 102 "
            pdb=" O5'   G C 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.81   -0.40 2.00e-01 2.50e+01 3.97e+00
  ... (remaining 1809 not shown)

  Planarity restraints: 1833
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A1350 "   -0.008 2.00e-02 2.50e+03   1.31e-02 3.02e+00
        pdb=" CG  PHE A1350 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 PHE A1350 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD2 PHE A1350 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE A1350 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE A1350 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE A1350 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A1337 "    0.008 2.00e-02 2.50e+03   1.62e-02 2.64e+00
        pdb=" C   ASP A1337 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   ASP A1337 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PHE A1338 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT T  15 "    0.016 2.00e-02 2.50e+03   8.85e-03 1.96e+00
        pdb=" N1   DT T  15 "    0.006 2.00e-02 2.50e+03
        pdb=" C2   DT T  15 "   -0.004 2.00e-02 2.50e+03
        pdb=" O2   DT T  15 "   -0.011 2.00e-02 2.50e+03
        pdb=" N3   DT T  15 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DT T  15 "    0.002 2.00e-02 2.50e+03
        pdb=" O4   DT T  15 "    0.014 2.00e-02 2.50e+03
        pdb=" C5   DT T  15 "   -0.007 2.00e-02 2.50e+03
        pdb=" C7   DT T  15 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DT T  15 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1830 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 751
        2.73 -     3.27: 11289
        3.27 -     3.82: 19694
        3.82 -     4.36: 22850
        4.36 -     4.90: 37585
  Nonbonded interactions: 92169
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 842 "
            pdb=" OG  SER A 845 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OG1 THR A1132 "
            pdb=" O   GLN A1135 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   PRO B 102 "
            pdb=" OH  TYR B 108 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OE2 GLU A1125 "
            pdb=" OG  SER A1140 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OG  SER B 124 "
            pdb=" OD1 ASP B 126 "
     model   vdw
     2.307 3.040
  ... (remaining 92164 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:             0.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     31.770
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.097  11836  Z= 0.255
  Angle     :  0.774  15.031  16348  Z= 0.437
  Chirality :  0.053   0.523   1812
  Planarity :  0.004   0.034   1833
  Dihedral  : 18.428 147.972   4614
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.24), residues: 1238
  helix:  1.75 (0.20), residues: 677
  sheet: -0.61 (0.49), residues: 110
  loop : -0.42 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 159 
 HIS   0.007   0.001   HIS A 943 
 PHE   0.028   0.001   PHE A1350 
 TYR   0.016   0.001   TYR A 496 
 ARG   0.004   0.000   ARG A1151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14963 (  595)
  hydrogen bonds       : angle       5.94133 ( 1642)
  covalent geometry    : bond        0.00484 (11835)
  covalent geometry    : angle       0.77365 (16348)
  Misc. bond           : bond        0.06276 (    1)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 1.110 
Fit side-chains
   revert: symmetry clash
REVERT: B   39 THR cc_start: 0.8684 (p) cc_final: 0.8133 (t)
REVERT: B  209 ASP cc_start: 0.8343 (t0) cc_final: 0.8111 (t0)
REVERT: B  329 MET cc_start: 0.7504 (tpp) cc_final: 0.7055 (tpp)
REVERT: A  796 ASP cc_start: 0.8136 (m-30) cc_final: 0.7778 (m-30)
REVERT: A  926 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7724 (tm-30)
REVERT: A  962 GLU cc_start: 0.8024 (tp30) cc_final: 0.7771 (tp30)
REVERT: A 1007 LYS cc_start: 0.7761 (pttt) cc_final: 0.7502 (pttt)
REVERT: A 1197 ASP cc_start: 0.8267 (m-30) cc_final: 0.8063 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.2258
  time to fit residues: 56.1347
Evaluate side-chains
  137 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 54 optimal weight:   10.0000
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:   20.0000
   chunk 52 optimal weight:   20.0000
   chunk 101 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 75 optimal weight:    0.0020
   chunk 117 optimal weight:   50.0000
