Starting phenix.real_space_refine
on Sat Aug 23 10:13:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c5u_16443/08_2025/8c5u_16443.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c5u_16443/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c5u_16443/08_2025/8c5u_16443.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c5u_16443/08_2025/8c5u_16443.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c5u_16443/08_2025/8c5u_16443.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c5u_16443/08_2025/8c5u_16443.map"
  }
  resolution = 3.62
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.011
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 3, 'GLU:plan': 9, 'ASP:plan': 6, 'GLN:plan1': 2, 'ASN:plan1': 1}
          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: 2.41, per 1000 atoms: 0.21
  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: 0.75
  Conformation dependent library (CDL) restraints added in 453.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.96
  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: 1.95

  Time building geometry restraints manager: 1.06 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:             0.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     10.780
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.250
-------------------------------------------------------------------------------
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 : 7.75
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.004   0.000   ARG A1151 
 TYR   0.016   0.001   TYR A 496 
 PHE   0.028   0.001   PHE A1350 
 TRP   0.012   0.001   TRP B 159 
 HIS   0.007   0.001   HIS A 943 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 (11835)
  covalent geometry    : angle       0.77365 (16348)
  hydrogen bonds       : bond        0.14963 (  595)
  hydrogen bonds       : angle       5.94133 ( 1642)
  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  : 0.403 
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: 0.7779 (m-30)
REVERT: A  926 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7725 (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: 0.7501 (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: 0.0911
  time to fit residues: 23.1529
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  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:   30.0000
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   overall best weight:    4.5990

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.127554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.094404 restraints weight = 20876.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.097454 restraints weight = 11280.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.099385 restraints weight = 7958.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.100593 restraints weight = 6523.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.101224 restraints weight = 5821.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.1171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  11836  Z= 0.188
  Angle     :  0.608   8.843  16348  Z= 0.324
  Chirality :  0.041   0.156   1812
  Planarity :  0.004   0.034   1833
  Dihedral  : 20.489 153.410   2195
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  8.43 %
    Favored  : 90.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.24), residues: 1238
  helix:  1.74 (0.20), residues: 678
  sheet: -0.60 (0.45), residues: 124
  loop : -0.43 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 533 
 TYR   0.025   0.001   TYR A 496 
 PHE   0.019   0.001   PHE A1350 
 TRP   0.017   0.001   TRP A 908 
 HIS   0.004   0.001   HIS A1188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (11835)
  covalent geometry    : angle       0.60768 (16348)
  hydrogen bonds       : bond        0.04637 (  595)
  hydrogen bonds       : angle       4.43463 ( 1642)
  Misc. bond           : bond        0.00089 (    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
  164 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: B  209 ASP cc_start: 0.8254 (t0) cc_final: 0.7965 (t0)
REVERT: B  329 MET cc_start: 0.7611 (tpp) cc_final: 0.7255 (tpp)
REVERT: A  533 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8285 (ttp-170)
REVERT: A  796 ASP cc_start: 0.8208 (m-30) cc_final: 0.7891 (m-30)
REVERT: A  905 ASP cc_start: 0.8146 (m-30) cc_final: 0.7898 (t0)
REVERT: A  962 GLU cc_start: 0.8041 (tp30) cc_final: 0.7709 (tp30)
REVERT: A 1078 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7197 (tm-30)
REVERT: A 1197 ASP cc_start: 0.8397 (m-30) cc_final: 0.8187 (m-30)
REVERT: A 1259 LEU cc_start: 0.8147 (tt) cc_final: 0.7626 (mt)
  outliers start: 16
  outliers final: 10
  residues processed: 159
