Starting phenix.real_space_refine
on Sat Aug 23 09:48:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8atw_15665/08_2025/8atw_15665.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8atw_15665/08_2025/8atw_15665.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/8atw_15665/08_2025/8atw_15665.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8atw_15665/08_2025/8atw_15665.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8atw_15665/08_2025/8atw_15665.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8atw_15665/08_2025/8atw_15665.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=   0.000 sd=   0.013
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      64      5.49       5
     S      36      5.16       5
     C    7024      2.51       5
     N    1957      2.21       5
     O    2202      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: 11283
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2758
          Classifications: {'peptide': 336}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 19, 'TRANS': 316}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 7235
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 922, 7235
          Classifications: {'peptide': 922}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 44, 'TRANS': 877}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 167
          Unresolved non-hydrogen angles: 202
          Unresolved non-hydrogen dihedrals: 132
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 6, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 80
    Chain: "N"
      Number of atoms: 582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 582
          Classifications: {'DNA': 28}
          Link IDs: {'rna3p': 27}
    Chain: "T"
      Number of atoms: 567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 567
          Classifications: {'DNA': 28}
          Link IDs: {'rna3p': 27}
    Chain: "C"
      Number of atoms: 109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 109
          Classifications: {'RNA': 5}
          Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 1}
          Link IDs: {'rna3p': 4}
    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: 3.20, per 1000 atoms: 0.28
  Number of scatterers: 11283
  At special positions: 0
  Unit cell: (106.7, 114.46, 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      36     16.00
     P      64     15.00
     O    2202      8.00
     N    1957      7.00
     C    7024      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: 1.09
  Conformation dependent library (CDL) restraints added in 560.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2380

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 10 sheets defined
      59.3% alpha, 8.8% beta
      23 base pairs and 42 stacking pairs defined.
    Time for finding SS restraints: 1.35
  Creating SS restraints...
    Processing helix  chain 'B' and resid 7 through 12
    Processing helix  chain 'B' and resid 25 through 37
    Processing helix  chain 'B' and resid 44 through 47
    Processing helix  chain 'B' and resid 58 through 69
    Processing helix  chain 'B' and resid 79 through 91
    Processing helix  chain 'B' and resid 104 through 114
      removed outlier: 4.228A  pdb=" N   TYR B 108 " --> pdb=" O   ASP B 104 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   SER B 109 " --> pdb=" O   TRP B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 157
      removed outlier: 3.670A  pdb=" N   ILE B 147 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 164
      removed outlier: 3.772A  pdb=" N   PHE B 163 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
    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 215
    Processing helix  chain 'B' and resid 217 through 225
    Processing helix  chain 'B' and resid 230 through 234
      removed outlier: 4.028A  pdb=" N   GLU B 233 " --> pdb=" O   SER B 230 " (cutoff:3.500A)
      removed outlier: 4.113A  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: 3.602A  pdb=" N   VAL B 277 " --> pdb=" O   PRO B 273 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   MET B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 273 through 278'
    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
      removed outlier: 3.793A  pdb=" N   LEU B 299 " --> pdb=" O   ASP B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 320
    Processing helix  chain 'B' and resid 326 through 330
      removed outlier: 3.659A  pdb=" N   MET B 329 " --> pdb=" O   ASP B 326 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ASP B 330 " --> pdb=" O   ILE B 327 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 326 through 330'
    Processing helix  chain 'A' and resid 387 through 395
    Processing helix  chain 'A' and resid 397 through 421
      removed outlier: 3.747A  pdb=" N   GLN A 413 " --> pdb=" O   ASN A 409 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   ASP A 414 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   ARG A 415 " --> pdb=" O   PHE A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 441
    Processing helix  chain 'A' and resid 446 through 477
      Proline residue:  A 463  - end of helix
    Processing helix  chain 'A' and resid 488 through 501
      removed outlier: 4.062A  pdb=" N   LEU A 494 " --> pdb=" O   ASP A 490 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   GLY A 495 " --> pdb=" O   THR A 491 " (cutoff:3.500A)
      Proline residue:  A 498  - end of helix
    Processing helix  chain 'A' and resid 504 through 519
    Processing helix  chain 'A' and resid 531 through 553