   overall best weight:    2.9996

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

Flipped N/Q/H residues before XYZ refinement:
B 308 ASN
A 520 ASN
A 791 ASN
A 925 ASN
A1070 HIS
A1129 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.129124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.095998 restraints weight = 20614.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.099075 restraints weight = 11149.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.101074 restraints weight = 7868.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.1183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  11836  Z= 0.159
  Angle     :  0.586   8.774  16348  Z= 0.312
  Chirality :  0.040   0.154   1812
  Planarity :  0.004   0.035   1833
  Dihedral  : 20.446 154.555   2195
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  7.97 %
    Favored  : 90.53 %
  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:  1.23 (0.24), residues: 1238
  helix:  1.86 (0.20), residues: 675
  sheet: -0.56 (0.45), residues: 124
  loop : -0.36 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 908 
 HIS   0.004   0.001   HIS A1188 
 PHE   0.016   0.001   PHE A1350 
 TYR   0.026   0.001   TYR A 496 
 ARG   0.003   0.000   ARG A 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04405 (  595)
  hydrogen bonds       : angle       4.31632 ( 1642)
  covalent geometry    : bond        0.00354 (11835)
  covalent geometry    : angle       0.58580 (16348)
  Misc. bond           : bond        0.00008 (    1)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 150
  time to evaluate  : 1.211 
Fit side-chains
   revert: symmetry clash
REVERT: B  209 ASP cc_start: 0.8247 (t0) cc_final: 0.7924 (t0)
REVERT: B  329 MET cc_start: 0.7652 (tpp) cc_final: 0.7248 (tpp)
REVERT: A  533 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8284 (ttp-170)
REVERT: A  796 ASP cc_start: 0.8196 (m-30) cc_final: 0.7870 (m-30)
REVERT: A  905 ASP cc_start: 0.8212 (m-30) cc_final: 0.7914 (t0)
REVERT: A  962 GLU cc_start: 0.8103 (tp30) cc_final: 0.7740 (tp30)
REVERT: A 1078 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7174 (tm-30)
REVERT: A 1259 LEU cc_start: 0.8107 (tt) cc_final: 0.7609 (mt)
  outliers start: 16
  outliers final: 12
  residues processed: 161
  average time/residue: 0.2306
  time to fit residues: 53.7390
Evaluate side-chains
  143 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  925 ASN
Chi-restraints excluded: chain A residue  931 ASP
Chi-restraints excluded: chain A residue  951 LEU
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1205 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 26 optimal weight:    9.9990
   chunk 18 optimal weight:   10.0000
   chunk 99 optimal weight:   30.0000
   chunk 42 optimal weight:    0.9990
   chunk 29 optimal weight:    7.9990
   chunk 24 optimal weight:   10.0000
   chunk 57 optimal weight:    7.9990
   chunk 61 optimal weight:   10.0000
   chunk 98 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
B  44 HIS
B 308 ASN
A 791 ASN
A 925 ASN
A1036 GLN
A1070 HIS
A1129 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.126989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.093600 restraints weight = 20714.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.096512 restraints weight = 11380.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.098373 restraints weight = 8160.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.1432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  11836  Z= 0.209
  Angle     :  0.600   9.379  16348  Z= 0.317
  Chirality :  0.041   0.154   1812
  Planarity :  0.004   0.034   1833
  Dihedral  : 20.413 162.813   2195
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  :  9.84 %
    Favored  : 87.72 %
  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:  1.07 (0.24), residues: 1238
  helix:  1.72 (0.20), residues: 679
  sheet: -0.59 (0.45), residues: 124
  loop : -0.44 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 908 
 HIS   0.004   0.001   HIS A1188 
 PHE   0.016   0.001   PHE A1350 
 TYR   0.024   0.002   TYR A 496 
 ARG   0.006   0.000   ARG A 533 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04444 (  595)
  hydrogen bonds       : angle       4.36028 ( 1642)
  covalent geometry    : bond        0.00478 (11835)
  covalent geometry    : angle       0.60005 (16348)