  average time/residue: 0.0889
  time to fit residues: 20.8307
Evaluate side-chains
  139 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 128
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
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  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 1205 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 75 optimal weight:    6.9990
   chunk 117 optimal weight:    0.0980
   chunk 125 optimal weight:   20.0000
   chunk 128 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 87 optimal weight:    9.9990
   chunk 71 optimal weight:   10.0000
   chunk 110 optimal weight:    0.6980
   chunk 127 optimal weight:   10.0000
   chunk 5 optimal weight:    8.9990
   overall best weight:    4.3586

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 791 ASN
A 925 ASN
A1036 GLN
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 = 0.3676 r_free = 0.3676 target = 0.127241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.093684 restraints weight = 20966.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.096779 restraints weight = 11303.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.098777 restraints weight = 7965.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.099965 restraints weight = 6513.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.100583 restraints weight = 5828.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.1454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  11836  Z= 0.176
  Angle     :  0.583   9.494  16348  Z= 0.308
  Chirality :  0.040   0.153   1812
  Planarity :  0.004   0.034   1833
  Dihedral  : 20.357 163.174   2195
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  :  9.84 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.24), residues: 1238
  helix:  1.76 (0.20), residues: 679
  sheet: -0.61 (0.45), residues: 124
  loop : -0.49 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 533 
 TYR   0.024   0.001   TYR A 496 
 PHE   0.014   0.001   PHE A1350 
 TRP   0.018   0.001   TRP B 235 
 HIS   0.003   0.001   HIS A1188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (11835)
  covalent geometry    : angle       0.58253 (16348)
  hydrogen bonds       : bond        0.04256 (  595)
  hydrogen bonds       : angle       4.29347 ( 1642)
  Misc. bond           : bond        0.00023 (    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
  159 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 ILE cc_start: 0.7273 (mm) cc_final: 0.6941 (mp)
REVERT: B  141 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7588 (tm-30)
REVERT: B  209 ASP cc_start: 0.8171 (t0) cc_final: 0.7869 (t0)
REVERT: B  329 MET cc_start: 0.7612 (tpp) cc_final: 0.7256 (tpp)
REVERT: A  533 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8312 (ttp-170)
REVERT: A  796 ASP cc_start: 0.8210 (m-30) cc_final: 0.7901 (m-30)
REVERT: A  962 GLU cc_start: 0.8103 (tp30) cc_final: 0.7772 (tp30)
REVERT: A  977 ASP cc_start: 0.7896 (t0) cc_final: 0.7685 (t0)
REVERT: A 1015 GLN cc_start: 0.8035 (mm110) cc_final: 0.7786 (mm-40)
REVERT: A 1078 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7018 (tm-30)
REVERT: A 1259 LEU cc_start: 0.8083 (tt) cc_final: 0.7567 (mp)
  outliers start: 25
  outliers final: 17
  residues processed: 149
  average time/residue: 0.0889
  time to fit residues: 19.4081
Evaluate side-chains
  144 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 65 optimal weight:    0.2980
   chunk 10 optimal weight:    8.9990
   chunk 4 optimal weight:    8.9990
   chunk 109 optimal weight:    0.5980
   chunk 42 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   chunk 121 optimal weight:    6.9990
   chunk 87 optimal weight:    5.9990
   chunk 126 optimal weight:   20.0000
   chunk 82 optimal weight:   10.0000
   overall best weight:    4.3786

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

Flipped N/Q/H residues before XYZ refinement:
B 275 ASN
** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 ASN
A 925 ASN
A1070 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.127155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.093592 restraints weight = 20898.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.096608 restraints weight = 11322.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.098567 restraints weight = 8041.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.099774 restraints weight = 6580.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.100046 restraints weight = 5863.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  11836  Z= 0.174
  Angle     :  0.578  12.226  16348  Z= 0.306
  Chirality :  0.040   0.164   1812
  Planarity :  0.004   0.034   1833
  Dihedral  : 20.258 172.539   2195