      removed outlier: 3.646A  pdb=" N   ILE A 536 " --> pdb=" O   ALA A 532 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU A 552 " --> pdb=" O   SER A 548 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LYS A 553 " --> pdb=" O   GLU A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 612
    Processing helix  chain 'A' and resid 652 through 661
      removed outlier: 4.427A  pdb=" N   GLY A 661 " --> pdb=" O   ARG A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 717
    Processing helix  chain 'A' and resid 719 through 732
      removed outlier: 3.975A  pdb=" N   THR A 732 " --> pdb=" O   VAL A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 737 through 751
      removed outlier: 3.537A  pdb=" N   GLY A 751 " --> pdb=" O   VAL A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 775 through 813
    Processing helix  chain 'A' and resid 842 through 848
    Processing helix  chain 'A' and resid 860 through 873
    Processing helix  chain 'A' and resid 879 through 890
    Processing helix  chain 'A' and resid 890 through 900
    Processing helix  chain 'A' and resid 907 through 911
    Processing helix  chain 'A' and resid 913 through 930
    Processing helix  chain 'A' and resid 932 through 935
      removed outlier: 3.560A  pdb=" N   GLU A 935 " --> pdb=" O   ASN A 932 " (cutoff:3.500A)
      No H-bonds generated for '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
    Processing helix  chain 'A' and resid 977 through 994
    Processing helix  chain 'A' and resid 998 through 1005
    Processing helix  chain 'A' and resid 1009 through 1021
      removed outlier: 4.285A  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 1047 through 1066
    Processing helix  chain 'A' and resid 1068 through 1085
    Processing helix  chain 'A' and resid 1090 through 1094
      removed outlier: 3.656A  pdb=" N   LYS A1094 " --> pdb=" O   VAL A1091 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1149 through 1181
      Proline residue:  A1158  - end of helix
    Processing helix  chain 'A' and resid 1197 through 1214
    Processing helix  chain 'A' and resid 1216 through 1229
    Processing helix  chain 'A' and resid 1242 through 1260
      removed outlier: 3.642A  pdb=" N   GLN A1246 " --> pdb=" O   THR A1242 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   LYS A1247 " --> pdb=" O   ASP A1243 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU A1259 " --> pdb=" O   LEU A1255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1264 through 1280
    Processing helix  chain 'A' and resid 1283 through 1293
    Processing helix  chain 'A' and resid 1295 through 1302
      removed outlier: 3.984A  pdb=" N   ASP A1302 " --> pdb=" O   SER A1298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1305 through 1310
      removed outlier: 4.212A  pdb=" N   LEU A1309 " --> pdb=" O   ASP A1305 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLU A1310 " --> pdb=" O   LEU A1306 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1305 through 1310'
    Processing helix  chain 'A' and resid 1340 through 1346
      removed outlier: 4.003A  pdb=" N   ASN A1345 " --> pdb=" O   VAL A1342 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.277A  pdb=" N   TYR B  73 " --> pdb=" O   GLN B  96 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   LEU B  98 " --> pdb=" O   TYR B  73 " (cutoff:3.500A)
      removed outlier: 5.634A  pdb=" N   LEU B  75 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   SER B  74 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU B  76 " --> pdb=" O   ASP B  52 " (cutoff:3.500A)
      removed outlier: 5.251A  pdb=" N   LYS B 167 " --> pdb=" O   ASN B 129 " (cutoff:3.500A)
      removed outlier: 9.372A  pdb=" N   LYS B 131 " --> pdb=" O   LYS B 167 " (cutoff:3.500A)
      removed outlier: 13.135A  pdb=" N   LEU B 169 " --> pdb=" O   LYS B 131 " (cutoff:3.500A)
      removed outlier: 10.105A  pdb=" N   LEU B 133 " --> pdb=" O   LEU B 169 " (cutoff:3.500A)
      removed outlier: 12.528A  pdb=" N   TRP B 171 " --> pdb=" O   LEU B 133 " (cutoff:3.500A)
      removed outlier: 9.968A  pdb=" N   VAL B 135 " --> pdb=" O   TRP B 171 " (cutoff:3.500A)
      removed outlier: 11.572A  pdb=" N   ASN B 137 " --> pdb=" O   PRO B 173 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   VAL B 166 " --> pdb=" O   PRO B 249 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   ALA B 206 " --> pdb=" O   LEU B 244 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   GLU B 246 " --> pdb=" O   LEU B 204 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   LEU B 204 " --> pdb=" O   GLU B 246 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   ASP B 248 " --> pdb=" O   THR B 202 " (cutoff:3.500A)
      removed outlier: 5.527A  pdb=" N   THR B 202 " --> pdb=" O   ASP B 248 " (cutoff:3.500A)
      removed outlier: 9.616A  pdb=" N   ILE B 227 " --> pdb=" O   LYS B 203 " (cutoff:3.500A)
      removed outlier: 7.271A  pdb=" N   ILE B 205 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 528 through 530
    Processing sheet with id=AA3, first strand: chain 'A' and resid 613 through 619
      removed outlier: 3.641A  pdb=" N   GLY A 629 " --> pdb=" O   VAL A 616 " (cutoff:3.500A)
    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 1087 through 1088
      removed outlier: 3.530A  pdb=" N   VAL A1323 " --> pdb=" O   GLY A1236 " (cutoff:3.500A)
    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 1127 through 1131
      removed outlier: 3.517A  pdb=" N   ILE A1139 " --> pdb=" O   LYS A1128 " (cutoff:3.500A)

    540 hydrogen bonds defined for protein.