  Misc. bond           : bond        0.00021 (    1)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 137
  time to evaluate  : 1.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 ILE cc_start: 0.7318 (mm) cc_final: 0.6983 (mp)
REVERT: B  141 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7637 (tm-30)
REVERT: B  209 ASP cc_start: 0.8254 (t0) cc_final: 0.7958 (t0)
REVERT: B  329 MET cc_start: 0.7638 (tpp) cc_final: 0.7258 (tpp)
REVERT: A  796 ASP cc_start: 0.8189 (m-30) cc_final: 0.7889 (m-30)
REVERT: A  905 ASP cc_start: 0.8136 (m-30) cc_final: 0.7902 (t0)
REVERT: A  962 GLU cc_start: 0.8107 (tp30) cc_final: 0.7769 (tp30)
REVERT: A 1015 GLN cc_start: 0.8064 (mm110) cc_final: 0.7813 (mm-40)
REVERT: A 1078 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7116 (tm-30)
REVERT: A 1259 LEU cc_start: 0.8097 (tt) cc_final: 0.7580 (mp)
  outliers start: 26
  outliers final: 20
  residues processed: 154
  average time/residue: 0.2227
  time to fit residues: 50.1457
Evaluate side-chains
  146 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  315 THR
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  652 HIS
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  665 ILE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  925 ASN
Chi-restraints excluded: chain A residue  931 ASP
Chi-restraints excluded: chain A residue  951 LEU
Chi-restraints excluded: chain A residue 1021 VAL
Chi-restraints excluded: chain A residue 1036 GLN
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1205 LEU
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1350 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 114 optimal weight:    8.9990
   chunk 103 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 118 optimal weight:   20.0000
   chunk 109 optimal weight:   10.0000
   chunk 91 optimal weight:    9.9990
   chunk 36 optimal weight:    8.9990
   chunk 123 optimal weight:   20.0000
   chunk 70 optimal weight:    0.9980
   chunk 40 optimal weight:   10.0000
   chunk 53 optimal weight:    9.9990
   overall best weight:    4.9986

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

Flipped N/Q/H residues before XYZ refinement:
** B  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 ASN
A 925 ASN
A1070 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.127094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.093610 restraints weight = 20626.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.096531 restraints weight = 11362.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.098404 restraints weight = 8141.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11836  Z= 0.189
  Angle     :  0.589  12.511  16348  Z= 0.311
  Chirality :  0.040   0.170   1812
  Planarity :  0.004   0.034   1833
  Dihedral  : 20.339 171.688   2195
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 11.72 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.24), residues: 1238
  helix:  1.63 (0.19), residues: 683
  sheet: -0.63 (0.45), residues: 128
  loop : -0.48 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 908 
 HIS   0.004   0.001   HIS A1188 
 PHE   0.016   0.001   PHE A1350 
 TYR   0.014   0.001   TYR A 496 
 ARG   0.007   0.000   ARG A 533 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04283 (  595)
  hydrogen bonds       : angle       4.32241 ( 1642)
  covalent geometry    : bond        0.00433 (11835)
  covalent geometry    : angle       0.58935 (16348)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 1.096 
Fit side-chains
   revert: symmetry clash
REVERT: B  128 ILE cc_start: 0.7240 (mm) cc_final: 0.6922 (mp)
REVERT: B  141 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7643 (tm-30)
REVERT: B  209 ASP cc_start: 0.8287 (t0) cc_final: 0.7977 (t0)
REVERT: B  329 MET cc_start: 0.7677 (tpp) cc_final: 0.7305 (tpp)
REVERT: A  533 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8287 (ttp-170)
REVERT: A  796 ASP cc_start: 0.8175 (m-30) cc_final: 0.7892 (m-30)
REVERT: A  905 ASP cc_start: 0.8143 (m-30) cc_final: 0.7928 (t0)
REVERT: A  962 GLU cc_start: 0.8110 (tp30) cc_final: 0.7791 (tp30)
REVERT: A 1259 LEU cc_start: 0.8108 (tt) cc_final: 0.7537 (mp)
  outliers start: 23
  outliers final: 14
  residues processed: 144
  average time/residue: 0.2319
  time to fit residues: 48.7355
Evaluate side-chains
  137 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 1.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  315 THR