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 11.34 %
    Favored  : 86.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.24), residues: 1238
  helix:  1.70 (0.20), residues: 684
  sheet: -0.56 (0.48), residues: 116
  loop : -0.48 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 533 
 TYR   0.013   0.001   TYR A 496 
 PHE   0.013   0.001   PHE A 826 
 TRP   0.019   0.001   TRP A 908 
 HIS   0.003   0.001   HIS A1188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (11835)
  covalent geometry    : angle       0.57778 (16348)
  hydrogen bonds       : bond        0.04158 (  595)
  hydrogen bonds       : angle       4.24461 ( 1642)
  Misc. bond           : bond        0.00015 (    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
  157 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 129
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 ILE cc_start: 0.7107 (mm) cc_final: 0.6827 (mp)
REVERT: B  141 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7592 (tm-30)
REVERT: B  209 ASP cc_start: 0.8208 (t0) cc_final: 0.7892 (t0)
REVERT: B  329 MET cc_start: 0.7645 (tpp) cc_final: 0.7290 (tpp)
REVERT: A  796 ASP cc_start: 0.8199 (m-30) cc_final: 0.7894 (m-30)
REVERT: A  962 GLU cc_start: 0.8123 (tp30) cc_final: 0.7796 (tp30)
REVERT: A  977 ASP cc_start: 0.7889 (t0) cc_final: 0.7678 (t0)
REVERT: A 1259 LEU cc_start: 0.8100 (tt) cc_final: 0.7522 (mp)
  outliers start: 28
  outliers final: 20
  residues processed: 146
  average time/residue: 0.0909
  time to fit residues: 19.4414
Evaluate side-chains
  140 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
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  315 THR
Chi-restraints excluded: chain A residue  465 VAL
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 1321 MET
Chi-restraints excluded: chain A residue 1350 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 97 optimal weight:    9.9990
   chunk 51 optimal weight:   20.0000
   chunk 33 optimal weight:    2.9990
   chunk 2 optimal weight:    8.9990
   chunk 110 optimal weight:    9.9990
   chunk 9 optimal weight:    8.9990
   chunk 68 optimal weight:    9.9990
   chunk 72 optimal weight:   10.0000
   chunk 48 optimal weight:    6.9990
   overall best weight:    7.5990

-------------------------------------------------------------------------------
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
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 = 0.124334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.090756 restraints weight = 21062.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.093642 restraints weight = 11560.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.095507 restraints weight = 8282.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.096688 restraints weight = 6842.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.097300 restraints weight = 6108.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063  11836  Z= 0.262
  Angle     :  0.641  10.030  16348  Z= 0.338
  Chirality :  0.042   0.166   1812
  Planarity :  0.004   0.034   1833
  Dihedral  : 20.296 172.409   2195
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 12.56 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.23), residues: 1238
  helix:  1.46 (0.19), residues: 683
  sheet: -0.70 (0.47), residues: 116
  loop : -0.56 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 533 
 TYR   0.023   0.002   TYR B 161 
 PHE   0.017   0.002   PHE A1349 
 TRP   0.020   0.002   TRP A 908 
 HIS   0.006   0.001   HIS A1188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00605 (11835)
  covalent geometry    : angle       0.64059 (16348)
  hydrogen bonds       : bond        0.04695 (  595)
  hydrogen bonds       : angle       4.48860 ( 1642)
  Misc. bond           : bond        0.00003 (    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
  161 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 133
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: B  141 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7719 (tm-30)
REVERT: B  329 MET cc_start: 0.7626 (tpp) cc_final: 0.7288 (tpp)
REVERT: A  533 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8529 (ttp-170)
REVERT: A  796 ASP cc_start: 0.8200 (m-30) cc_final: 0.7874 (m-30)
REVERT: A  962 GLU cc_start: 0.8145 (tp30) cc_final: 0.7863 (tp30)
REVERT: A  977 ASP cc_start: 0.7878 (t0) cc_final: 0.7655 (t0)
REVERT: A 1259 LEU cc_start: 0.8098 (tt) cc_final: 0.7517 (mp)
  outliers start: 28
  outliers final: 19
  residues processed: 150
  average time/residue: 0.0924
  time to fit residues: 20.2631
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  : 0.332 
-------------------------------------------------------------------------------
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  315 THR