    1563 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      52 hydrogen bonds
      104 hydrogen bond angles
      0 basepair planarities
      23 basepair parallelities
      42 stacking parallelities
  Total time for adding SS restraints: 2.25

  Time building geometry restraints manager: 1.41 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: 2617
        1.33 -     1.45: 2671
        1.45 -     1.57: 6212
        1.57 -     1.69: 116
        1.69 -     1.81: 61
  Bond restraints: 11677
  Sorted by residual:
  bond pdb=" O3'  DT N 109 "
       pdb=" P    DA N 110 "
    ideal  model  delta    sigma   weight residual
    1.607  1.436  0.171 1.50e-02 4.44e+03 1.30e+02
  bond pdb=" C4'  DT T  20 "
       pdb=" O4'  DT T  20 "
    ideal  model  delta    sigma   weight residual
    1.450  1.621 -0.171 2.00e-02 2.50e+03 7.32e+01
  bond pdb=" C4'  DT T  21 "
       pdb=" O4'  DT T  21 "
    ideal  model  delta    sigma   weight residual
    1.450  1.568 -0.118 2.00e-02 2.50e+03 3.47e+01
  bond pdb=" O3'  DT T  12 "
       pdb=" P    DT T  13 "
    ideal  model  delta    sigma   weight residual
    1.607  1.690 -0.083 1.50e-02 4.44e+03 3.03e+01
  bond pdb=" O3'  DA T  27 "
       pdb=" P    DA T  28 "
    ideal  model  delta    sigma   weight residual
    1.607  1.539  0.068 1.50e-02 4.44e+03 2.03e+01
  ... (remaining 11672 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.78: 15885
        2.78 -     5.56: 178
        5.56 -     8.34: 19
        8.34 -    11.12: 6
       11.12 -    13.90: 6
  Bond angle restraints: 16094
  Sorted by residual:
  angle pdb=" C5'  DA T  34 "
        pdb=" C4'  DA T  34 "
        pdb=" O4'  DA T  34 "
      ideal   model   delta    sigma   weight residual
     109.40  123.30  -13.90 1.50e+00 4.44e-01 8.59e+01
  angle pdb=" O3'  DA T  28 "
        pdb=" C3'  DA T  28 "
        pdb=" C2'  DA T  28 "
      ideal   model   delta    sigma   weight residual
     111.50   98.72   12.78 1.50e+00 4.44e-01 7.25e+01
  angle pdb=" C5'  DT N 112 "
        pdb=" C4'  DT N 112 "
        pdb=" O4'  DT N 112 "
      ideal   model   delta    sigma   weight residual
     109.40  121.24  -11.84 1.50e+00 4.44e-01 6.23e+01
  angle pdb=" C5'  DT T  29 "
        pdb=" C4'  DT T  29 "
        pdb=" O4'  DT T  29 "
      ideal   model   delta    sigma   weight residual
     109.40  119.88  -10.48 1.50e+00 4.44e-01 4.88e+01
  angle pdb=" O4'  DT T  20 "
        pdb=" C4'  DT T  20 "
        pdb=" C3'  DT T  20 "
      ideal   model   delta    sigma   weight residual
     105.40   95.72    9.68 1.50e+00 4.44e-01 4.16e+01
  ... (remaining 16089 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.65: 6053
       21.65 -    43.30: 641
       43.30 -    64.95: 169
       64.95 -    86.60: 20
       86.60 -   108.26: 5
  Dihedral angle restraints: 6888
    sinusoidal: 3214
      harmonic: 3674
  Sorted by residual:
  dihedral pdb=" O5' GTP C 201 "
           pdb=" O3A GTP C 201 "
           pdb=" PA  GTP C 201 "
           pdb=" PB  GTP C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     274.12  165.87  108.26     1      2.00e+01 2.50e-03 3.15e+01
  dihedral pdb=" C8  GTP C 201 "
           pdb=" C1' GTP C 201 "
           pdb=" N9  GTP C 201 "
           pdb=" O4' GTP C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59    2.87  101.72     1      2.00e+01 2.50e-03 2.89e+01
  dihedral pdb=" CA  MET B 267 "
           pdb=" C   MET B 267 "
           pdb=" N   ILE B 268 "
           pdb=" CA  ILE B 268 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.14   18.86     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 6885 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.131: 1756
       0.131 -    0.262: 16
       0.262 -    0.393: 6
       0.393 -    0.524: 2
       0.524 -    0.655: 2
  Chirality restraints: 1782
  Sorted by residual:
  chirality pdb=" C4'  DT T  20 "
            pdb=" C5'  DT T  20 "
            pdb=" O4'  DT T  20 "
            pdb=" C3'  DT T  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -3.18    0.66 2.00e-01 2.50e+01 1.07e+01
  chirality pdb=" P    DG N 108 "
            pdb=" OP1  DG N 108 "
            pdb=" OP2  DG N 108 "
            pdb=" O5'  DG N 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.99   -0.65 2.00e-01 2.50e+01 1.04e+01
  chirality pdb=" C4'  DT T  29 "
            pdb=" C5'  DT T  29 "
            pdb=" O4'  DT T  29 "
            pdb=" C3'  DT T  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.02   -0.51 2.00e-01 2.50e+01 6.41e+00
  ... (remaining 1779 not shown)

  Planarity restraints: 1838
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA T  28 "   -0.022 2.00e-02 2.50e+03   1.21e-02 4.02e+00
        pdb=" N9   DA T  28 "    0.027 2.00e-02 2.50e+03
        pdb=" C8   DA T  28 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7   DA T  28 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5   DA T  28 "    0.004 2.00e-02 2.50e+03
        pdb=" C6   DA T  28 "   -0.001 2.00e-02 2.50e+03
        pdb=" N6   DA T  28 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1   DA T  28 "    0.004 2.00e-02 2.50e+03
        pdb=" C2   DA T  28 "   -0.010 2.00e-02 2.50e+03
        pdb=" N3   DA T  28 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DA T  28 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 272 "   -0.033 5.00e-02 4.00e+02   4.85e-02 3.77e+00
        pdb=" N   PRO B 273 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 273 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 273 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 119 "    0.024 5.00e-02 4.00e+02   3.70e-02 2.19e+00
        pdb=" N   PRO B 120 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B 120 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 120 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1835 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 828
        2.74 -     3.28: 11157
        3.28 -     3.82: 19479
        3.82 -     4.36: 22248
        4.36 -     4.90: 37648
  Nonbonded interactions: 91360
  Sorted by model distance:
  nonbonded pdb=" O   LEU B  23 "
            pdb=" OH  TYR B  29 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OG1 THR A1132 "