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  652 HIS
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  925 ASN
Chi-restraints excluded: chain A residue  951 LEU
Chi-restraints excluded: chain A residue 1021 VAL
Chi-restraints excluded: chain A residue 1186 SER
Chi-restraints excluded: chain A residue 1205 LEU
Chi-restraints excluded: chain A residue 1296 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 93 optimal weight:    8.9990
   chunk 1 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 27 optimal weight:    8.9990
   chunk 117 optimal weight:   30.0000
   chunk 33 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 54 optimal weight:   10.0000
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 925 ASN
A1070 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.128355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.095029 restraints weight = 20443.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.097998 restraints weight = 11172.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.099910 restraints weight = 7983.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11836  Z= 0.142
  Angle     :  0.562  10.553  16348  Z= 0.296
  Chirality :  0.039   0.163   1812
  Planarity :  0.003   0.034   1833
  Dihedral  : 20.139 174.687   2195
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.03 %
    Favored  : 84.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.24), residues: 1238
  helix:  1.77 (0.20), residues: 683
  sheet: -0.53 (0.46), residues: 120
  loop : -0.46 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 908 
 HIS   0.003   0.001   HIS A 953 
 PHE   0.014   0.001   PHE A 826 
 TYR   0.015   0.001   TYR A 496 
 ARG   0.007   0.000   ARG A 533 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03941 (  595)
  hydrogen bonds       : angle       4.15085 ( 1642)
  covalent geometry    : bond        0.00319 (11835)
  covalent geometry    : angle       0.56163 (16348)
  Misc. bond           : bond        0.00020 (    1)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 139
  time to evaluate  : 1.252 
Fit side-chains
   revert: symmetry clash
REVERT: B  128 ILE cc_start: 0.7206 (mm) cc_final: 0.6888 (mp)
REVERT: B  141 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7628 (tm-30)
REVERT: B  329 MET cc_start: 0.7595 (tpp) cc_final: 0.7227 (tpp)
REVERT: A  533 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8375 (ttp-170)
REVERT: A  796 ASP cc_start: 0.8136 (m-30) cc_final: 0.7821 (m-30)
REVERT: A  905 ASP cc_start: 0.8142 (m-30) cc_final: 0.7928 (t0)
REVERT: A  962 GLU cc_start: 0.8094 (tp30) cc_final: 0.7761 (tp30)
REVERT: A 1259 LEU cc_start: 0.8085 (tt) cc_final: 0.7500 (mp)
  outliers start: 23
  outliers final: 16
  residues processed: 154
  average time/residue: 0.2260
  time to fit residues: 50.8304
Evaluate side-chains
  147 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  652 HIS
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  665 ILE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  925 ASN
Chi-restraints excluded: chain A residue  931 ASP
Chi-restraints excluded: chain A residue  951 LEU
Chi-restraints excluded: chain A residue 1021 VAL
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1205 LEU
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1350 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 127 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 70 optimal weight:    9.9990
   chunk 95 optimal weight:   20.0000
   chunk 92 optimal weight:    8.9990
   chunk 20 optimal weight:   20.0000
   chunk 97 optimal weight:    9.9990
   chunk 100 optimal weight:    9.9990
   chunk 91 optimal weight:    9.9990
   chunk 38 optimal weight:    6.9990
   chunk 86 optimal weight:    6.9990
   overall best weight:    8.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 258 ASN
** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 925 ASN
A1070 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.123952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.090834 restraints weight = 21093.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.093525 restraints weight = 12079.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.095231 restraints weight = 8834.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.067  11836  Z= 0.290
  Angle     :  0.673   8.654  16348  Z= 0.354
  Chirality :  0.043   0.184   1812
  Planarity :  0.004   0.034   1833