Chi-restraints excluded: chain A residue  465 VAL
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 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 1351 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 40 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9990
   chunk 61 optimal weight:    9.9990
   chunk 11 optimal weight:    0.5980
   chunk 120 optimal weight:   50.0000
   chunk 60 optimal weight:    6.9990
   chunk 94 optimal weight:   20.0000
   chunk 112 optimal weight:    1.9990
   chunk 118 optimal weight:    9.9990
   chunk 111 optimal weight:    5.9990
   overall best weight:    3.1188

-------------------------------------------------------------------------------
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
A 925 ASN
A1070 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.127367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.093712 restraints weight = 20854.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.096765 restraints weight = 11338.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.098698 restraints weight = 8028.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.099882 restraints weight = 6617.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.100362 restraints weight = 5906.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11836  Z= 0.148
  Angle     :  0.582  13.234  16348  Z= 0.304
  Chirality :  0.039   0.194   1812
  Planarity :  0.004   0.034   1833
  Dihedral  : 19.859 142.415   2195
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 13.87 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.24), residues: 1238
  helix:  1.68 (0.20), residues: 682
  sheet: -0.63 (0.45), residues: 124
  loop : -0.57 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 533 
 TYR   0.024   0.001   TYR B 161 
 PHE   0.015   0.001   PHE A 826 
 TRP   0.023   0.001   TRP A 908 
 HIS   0.003   0.001   HIS A 953 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (11835)
  covalent geometry    : angle       0.58209 (16348)
  hydrogen bonds       : bond        0.04006 (  595)
  hydrogen bonds       : angle       4.20461 ( 1642)
  Misc. bond           : bond        0.00034 (    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
  168 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 140
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: B   66 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7383 (m-40)
REVERT: B  128 ILE cc_start: 0.7066 (mm) cc_final: 0.6783 (mp)
REVERT: B  141 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7632 (tm-30)
REVERT: B  329 MET cc_start: 0.7615 (tpp) cc_final: 0.7261 (tpp)
REVERT: A  533 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8347 (ttp-170)
REVERT: A  796 ASP cc_start: 0.8222 (m-30) cc_final: 0.7879 (m-30)
REVERT: A  856 LYS cc_start: 0.8263 (mmtp) cc_final: 0.8027 (mmmm)
REVERT: A  962 GLU cc_start: 0.8129 (tp30) cc_final: 0.7824 (tp30)
REVERT: A  977 ASP cc_start: 0.7784 (t0) cc_final: 0.7556 (t0)
REVERT: A 1176 GLU cc_start: 0.8570 (tp30) cc_final: 0.8329 (tp30)
REVERT: A 1259 LEU cc_start: 0.8033 (tt) cc_final: 0.7461 (mp)
  outliers start: 28
  outliers final: 17
  residues processed: 158
  average time/residue: 0.0961
  time to fit residues: 21.8783
Evaluate side-chains
  152 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 ASN
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  175 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  652 HIS
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  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 1186 SER
Chi-restraints excluded: chain A residue 1187 VAL
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 45 optimal weight:   10.0000
   chunk 69 optimal weight:    9.9990
   chunk 38 optimal weight:    8.9990
   chunk 3 optimal weight:    7.9990
   chunk 66 optimal weight:   40.0000
   chunk 37 optimal weight:    9.9990
   chunk 54 optimal weight:    6.9990
   chunk 59 optimal weight:    9.9990
   chunk 47 optimal weight:    6.9990
   chunk 85 optimal weight:    9.9990
   chunk 114 optimal weight:   20.0000
   overall best weight:    8.1990

-------------------------------------------------------------------------------
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**
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 = 0.3629 r_free = 0.3629 target = 0.123861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.090286 restraints weight = 21104.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.093130 restraints weight = 11709.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.094973 restraints weight = 8456.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.095937 restraints weight = 6995.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.096692 restraints weight = 6316.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