            pdb=" O   GLN A1135 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" NH2 ARG A1206 "
            pdb=" O   SER A1346 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" OD2 ASP A 775 "
            pdb=" OG  SER A 777 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   PRO B 102 "
            pdb=" OH  TYR B 108 "
     model   vdw
     2.283 3.040
  ... (remaining 91355 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:             0.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.860
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
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   0.171  11678  Z= 0.275
  Angle     :  0.737  13.899  16094  Z= 0.407
  Chirality :  0.054   0.655   1782
  Planarity :  0.004   0.049   1838
  Dihedral  : 18.135 108.255   4508
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: 1250
  helix:  1.59 (0.20), residues: 708
  sheet:  0.27 (0.56), residues: 85
  loop : -0.58 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 984 
 TYR   0.021   0.002   TYR A 979 
 PHE   0.020   0.001   PHE A1300 
 TRP   0.014   0.001   TRP B 159 
 HIS   0.004   0.001   HIS A1169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 (11677)
  covalent geometry    : angle       0.73670 (16094)
  hydrogen bonds       : bond        0.14427 (  592)
  hydrogen bonds       : angle       5.76474 ( 1667)
  Misc. bond           : bond        0.09025 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.432 
Fit side-chains
REVERT: B   52 ASP cc_start: 0.6643 (t70) cc_final: 0.6442 (t70)
REVERT: B   71 ARG cc_start: 0.7645 (ptp-110) cc_final: 0.7430 (ptt180)
REVERT: B  247 MET cc_start: 0.8059 (mmt) cc_final: 0.7852 (mmp)
REVERT: A  398 LEU cc_start: 0.8355 (mt) cc_final: 0.8045 (mt)
REVERT: A  402 LYS cc_start: 0.8556 (mptt) cc_final: 0.8352 (mptt)
REVERT: A  514 LEU cc_start: 0.8787 (mt) cc_final: 0.7974 (tp)
REVERT: A 1057 HIS cc_start: 0.6975 (m90) cc_final: 0.6355 (m90)
REVERT: A 1325 LEU cc_start: 0.8353 (mm) cc_final: 0.8106 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.1035
  time to fit residues: 31.1395
Evaluate side-chains
  153 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    0.5980
   chunk 124 optimal weight:   20.0000
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    9.9990
   chunk 91 optimal weight:   20.0000
   chunk 55 optimal weight:    9.9990
   chunk 35 optimal weight:    9.9990
   overall best weight:    5.5188

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

Flipped N/Q/H residues before XYZ refinement:
B 265 HIS
** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1129 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.141963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.111503 restraints weight = 18092.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.114993 restraints weight = 10010.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.117258 restraints weight = 6968.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.118758 restraints weight = 5584.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.119421 restraints weight = 4858.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.1260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.086  11678  Z= 0.217
  Angle     :  0.616   9.446  16094  Z= 0.326
  Chirality :  0.042   0.189   1782
  Planarity :  0.005   0.039   1838
  Dihedral  : 18.636 100.006   2081
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 10.16 %
    Favored  : 88.54 %
  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:  0.80 (0.24), residues: 1250
  helix:  1.45 (0.20), residues: 710
  sheet:  0.06 (0.44), residues: 129
  loop : -0.88 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 827 
 TYR   0.016   0.002   TYR A1229 
 PHE   0.019   0.002   PHE A1138 
 TRP   0.010   0.001   TRP A1110 
 HIS   0.007   0.001   HIS B 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 (11677)
  covalent geometry    : angle       0.61551 (16094)
  hydrogen bonds       : bond        0.05029 (  592)
  hydrogen bonds       : angle       4.59187 ( 1667)
  Misc. bond           : bond        0.00764 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 159
  time to evaluate  : 0.441 
Fit side-chains
REVERT: B   60 GLN cc_start: 0.7120 (tm-30) cc_final: 0.6730 (tm-30)
REVERT: A  922 PHE cc_start: 0.8502 (m-10) cc_final: 0.8141 (m-10)
REVERT: A 1057 HIS cc_start: 0.7021 (m90) cc_final: 0.6576 (m90)
  outliers start: 14
  outliers final: 11
  residues processed: 168
  average time/residue: 0.1031
  time to fit residues: 25.8281
Evaluate side-chains
  150 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 139
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  684 ASN
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1233 VAL
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 93 optimal weight:    5.9990
   chunk 92 optimal weight:    8.9990
   chunk 51 optimal weight:   10.0000
   chunk 9 optimal weight:    7.9990
   chunk 83 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 95 optimal weight:   20.0000
   chunk 64 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 21 optimal weight:    6.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.140145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.108630 restraints weight = 18310.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.112018 restraints weight = 10246.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.114294 restraints weight = 7278.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.115611 restraints weight = 5886.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.116733 restraints weight = 5188.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  11678  Z= 0.239
  Angle     :  0.620   9.693  16094  Z= 0.329
  Chirality :  0.042   0.173   1782
  Planarity :  0.005   0.039   1838
  Dihedral  : 18.740 104.636   2081
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.61 %
    Favored  : 84.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.60 (0.24), residues: 1250
  helix:  1.30 (0.19), residues: 711
  sheet: -0.06 (0.45), residues: 129
  loop : -0.98 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 827 
 TYR   0.018   0.002   TYR B 161 
 PHE   0.019   0.002   PHE A1138 