  Dihedral  : 20.139 144.761   2195
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.55 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 13.96 %
    Favored  : 83.32 %
  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:  0.69 (0.23), residues: 1238
  helix:  1.37 (0.19), residues: 682
  sheet: -0.74 (0.46), residues: 116
  loop : -0.56 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 908 
 HIS   0.006   0.001   HIS A1188 
 PHE   0.017   0.002   PHE A1349 
 TYR   0.029   0.002   TYR B 161 
 ARG   0.007   0.001   ARG A 533 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04906 (  595)
  hydrogen bonds       : angle       4.57043 ( 1642)
  covalent geometry    : bond        0.00669 (11835)
  covalent geometry    : angle       0.67287 (16348)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 135
  time to evaluate  : 1.128 
Fit side-chains
   revert: symmetry clash
REVERT: B   43 LYS cc_start: 0.8546 (ptmm) cc_final: 0.8187 (tptp)
REVERT: B  128 ILE cc_start: 0.7265 (mm) cc_final: 0.6940 (mp)
REVERT: B  141 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7794 (tm-30)
REVERT: B  329 MET cc_start: 0.7627 (tpp) cc_final: 0.7278 (tpp)
REVERT: A  533 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8485 (ttp-170)
REVERT: A  796 ASP cc_start: 0.8171 (m-30) cc_final: 0.7896 (m-30)
REVERT: A  905 ASP cc_start: 0.8198 (m-30) cc_final: 0.7930 (t0)
REVERT: A  962 GLU cc_start: 0.8157 (tp30) cc_final: 0.7868 (tp30)
REVERT: A 1176 GLU cc_start: 0.8602 (tp30) cc_final: 0.8362 (tp30)
  outliers start: 29
  outliers final: 19
  residues processed: 153
  average time/residue: 0.2291
  time to fit residues: 50.5820
Evaluate side-chains
  149 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  315 THR
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  665 ILE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  925 ASN
Chi-restraints excluded: chain A residue  931 ASP
Chi-restraints excluded: chain A residue  951 LEU
Chi-restraints excluded: chain A residue 1021 VAL
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1186 SER
Chi-restraints excluded: chain A residue 1271 PHE
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1350 PHE
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 46 optimal weight:    6.9990
   chunk 70 optimal weight:    6.9990
   chunk 112 optimal weight:    7.9990
   chunk 37 optimal weight:    5.9990
   chunk 101 optimal weight:    0.8980
   chunk 81 optimal weight:   10.0000
   chunk 105 optimal weight:    0.9990
   chunk 117 optimal weight:    9.9990
   chunk 74 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
B  66 ASN
** B  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 449 ASN
A 925 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.126782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.093533 restraints weight = 20760.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.096444 restraints weight = 11296.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.098277 restraints weight = 8066.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11836  Z= 0.167
  Angle     :  0.607  13.652  16348  Z= 0.318
  Chirality :  0.040   0.181   1812
  Planarity :  0.004   0.034   1833
  Dihedral  : 19.650 143.378   2195
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 14.53 %
    Favored  : 83.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.24), residues: 1238
  helix:  1.54 (0.20), residues: 682
  sheet: -0.53 (0.46), residues: 118
  loop : -0.59 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 908 
 HIS   0.005   0.001   HIS A 953 
 PHE   0.014   0.001   PHE A1350 
 TYR   0.029   0.001   TYR B 161 
 ARG   0.008   0.000   ARG A 533 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04235 (  595)
  hydrogen bonds       : angle       4.30926 ( 1642)
  covalent geometry    : bond        0.00382 (11835)
  covalent geometry    : angle       0.60703 (16348)
  Misc. bond           : bond        0.00057 (    1)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 1.116 
Fit side-chains
   revert: symmetry clash
REVERT: B   43 LYS cc_start: 0.8514 (ptmm) cc_final: 0.8175 (tptp)
REVERT: B  128 ILE cc_start: 0.7197 (mm) cc_final: 0.6879 (mp)
REVERT: B  141 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7758 (tm-30)
REVERT: B  329 MET cc_start: 0.7628 (tpp) cc_final: 0.7261 (tpp)
REVERT: A  533 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8339 (ttp-170)