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      :  0.006   0.068  11836  Z= 0.277
  Angle     :  0.675  11.759  16348  Z= 0.354
  Chirality :  0.043   0.198   1812
  Planarity :  0.004   0.034   1833
  Dihedral  : 19.730 143.694   2195
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.28 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.23), residues: 1238
  helix:  1.41 (0.20), residues: 676
  sheet: -0.81 (0.47), residues: 116
  loop : -0.64 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 533 
 TYR   0.018   0.002   TYR A 954 
 PHE   0.016   0.002   PHE A1349 
 TRP   0.023   0.002   TRP A 908 
 HIS   0.005   0.001   HIS A 943 

Details of bonding type rmsd
  covalent geometry    : bond        0.00643 (11835)
  covalent geometry    : angle       0.67534 (16348)
  hydrogen bonds       : bond        0.04823 (  595)
  hydrogen bonds       : angle       4.50896 ( 1642)
  Misc. bond           : bond        0.00047 (    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
  147 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: B  141 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7821 (tm-30)
REVERT: B  209 ASP cc_start: 0.8165 (t0) cc_final: 0.7749 (t0)
REVERT: B  329 MET cc_start: 0.7616 (tpp) cc_final: 0.7278 (tpp)
REVERT: A  533 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8453 (ttp-170)
REVERT: A  796 ASP cc_start: 0.8198 (m-30) cc_final: 0.7842 (m-30)
REVERT: A  962 GLU cc_start: 0.8151 (tp30) cc_final: 0.7889 (tp30)
REVERT: A 1176 GLU cc_start: 0.8610 (tp30) cc_final: 0.8356 (tp30)
  outliers start: 22
  outliers final: 17
  residues processed: 138
  average time/residue: 0.0947
  time to fit residues: 18.7821
Evaluate side-chains
  142 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
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  315 THR
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  551 VAL
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  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 1162 ILE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9980
   chunk 47 optimal weight:    6.9990
   chunk 105 optimal weight:    1.9990
   chunk 63 optimal weight:    8.9990
   chunk 71 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 121 optimal weight:    7.9990
   chunk 58 optimal weight:    8.9990
   chunk 94 optimal weight:    0.8980
   chunk 48 optimal weight:   10.0000
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** B  72 GLN ** 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 = 0.3694 r_free = 0.3694 target = 0.128655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.095192 restraints weight = 20667.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.098248 restraints weight = 11248.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.100235 restraints weight = 7997.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.101420 restraints weight = 6559.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.102114 restraints weight = 5865.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11836  Z= 0.127
  Angle     :  0.597  11.990  16348  Z= 0.310
  Chirality :  0.039   0.187   1812
  Planarity :  0.004   0.035   1833
  Dihedral  : 19.477 146.086   2195
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 16.49 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.24), residues: 1238
  helix:  1.68 (0.20), residues: 682
  sheet: -0.48 (0.47), residues: 118
  loop : -0.64 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 533 
 TYR   0.014   0.001   TYR A 496 
 PHE   0.016   0.001   PHE A 826 
 TRP   0.028   0.001   TRP A 908 
 HIS   0.003   0.001   HIS A 953 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (11835)
  covalent geometry    : angle       0.59721 (16348)
  hydrogen bonds       : bond        0.03852 (  595)
  hydrogen bonds       : angle       4.13608 ( 1642)
  Misc. bond           : bond        0.00062 (    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
  162 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: B  128 ILE cc_start: 0.7050 (mm) cc_final: 0.6755 (mp)
REVERT: B  141 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7679 (tm-30)
REVERT: B  209 ASP cc_start: 0.8121 (t0) cc_final: 0.7709 (t0)
REVERT: B  329 MET cc_start: 0.7531 (tpp) cc_final: 0.7184 (tpp)
REVERT: A  533 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8313 (ttp-170)
REVERT: A  796 ASP cc_start: 0.8208 (m-30) cc_final: 0.7884 (m-30)
REVERT: A  856 LYS cc_start: 0.8257 (mmtp) cc_final: 0.8011 (mmmm)
REVERT: A  926 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7913 (tm-30)
REVERT: A  962 GLU cc_start: 0.8125 (tp30) cc_final: 0.7835 (tp30)