 TRP   0.014   0.001   TRP B  24 
 HIS   0.018   0.001   HIS B 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00551 (11677)
  covalent geometry    : angle       0.62041 (16094)
  hydrogen bonds       : bond        0.05104 (  592)
  hydrogen bonds       : angle       4.54376 ( 1667)
  Misc. bond           : bond        0.00033 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 152
  time to evaluate  : 0.423 
Fit side-chains
REVERT: B   60 GLN cc_start: 0.7352 (tm-30) cc_final: 0.6786 (tm-30)
REVERT: B  319 MET cc_start: 0.8305 (mmp) cc_final: 0.8095 (mmp)
REVERT: A 1057 HIS cc_start: 0.6877 (m90) cc_final: 0.6441 (m90)
REVERT: A 1096 PHE cc_start: 0.7546 (p90) cc_final: 0.7299 (p90)
  outliers start: 20
  outliers final: 15
  residues processed: 167
  average time/residue: 0.1018
  time to fit residues: 25.1057
Evaluate side-chains
  152 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  214 LYS
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  684 ASN
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1233 VAL
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1325 LEU
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 11 optimal weight:    0.4980
   chunk 103 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 31 optimal weight:    7.9990
   chunk 79 optimal weight:   20.0000
   chunk 53 optimal weight:    3.9990
   chunk 94 optimal weight:    7.9990
   chunk 93 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    2.4988

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

Flipped N/Q/H residues before XYZ refinement:
A 791 ASN
** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.143321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.111854 restraints weight = 18297.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.115450 restraints weight = 10136.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.117823 restraints weight = 7095.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.119275 restraints weight = 5696.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.120352 restraints weight = 4977.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11678  Z= 0.136
  Angle     :  0.547   8.749  16094  Z= 0.290
  Chirality :  0.039   0.190   1782
  Planarity :  0.004   0.040   1838
  Dihedral  : 18.530 104.957   2081
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 15.56 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.24), residues: 1250
  helix:  1.53 (0.20), residues: 698
  sheet:  0.32 (0.46), residues: 120
  loop : -0.95 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 984 
 TYR   0.025   0.002   TYR B 335 
 PHE   0.015   0.001   PHE A1300 
 TRP   0.014   0.001   TRP B  24 
 HIS   0.003   0.001   HIS A1163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (11677)
  covalent geometry    : angle       0.54705 (16094)
  hydrogen bonds       : bond        0.04208 (  592)
  hydrogen bonds       : angle       4.23879 ( 1667)
  Misc. bond           : bond        0.00042 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 163
  time to evaluate  : 0.456 
Fit side-chains
REVERT: B   60 GLN cc_start: 0.7257 (tm-30) cc_final: 0.6752 (tm-30)
REVERT: B   73 TYR cc_start: 0.8438 (t80) cc_final: 0.8180 (t80)
REVERT: B  329 MET cc_start: 0.6820 (mtm) cc_final: 0.6289 (mmm)
REVERT: A  529 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.7735 (ppp)
REVERT: A 1057 HIS cc_start: 0.6829 (m90) cc_final: 0.6391 (m90)
REVERT: A 1096 PHE cc_start: 0.7518 (p90) cc_final: 0.7190 (p90)
REVERT: A 1299 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8156 (tp)
  outliers start: 24
  outliers final: 18
  residues processed: 179
  average time/residue: 0.0982
  time to fit residues: 26.5406
Evaluate side-chains
  163 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 143
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  214 LYS
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  529 MET
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  867 ILE
Chi-restraints excluded: chain A residue  893 ASP
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1233 VAL
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1325 LEU
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 21 optimal weight:    8.9990
   chunk 53 optimal weight:    7.9990
   chunk 50 optimal weight:    7.9990
   chunk 31 optimal weight:    9.9990
   chunk 118 optimal weight:   20.0000
   chunk 92 optimal weight:    9.9990
   chunk 121 optimal weight:   20.0000
   chunk 90 optimal weight:    8.9990
   chunk 74 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 57 optimal weight:    6.9990
   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  72 GLN
B 265 HIS
** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 791 ASN
** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.137814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.106012 restraints weight = 18336.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.109390 restraints weight = 10457.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.111636 restraints weight = 7472.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.112967 restraints weight = 6061.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.113973 restraints weight = 5349.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.064  11678  Z= 0.291
  Angle     :  0.668   9.387  16094  Z= 0.354
  Chirality :  0.044   0.154   1782
  Planarity :  0.005   0.041   1838
  Dihedral  : 18.817 112.507   2081
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 17.71 %
    Favored  : 78.94 %
  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:  0.35 (0.23), residues: 1250
  helix:  1.13 (0.19), residues: 702
  sheet: -0.21 (0.45), residues: 121
  loop : -1.08 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 827 
 TYR   0.020   0.002   TYR B 161 
 PHE   0.024   0.002   PHE A1300 
 TRP   0.024   0.002   TRP B  24 
 HIS   0.009   0.001   HIS B 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00674 (11677)
  covalent geometry    : angle       0.66849 (16094)
  hydrogen bonds       : bond        0.05519 (  592)
  hydrogen bonds       : angle       4.61217 ( 1667)
  Misc. bond           : bond        0.00016 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 142