REVERT: A  796 ASP cc_start: 0.8152 (m-30) cc_final: 0.7851 (m-30)
REVERT: A  856 LYS cc_start: 0.8218 (mmtp) cc_final: 0.8002 (mmmm)
REVERT: A  905 ASP cc_start: 0.8137 (m-30) cc_final: 0.7899 (t0)
REVERT: A  926 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7954 (tm-30)
REVERT: A  962 GLU cc_start: 0.8127 (tp30) cc_final: 0.7833 (tp30)
REVERT: A 1176 GLU cc_start: 0.8582 (tp30) cc_final: 0.8351 (tp30)
REVERT: A 1259 LEU cc_start: 0.7937 (tt) cc_final: 0.7292 (mp)
  outliers start: 25
  outliers final: 18
  residues processed: 152
  average time/residue: 0.2455
  time to fit residues: 53.3221
Evaluate side-chains
  151 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  652 HIS
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  665 ILE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  925 ASN
Chi-restraints excluded: chain A residue  931 ASP
Chi-restraints excluded: chain A residue  951 LEU
Chi-restraints excluded: chain A residue 1021 VAL
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1186 SER
Chi-restraints excluded: chain A residue 1296 THR
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 65 optimal weight:    0.9990
   chunk 124 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 64 optimal weight:    5.9990
   chunk 59 optimal weight:   10.0000
   chunk 85 optimal weight:    9.9990
   chunk 48 optimal weight:   20.0000
   chunk 114 optimal weight:    8.9990
   chunk 122 optimal weight:    5.9990
   chunk 95 optimal weight:    9.9990
   chunk 112 optimal weight:    0.7980
   overall best weight:    4.5588

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

Flipped N/Q/H residues before XYZ refinement:
B  66 ASN
A 925 ASN
A1070 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.126573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.093426 restraints weight = 20689.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.096300 restraints weight = 11315.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.098162 restraints weight = 8115.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  11836  Z= 0.182
  Angle     :  0.625  12.841  16348  Z= 0.324
  Chirality :  0.040   0.227   1812
  Planarity :  0.004   0.034   1833
  Dihedral  : 19.575 145.241   2195
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.65 %
    Favored  : 82.19 %
  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:  0.86 (0.24), residues: 1238
  helix:  1.53 (0.19), residues: 683
  sheet: -0.64 (0.45), residues: 124
  loop : -0.52 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 908 
 HIS   0.004   0.001   HIS A 953 
 PHE   0.016   0.001   PHE A1350 
 TYR   0.032   0.001   TYR B 161 
 ARG   0.008   0.000   ARG A 533 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04255 (  595)
  hydrogen bonds       : angle       4.30044 ( 1642)
  covalent geometry    : bond        0.00419 (11835)
  covalent geometry    : angle       0.62503 (16348)
  Misc. bond           : bond        0.00052 (    1)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
REVERT: B   43 LYS cc_start: 0.8511 (ptmm) cc_final: 0.8181 (tptp)
REVERT: B  128 ILE cc_start: 0.7139 (mm) cc_final: 0.6860 (mp)
REVERT: B  141 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7788 (tm-30)
REVERT: B  329 MET cc_start: 0.7607 (tpp) cc_final: 0.7238 (tpp)
REVERT: A  533 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8344 (ttp-170)
REVERT: A  796 ASP cc_start: 0.8145 (m-30) cc_final: 0.7854 (m-30)
REVERT: A  856 LYS cc_start: 0.8223 (mmtp) cc_final: 0.8002 (mmmm)
REVERT: A  905 ASP cc_start: 0.8152 (m-30) cc_final: 0.7903 (t0)
REVERT: A  962 GLU cc_start: 0.8163 (tp30) cc_final: 0.7887 (tp30)
REVERT: A 1078 GLU cc_start: 0.7434 (tm-30) cc_final: 0.6920 (tm-30)
REVERT: A 1176 GLU cc_start: 0.8554 (tp30) cc_final: 0.8332 (tp30)
REVERT: A 1259 LEU cc_start: 0.7923 (tt) cc_final: 0.7235 (mp)
  outliers start: 23
  outliers final: 18
  residues processed: 145
  average time/residue: 0.2369
  time to fit residues: 49.0834
Evaluate side-chains
  148 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 1.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  652 HIS
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  665 ILE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  925 ASN
Chi-restraints excluded: chain A residue  931 ASP
Chi-restraints excluded: chain A residue  951 LEU