REVERT: A 1078 GLU cc_start: 0.7348 (tm-30) cc_final: 0.6823 (tm-30)
REVERT: A 1176 GLU cc_start: 0.8547 (tp30) cc_final: 0.8331 (tp30)
REVERT: A 1259 LEU cc_start: 0.7921 (tt) cc_final: 0.7270 (mp)
  outliers start: 18
  outliers final: 14
  residues processed: 155
  average time/residue: 0.0968
  time to fit residues: 21.2528
Evaluate side-chains
  149 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 HIS
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  652 HIS
Chi-restraints excluded: chain A residue  656 ILE
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  954 TYR
Chi-restraints excluded: chain A residue 1186 SER
Chi-restraints excluded: chain A residue 1205 LEU
Chi-restraints excluded: chain A residue 1271 PHE
Chi-restraints excluded: chain A residue 1296 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 51 optimal weight:   20.0000
   chunk 109 optimal weight:   10.0000
   chunk 23 optimal weight:    0.8980
   chunk 96 optimal weight:   20.0000
   chunk 1 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 65 optimal weight:    8.9990
   chunk 92 optimal weight:   20.0000
   chunk 74 optimal weight:    6.9990
   chunk 126 optimal weight:   20.0000
   overall best weight:    5.1788

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

Flipped N/Q/H residues before XYZ refinement:
B 308 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 = 0.3660 r_free = 0.3660 target = 0.126134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.092551 restraints weight = 20672.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.095504 restraints weight = 11353.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.097411 restraints weight = 8103.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.098595 restraints weight = 6669.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.099241 restraints weight = 5952.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  11836  Z= 0.197
  Angle     :  0.620  11.044  16348  Z= 0.324
  Chirality :  0.041   0.226   1812
  Planarity :  0.004   0.034   1833
  Dihedral  : 19.545 148.439   2195
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 16.12 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.24), residues: 1238
  helix:  1.67 (0.20), residues: 683
  sheet: -0.54 (0.47), residues: 118
  loop : -0.68 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 533 
 TYR   0.029   0.002   TYR B 161 
 PHE   0.015   0.001   PHE A 826 
 TRP   0.027   0.001   TRP A 908 
 HIS   0.004   0.001   HIS A1188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 (11835)
  covalent geometry    : angle       0.61978 (16348)
  hydrogen bonds       : bond        0.04239 (  595)
  hydrogen bonds       : angle       4.25206 ( 1642)
  Misc. bond           : bond        0.00049 (    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
  159 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
REVERT: B   72 GLN cc_start: 0.6178 (tt0) cc_final: 0.5860 (tt0)
REVERT: B  128 ILE cc_start: 0.7099 (mm) cc_final: 0.6819 (mp)
REVERT: B  141 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7757 (tm-30)
REVERT: B  329 MET cc_start: 0.7619 (tpp) cc_final: 0.7262 (tpp)
REVERT: A  533 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8336 (ttp-170)
REVERT: A  796 ASP cc_start: 0.8176 (m-30) cc_final: 0.7860 (m-30)
REVERT: A  856 LYS cc_start: 0.8263 (mmtp) cc_final: 0.8003 (mmmm)
REVERT: A  926 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7915 (tm-30)
REVERT: A  962 GLU cc_start: 0.8154 (tp30) cc_final: 0.7889 (tp30)
REVERT: A 1176 GLU cc_start: 0.8585 (tp30) cc_final: 0.8363 (tp30)
REVERT: A 1259 LEU cc_start: 0.7941 (tt) cc_final: 0.7281 (mp)
  outliers start: 24
  outliers final: 18
  residues processed: 148
  average time/residue: 0.0973
  time to fit residues: 20.4976
Evaluate side-chains
  152 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 HIS
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  551 VAL
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  925 ASN
Chi-restraints excluded: chain A residue  931 ASP
Chi-restraints excluded: chain A residue  951 LEU
Chi-restraints excluded: chain A residue  954 TYR
Chi-restraints excluded: chain A residue 1105 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 60 optimal weight:    8.9990
   chunk 71 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 61 optimal weight:    9.9990
   chunk 35 optimal weight:    7.9990
   chunk 113 optimal weight:   10.0000
   chunk 105 optimal weight:    2.9990
   chunk 7 optimal weight:    7.9990
   chunk 101 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 121 optimal weight:    9.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