  time to evaluate  : 0.421 
Fit side-chains
REVERT: A  402 LYS cc_start: 0.8630 (mptt) cc_final: 0.8160 (mmtp)
REVERT: A  529 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.7921 (ppp)
REVERT: A  926 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7442 (mm-30)
REVERT: A 1096 PHE cc_start: 0.7554 (p90) cc_final: 0.7282 (p90)
REVERT: A 1170 MET cc_start: 0.8297 (tmm) cc_final: 0.8008 (tmm)
REVERT: A 1299 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8047 (tp)
  outliers start: 36
  outliers final: 24
  residues processed: 169
  average time/residue: 0.0922
  time to fit residues: 23.2749
Evaluate side-chains
  160 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 134
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 ASP
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  529 MET
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  684 ASN
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  893 ASP
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1233 VAL
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1325 LEU
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   chunk 124 optimal weight:    8.9990
   chunk 38 optimal weight:   20.0000
   chunk 78 optimal weight:    8.9990
   chunk 43 optimal weight:    7.9990
   chunk 98 optimal weight:    9.9990
   chunk 49 optimal weight:    8.9990
   chunk 32 optimal weight:    9.9990
   chunk 109 optimal weight:    1.9990
   chunk 70 optimal weight:    9.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 791 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.138617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.106875 restraints weight = 18222.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.110318 restraints weight = 10322.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.112540 restraints weight = 7337.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.114052 restraints weight = 5967.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.114992 restraints weight = 5214.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  11678  Z= 0.237
  Angle     :  0.625   9.817  16094  Z= 0.330
  Chirality :  0.042   0.168   1782
  Planarity :  0.005   0.045   1838
  Dihedral  : 18.797 115.264   2081
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 19.38 %
    Favored  : 77.63 %
  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:  0.37 (0.23), residues: 1250
  helix:  1.13 (0.19), residues: 703
  sheet: -0.06 (0.46), residues: 118
  loop : -1.09 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 493 
 TYR   0.019   0.002   TYR B 161 
 PHE   0.021   0.002   PHE A1300 
 TRP   0.023   0.002   TRP B  24 
 HIS   0.004   0.001   HIS B 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00548 (11677)
  covalent geometry    : angle       0.62465 (16094)
  hydrogen bonds       : bond        0.05080 (  592)
  hydrogen bonds       : angle       4.51285 ( 1667)
  Misc. bond           : bond        0.00027 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 147
  time to evaluate  : 0.426 
Fit side-chains
REVERT: B  329 MET cc_start: 0.6838 (mtm) cc_final: 0.6278 (mmm)
REVERT: A  402 LYS cc_start: 0.8632 (mptt) cc_final: 0.8137 (mmtp)
REVERT: A  529 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.7968 (ppp)
REVERT: A  926 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7422 (mm-30)
REVERT: A  930 MET cc_start: 0.7570 (ttm) cc_final: 0.7349 (ttt)
REVERT: A 1096 PHE cc_start: 0.7512 (p90) cc_final: 0.7116 (p90)
REVERT: A 1299 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8048 (tp)
  outliers start: 32
  outliers final: 24
  residues processed: 167
  average time/residue: 0.0881
  time to fit residues: 21.8276
Evaluate side-chains
  165 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  529 MET
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  684 ASN
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  893 ASP
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue 1025 THR
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1233 VAL
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1300 PHE
Chi-restraints excluded: chain A residue 1325 LEU
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 121 optimal weight:    0.7980
   chunk 119 optimal weight:   40.0000
   chunk 98 optimal weight:    6.9990
   chunk 8 optimal weight:    9.9990
   chunk 36 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 7 optimal weight:    2.9990
   chunk 82 optimal weight:   10.0000
   chunk 102 optimal weight:    4.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 791 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.141101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.109890 restraints weight = 17996.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.113367 restraints weight = 9980.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.115723 restraints weight = 7023.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.117154 restraints weight = 5645.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.118063 restraints weight = 4944.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074  11678  Z= 0.157
  Angle     :  0.579   8.921  16094  Z= 0.304
  Chirality :  0.039   0.172   1782
  Planarity :  0.004   0.051   1838
  Dihedral  : 18.612 115.746   2081
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 20.22 %
    Favored  : 76.89 %
  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:  0.62 (0.24), residues: 1250
  helix:  1.34 (0.20), residues: 703
  sheet: -0.06 (0.44), residues: 120
  loop : -0.96 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 984 
 TYR   0.018   0.002   TYR A 819 
 PHE   0.016   0.001   PHE A1300 
 TRP   0.016   0.001   TRP B  24 
 HIS   0.004   0.001   HIS B 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (11677)
  covalent geometry    : angle       0.57885 (16094)
  hydrogen bonds       : bond        0.04480 (  592)
  hydrogen bonds       : angle       4.29880 ( 1667)
  Misc. bond           : bond        0.00049 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 154
  time to evaluate  : 0.468 
Fit side-chains
REVERT: B  116 ARG cc_start: 0.7377 (mmp80) cc_final: 0.6883 (mmp-170)