Chi-restraints excluded: chain A residue 1021 VAL
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1186 SER
Chi-restraints excluded: chain A residue 1271 PHE
Chi-restraints excluded: chain A residue 1296 THR
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 64 optimal weight:   10.0000
   chunk 38 optimal weight:    9.9990
   chunk 108 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 113 optimal weight:    0.0000
   chunk 128 optimal weight:   10.0000
   chunk 81 optimal weight:    9.9990
   chunk 119 optimal weight:   20.0000
   chunk 53 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    3.3992

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

Flipped N/Q/H residues before XYZ refinement:
A 925 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.127649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.094504 restraints weight = 20734.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.097451 restraints weight = 11259.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.099357 restraints weight = 8020.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11836  Z= 0.156
  Angle     :  0.612  12.533  16348  Z= 0.318
  Chirality :  0.040   0.217   1812
  Planarity :  0.004   0.034   1833
  Dihedral  : 19.507 147.387   2195
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 15.93 %
    Favored  : 82.19 %
  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:  0.96 (0.24), residues: 1238
  helix:  1.61 (0.20), residues: 683
  sheet: -0.47 (0.47), residues: 118
  loop : -0.54 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 908 
 HIS   0.004   0.001   HIS A 953 
 PHE   0.017   0.001   PHE A1350 
 TYR   0.014   0.001   TYR A 496 
 ARG   0.008   0.000   ARG A 533 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04065 (  595)
  hydrogen bonds       : angle       4.22095 ( 1642)
  covalent geometry    : bond        0.00355 (11835)
  covalent geometry    : angle       0.61190 (16348)
  Misc. bond           : bond        0.00054 (    1)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 1.111 
Fit side-chains
   revert: symmetry clash
REVERT: B   43 LYS cc_start: 0.8406 (ptmm) cc_final: 0.8109 (tptp)
REVERT: B   72 GLN cc_start: 0.6251 (tt0) cc_final: 0.5962 (tt0)
REVERT: B  128 ILE cc_start: 0.7114 (mm) cc_final: 0.6824 (mp)
REVERT: B  141 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7765 (tm-30)
REVERT: B  209 ASP cc_start: 0.8310 (t0) cc_final: 0.7931 (t0)
REVERT: B  329 MET cc_start: 0.7585 (tpp) cc_final: 0.7217 (tpp)
REVERT: A  533 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8332 (ttp-170)
REVERT: A  796 ASP cc_start: 0.8148 (m-30) cc_final: 0.7855 (m-30)
REVERT: A  856 LYS cc_start: 0.8259 (mmtp) cc_final: 0.8026 (mmmm)
REVERT: A  905 ASP cc_start: 0.8148 (m-30) cc_final: 0.7900 (t0)
REVERT: A  926 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7908 (tm-30)
REVERT: A  962 GLU cc_start: 0.8149 (tp30) cc_final: 0.7873 (tp30)
REVERT: A 1259 LEU cc_start: 0.7929 (tt) cc_final: 0.7274 (mp)
  outliers start: 20
  outliers final: 18
  residues processed: 154
  average time/residue: 0.2407
  time to fit residues: 53.3672
Evaluate side-chains
  153 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 1.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  315 THR
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  652 HIS
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  925 ASN
Chi-restraints excluded: chain A residue  951 LEU
Chi-restraints excluded: chain A residue 1021 VAL
Chi-restraints excluded: chain A residue 1186 SER
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1271 PHE
Chi-restraints excluded: chain A residue 1296 THR
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 94 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 123 optimal weight:   20.0000
   chunk 111 optimal weight:   10.0000
   chunk 86 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 104 optimal weight:    7.9990
   chunk 68 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   chunk 27 optimal weight:    8.9990
   chunk 33 optimal weight:    7.9990
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 925 ASN
A1070 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.126704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.093329 restraints weight = 20735.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.096196 restraints weight = 11432.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.098009 restraints weight = 8220.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11836  Z= 0.189