B  66 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 = 0.3670 r_free = 0.3670 target = 0.126904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.093322 restraints weight = 20865.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.096288 restraints weight = 11397.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.098213 restraints weight = 8143.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.099348 restraints weight = 6706.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.099900 restraints weight = 5995.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11836  Z= 0.168
  Angle     :  0.613  11.110  16348  Z= 0.319
  Chirality :  0.040   0.220   1812
  Planarity :  0.004   0.034   1833
  Dihedral  : 19.514 150.917   2195
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 16.59 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.24), residues: 1238
  helix:  1.66 (0.20), residues: 683
  sheet: -0.45 (0.47), residues: 118
  loop : -0.70 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 533 
 TYR   0.019   0.001   TYR A 954 
 PHE   0.016   0.001   PHE A1350 
 TRP   0.029   0.001   TRP A 908 
 HIS   0.003   0.001   HIS A 943 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (11835)
  covalent geometry    : angle       0.61268 (16348)
  hydrogen bonds       : bond        0.04095 (  595)
  hydrogen bonds       : angle       4.20915 ( 1642)
  Misc. bond           : bond        0.00053 (    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
  152 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
REVERT: B  128 ILE cc_start: 0.7067 (mm) cc_final: 0.6784 (mp)
REVERT: B  141 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7744 (tm-30)
REVERT: B  209 ASP cc_start: 0.8246 (t0) cc_final: 0.7855 (t0)
REVERT: B  329 MET cc_start: 0.7604 (tpp) cc_final: 0.7244 (tpp)
REVERT: A  533 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8342 (ttp-170)
REVERT: A  796 ASP cc_start: 0.8165 (m-30) cc_final: 0.7861 (m-30)
REVERT: A  856 LYS cc_start: 0.8274 (mmtp) cc_final: 0.8011 (mmmm)
REVERT: A  926 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7919 (tm-30)
REVERT: A  962 GLU cc_start: 0.8156 (tp30) cc_final: 0.7891 (tp30)
REVERT: A 1078 GLU cc_start: 0.7382 (tm-30) cc_final: 0.6918 (tm-30)
REVERT: A 1259 LEU cc_start: 0.7935 (tt) cc_final: 0.7267 (mp)
  outliers start: 18
  outliers final: 16
  residues processed: 143
  average time/residue: 0.0950
  time to fit residues: 19.5965
Evaluate side-chains
  150 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 HIS
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain A residue  489 VAL
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  675 MET
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  954 TYR
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 24 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 54 optimal weight:    9.9990
   chunk 37 optimal weight:    6.9990
   chunk 104 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 125 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 21 optimal weight:   20.0000
   chunk 105 optimal weight:    0.9990
   overall best weight:    3.1388

-------------------------------------------------------------------------------
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 = 0.3680 r_free = 0.3680 target = 0.127604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.094039 restraints weight = 20911.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.097103 restraints weight = 11369.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.098978 restraints weight = 8045.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.100225 restraints weight = 6654.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.100901 restraints weight = 5942.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11836  Z= 0.151
  Angle     :  0.605  10.990  16348  Z= 0.314
  Chirality :  0.040   0.215   1812
  Planarity :  0.004   0.035   1833
  Dihedral  : 19.436 153.124   2195
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 16.59 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.24), residues: 1238
  helix:  1.68 (0.20), residues: 683
  sheet: -0.42 (0.47), residues: 118
  loop : -0.68 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 533 
 TYR   0.017   0.001   TYR A 954 
 PHE   0.025   0.001   PHE A1350 
 TRP   0.030   0.001   TRP A 908 
 HIS   0.003   0.001   HIS A 953 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (11835)
  covalent geometry    : angle       0.60461 (16348)
  hydrogen bonds       : bond        0.03961 (  595)
  hydrogen bonds       : angle       4.15368 ( 1642)
  Misc. bond           : bond        0.00055 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1634.87 seconds
wall clock time: 28 minutes 58.11 seconds (1738.11 seconds total)