REVERT: B  329 MET cc_start: 0.6834 (mtm) cc_final: 0.6289 (mmm)
REVERT: A  529 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.7907 (ppp)
REVERT: A  926 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7379 (mm-30)
REVERT: A 1018 MET cc_start: 0.8766 (ttp) cc_final: 0.8447 (ttp)
REVERT: A 1096 PHE cc_start: 0.7445 (p90) cc_final: 0.6939 (p90)
REVERT: A 1299 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8101 (tp)
  outliers start: 31
  outliers final: 24
  residues processed: 174
  average time/residue: 0.1057
  time to fit residues: 27.3336
Evaluate side-chains
  168 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 142
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  214 LYS
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  529 MET
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  893 ASP
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1166 ASP
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1233 VAL
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1300 PHE
Chi-restraints excluded: chain A residue 1325 LEU
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 85 optimal weight:    9.9990
   chunk 110 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 37 optimal weight:    9.9990
   chunk 122 optimal weight:    4.9990
   chunk 75 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 60 optimal weight:    7.9990
   chunk 108 optimal weight:    7.9990
   chunk 31 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.139677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.108220 restraints weight = 18061.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.111655 restraints weight = 10135.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.113954 restraints weight = 7174.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.115397 restraints weight = 5791.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.116204 restraints weight = 5079.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  11678  Z= 0.207
  Angle     :  0.615   8.704  16094  Z= 0.324
  Chirality :  0.042   0.315   1782
  Planarity :  0.004   0.049   1838
  Dihedral  : 18.708 117.351   2081
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 20.78 %
    Favored  : 76.05 %
  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:  0.47 (0.24), residues: 1250
  helix:  1.22 (0.20), residues: 705
  sheet: -0.09 (0.45), residues: 118
  loop : -1.06 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 984 
 TYR   0.019   0.002   TYR A 979 
 PHE   0.019   0.002   PHE A1300 
 TRP   0.026   0.001   TRP B  24 
 HIS   0.004   0.001   HIS B 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 (11677)
  covalent geometry    : angle       0.61458 (16094)
  hydrogen bonds       : bond        0.04847 (  592)
  hydrogen bonds       : angle       4.41334 ( 1667)
  Misc. bond           : bond        0.00042 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 146
  time to evaluate  : 0.442 
Fit side-chains
REVERT: B  329 MET cc_start: 0.6834 (mtm) cc_final: 0.6246 (mmm)
REVERT: A  437 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6755 (pp20)
REVERT: A  529 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.7896 (ppp)
REVERT: A  926 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7443 (mm-30)
REVERT: A 1018 MET cc_start: 0.8828 (ttp) cc_final: 0.8589 (ttp)
REVERT: A 1057 HIS cc_start: 0.6916 (m90) cc_final: 0.6670 (m90)
REVERT: A 1096 PHE cc_start: 0.7465 (p90) cc_final: 0.6864 (p90)
REVERT: A 1299 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7982 (tp)
  outliers start: 34
  outliers final: 27
  residues processed: 168
  average time/residue: 0.1039
  time to fit residues: 26.0659
Evaluate side-chains
  170 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 140
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 TYR
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  529 MET
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  893 ASP
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1166 ASP
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1205 LEU
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1233 VAL
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1300 PHE
Chi-restraints excluded: chain A residue 1325 LEU
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 116 optimal weight:    5.9990
   chunk 56 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 88 optimal weight:    8.9990
   chunk 64 optimal weight:    4.9990
   chunk 54 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.141054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.110361 restraints weight = 17940.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.113943 restraints weight = 9931.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.116235 restraints weight = 6879.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.117611 restraints weight = 5522.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.118578 restraints weight = 4836.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  11678  Z= 0.162
  Angle     :  0.595   8.876  16094  Z= 0.313
  Chirality :  0.040   0.192   1782
  Planarity :  0.004   0.051   1838
  Dihedral  : 18.590 117.747   2081
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 21.16 %
    Favored  : 75.40 %
  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:  0.60 (0.24), residues: 1250
  helix:  1.38 (0.20), residues: 698
  sheet: -0.07 (0.44), residues: 120
  loop : -1.05 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 984 
 TYR   0.026   0.002   TYR A 979 
 PHE   0.017   0.001   PHE A1300 
 TRP   0.027   0.001   TRP B  24 
 HIS   0.004   0.001   HIS B 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (11677)
  covalent geometry    : angle       0.59486 (16094)
  hydrogen bonds       : bond        0.04476 (  592)
  hydrogen bonds       : angle       4.29745 ( 1667)
  Misc. bond           : bond        0.00050 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 144
  time to evaluate  : 0.476 
Fit side-chains
REVERT: B  329 MET cc_start: 0.6847 (mtm) cc_final: 0.6225 (mmm)
REVERT: A  402 LYS cc_start: 0.8611 (mptt) cc_final: 0.8067 (mmtp)
REVERT: A  437 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6764 (pp20)