  Angle     :  0.633  12.208  16348  Z= 0.329
  Chirality :  0.041   0.208   1812
  Planarity :  0.004   0.034   1833
  Dihedral  : 19.527 149.896   2195
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 16.03 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.24), residues: 1238
  helix:  1.55 (0.20), residues: 683
  sheet: -0.50 (0.47), residues: 118
  loop : -0.57 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 908 
 HIS   0.004   0.001   HIS A 953 
 PHE   0.025   0.001   PHE A1350 
 TYR   0.015   0.001   TYR A 496 
 ARG   0.008   0.000   ARG A 533 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04240 (  595)
  hydrogen bonds       : angle       4.28209 ( 1642)
  covalent geometry    : bond        0.00436 (11835)
  covalent geometry    : angle       0.63321 (16348)
  Misc. bond           : bond        0.00051 (    1)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 1.212 
Fit side-chains
   revert: symmetry clash
REVERT: B  128 ILE cc_start: 0.7133 (mm) cc_final: 0.6854 (mp)
REVERT: B  141 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7819 (tm-30)
REVERT: B  329 MET cc_start: 0.7603 (tpp) cc_final: 0.7227 (tpp)
REVERT: A  533 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8358 (ttp-170)
REVERT: A  796 ASP cc_start: 0.8141 (m-30) cc_final: 0.7849 (m-30)
REVERT: A  856 LYS cc_start: 0.8231 (mmtp) cc_final: 0.8026 (mmmm)
REVERT: A  905 ASP cc_start: 0.8137 (m-30) cc_final: 0.7895 (t0)
REVERT: A  926 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7947 (tm-30)
REVERT: A  962 GLU cc_start: 0.8154 (tp30) cc_final: 0.7894 (tp30)
REVERT: A 1078 GLU cc_start: 0.7435 (tm-30) cc_final: 0.6979 (tm-30)
REVERT: A 1259 LEU cc_start: 0.8005 (tt) cc_final: 0.7342 (mp)
  outliers start: 22
  outliers final: 16
  residues processed: 144
  average time/residue: 0.2437
  time to fit residues: 50.2132
Evaluate side-chains
  147 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  315 THR
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  652 HIS
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  665 ILE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  925 ASN
Chi-restraints excluded: chain A residue  931 ASP
Chi-restraints excluded: chain A residue  951 LEU
Chi-restraints excluded: chain A residue 1021 VAL
Chi-restraints excluded: chain A residue 1296 THR
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 23 optimal weight:    1.9990
   chunk 73 optimal weight:   10.0000
   chunk 82 optimal weight:    5.9990
   chunk 63 optimal weight:    7.9990
   chunk 66 optimal weight:    0.1980
   chunk 15 optimal weight:    7.9990
   chunk 24 optimal weight:    7.9990
   chunk 85 optimal weight:    9.9990
   chunk 125 optimal weight:   20.0000
   chunk 62 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    3.0388

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

Flipped N/Q/H residues before XYZ refinement:
A 925 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.127960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.094929 restraints weight = 20569.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.097866 restraints weight = 11221.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.099757 restraints weight = 7985.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11836  Z= 0.150
  Angle     :  0.617  12.215  16348  Z= 0.319
  Chirality :  0.040   0.203   1812
  Planarity :  0.004   0.035   1833
  Dihedral  : 19.444 152.170   2195
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 16.12 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.24), residues: 1238
  helix:  1.65 (0.20), residues: 683
  sheet: -0.59 (0.46), residues: 124
  loop : -0.46 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 908 
 HIS   0.004   0.001   HIS A 953 
 PHE   0.030   0.001   PHE A1350 
 TYR   0.015   0.001   TYR A 954 
 ARG   0.008   0.000   ARG A 533 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04017 (  595)
  hydrogen bonds       : angle       4.18539 ( 1642)
  covalent geometry    : bond        0.00343 (11835)
  covalent geometry    : angle       0.61715 (16348)
  Misc. bond           : bond        0.00056 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3347.57 seconds
wall clock time: 59 minutes 46.64 seconds (3586.64 seconds total)