REVERT: A  529 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.7901 (ppp)
REVERT: A  926 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7376 (mm-30)
REVERT: A 1057 HIS cc_start: 0.6874 (m90) cc_final: 0.6606 (m90)
REVERT: A 1096 PHE cc_start: 0.7417 (p90) cc_final: 0.6928 (p90)
REVERT: A 1299 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8116 (tp)
  outliers start: 37
  outliers final: 29
  residues processed: 168
  average time/residue: 0.0884
  time to fit residues: 22.2279
Evaluate side-chains
  174 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 142
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 TYR
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue  116 ARG
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  529 MET
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  893 ASP
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1166 ASP
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1233 VAL
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1300 PHE
Chi-restraints excluded: chain A residue 1325 LEU
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 83 optimal weight:    9.9990
   chunk 68 optimal weight:    9.9990
   chunk 57 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 74 optimal weight:    8.9990
   chunk 104 optimal weight:    6.9990
   chunk 52 optimal weight:    7.9990
   chunk 1 optimal weight:    9.9990
   chunk 14 optimal weight:    0.2980
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.143406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.112818 restraints weight = 17845.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.116307 restraints weight = 9758.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.118703 restraints weight = 6827.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.120117 restraints weight = 5433.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.121179 restraints weight = 4741.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080  11678  Z= 0.130
  Angle     :  0.576   8.897  16094  Z= 0.301
  Chirality :  0.039   0.160   1782
  Planarity :  0.004   0.052   1838
  Dihedral  : 18.415 116.864   2081
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 22.18 %
    Favored  : 75.49 %
  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 (0.24), residues: 1250
  helix:  1.54 (0.20), residues: 698
  sheet: -0.01 (0.44), residues: 120
  loop : -1.00 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1275 
 TYR   0.024   0.002   TYR A 979 
 PHE   0.014   0.001   PHE B  85 
 TRP   0.025   0.001   TRP B  24 
 HIS   0.004   0.001   HIS B 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (11677)
  covalent geometry    : angle       0.57636 (16094)
  hydrogen bonds       : bond        0.04095 (  592)
  hydrogen bonds       : angle       4.17012 ( 1667)
  Misc. bond           : bond        0.00058 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 161
  time to evaluate  : 0.343 
Fit side-chains
REVERT: B  329 MET cc_start: 0.6837 (mtm) cc_final: 0.6310 (mmm)
REVERT: A  437 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6745 (pp20)
REVERT: A  529 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.7849 (ppp)
REVERT: A  926 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7261 (mm-30)
REVERT: A 1057 HIS cc_start: 0.6899 (m90) cc_final: 0.6640 (m90)
REVERT: A 1096 PHE cc_start: 0.7370 (p90) cc_final: 0.6910 (p90)
REVERT: A 1299 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8147 (tp)
  outliers start: 25
  outliers final: 21
  residues processed: 177
  average time/residue: 0.0885
  time to fit residues: 23.1373
Evaluate side-chains
  172 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue  116 ARG
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  220 CYS
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  529 MET
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  755 LEU
Chi-restraints excluded: chain A residue  893 ASP
Chi-restraints excluded: chain A residue 1103 ASP
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1233 VAL
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1300 PHE
Chi-restraints excluded: chain A residue 1325 LEU
Chi-restraints excluded: chain A residue 1332 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 43 optimal weight:    8.9990
   chunk 124 optimal weight:    0.5980
   chunk 50 optimal weight:    8.9990
   chunk 61 optimal weight:    2.9990
   chunk 120 optimal weight:   20.0000
   chunk 53 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 127 optimal weight:   10.0000
   chunk 66 optimal weight:    8.9990
   chunk 89 optimal weight:    8.9990
   chunk 20 optimal weight:   10.0000
   overall best weight:    4.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.140844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.109420 restraints weight = 18222.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.112941 restraints weight = 10169.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.115238 restraints weight = 7153.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.116736 restraints weight = 5768.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.117570 restraints weight = 5039.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078  11678  Z= 0.191
  Angle     :  0.608   8.893  16094  Z= 0.319
  Chirality :  0.041   0.166   1782
  Planarity :  0.004   0.048   1838
  Dihedral  : 18.561 117.495   2081
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 23.02 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.65 (0.24), residues: 1250
  helix:  1.41 (0.20), residues: 697
  sheet: -0.15 (0.44), residues: 123
  loop : -0.97 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1275 
 TYR   0.023   0.002   TYR A 979 
 PHE   0.017   0.002   PHE A1300 
 TRP   0.030   0.001   TRP B  24 
 HIS   0.004   0.001   HIS B 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 (11677)
  covalent geometry    : angle       0.60773 (16094)
  hydrogen bonds       : bond        0.04590 (  592)
  hydrogen bonds       : angle       4.31282 ( 1667)
  Misc. bond           : bond        0.00051 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1780.18 seconds
wall clock time: 31 minutes 33.02 seconds (1893.02 seconds total)