Starting phenix.real_space_refine
on Sat Oct 11 03:38:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q63_18183/10_2025/8q63_18183.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q63_18183/10_2025/8q63_18183.map

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

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

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


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

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

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11346
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2698
          Classifications: {'peptide': 329}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 309}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "A"
      Number of atoms: 7200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 915, 7200
          Classifications: {'peptide': 915}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 44}
          Link IDs: {'PTRANS': 44, 'TRANS': 870}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 152
          Unresolved non-hydrogen angles: 185
          Unresolved non-hydrogen dihedrals: 119
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 8, 'ASP:plan': 5, 'GLN:plan1': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 73
    Chain: "N"
      Number of atoms: 642
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 642
          Classifications: {'DNA': 31}
          Link IDs: {'rna3p': 30}
    Chain: "T"
      Number of atoms: 630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 630
          Classifications: {'DNA': 31}
          Link IDs: {'rna3p': 30}
    Chain: "C"
      Number of atoms: 152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 152
          Classifications: {'RNA': 7}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 2}
          Link IDs: {'rna3p': 6}
    Chain: "C"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 2.92, per 1000 atoms: 0.26
  Number of scatterers: 11346
  At special positions: 0
  Unit cell: (103.79, 116.4, 118.34, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      35     16.00
     P      70     15.00
     O    2229      8.00
     N    1971      7.00
     C    7041      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.10
  Conformation dependent library (CDL) restraints added in 497.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 11 sheets defined
      59.8% alpha, 7.3% beta
      26 base pairs and 47 stacking pairs defined.
    Time for finding SS restraints: 1.39
  Creating SS restraints...
    Processing helix  chain 'B' and resid 7 through 14
      removed outlier: 3.890A  pdb=" N   LEU B  14 " --> pdb=" O   ASP B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 37
    Processing helix  chain 'B' and resid 38 through 41
    Processing helix  chain 'B' and resid 44 through 47
      removed outlier: 3.762A  pdb=" N   GLU B  47 " --> pdb=" O   HIS B  44 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 44 through 47'
    Processing helix  chain 'B' and resid 58 through 69
    Processing helix  chain 'B' and resid 79 through 90
    Processing helix  chain 'B' and resid 104 through 113
      removed outlier: 3.834A  pdb=" N   TYR B 108 " --> pdb=" O   ASP B 104 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   ASP B 113 " --> pdb=" O   SER B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 157
      removed outlier: 3.960A  pdb=" N   MET B 148 " --> pdb=" O   GLU B 144 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ILE B 154 " --> pdb=" O   TRP B 150 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   GLY B 155 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 164
      removed outlier: 3.729A  pdb=" N   GLY B 164 " --> pdb=" O   TYR B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 182
    Processing helix  chain 'B' and resid 190 through 199
    Processing helix  chain 'B' and resid 209 through 215
      removed outlier: 3.521A  pdb=" N   GLU B 212 " --> pdb=" O   ASP B 209 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LYS B 214 " --> pdb=" O   ASN B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 225
    Processing helix  chain 'B' and resid 230 through 234
      removed outlier: 4.297A  pdb=" N   ILE B 234 " --> pdb=" O   ALA B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 267
    Processing helix  chain 'B' and resid 268 through 270
      No H-bonds generated for 'chain 'B' and resid 268 through 270'
    Processing helix  chain 'B' and resid 273 through 278
      removed outlier: 4.141A  pdb=" N   MET B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 282
    Processing helix  chain 'B' and resid 284 through 293
    Processing helix  chain 'B' and resid 295 through 301
      removed outlier: 3.573A  pdb=" N   LEU B 299 " --> pdb=" O   ASP B 295 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LYS B 300 " --> pdb=" O   LYS B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 321
    Processing helix  chain 'A' and resid 387 through 395
    Processing helix  chain 'A' and resid 397 through 421
      removed outlier: 4.247A  pdb=" N   ASP A 414 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ARG A 415 " --> pdb=" O   PHE A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 442
    Processing helix  chain 'A' and resid 448 through 476
      removed outlier: 4.518A  pdb=" N   VAL A 452 " --> pdb=" O   LYS A 448 " (cutoff:3.500A)
      Proline residue:  A 463  - end of helix
    Processing helix  chain 'A' and resid 490 through 497
      removed outlier: 3.764A  pdb=" N   GLY A 495 " --> pdb=" O   THR A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 515
      removed outlier: 4.529A  pdb=" N   GLY A 506 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 552
      removed outlier: 3.855A  pdb=" N   ILE A 536 " --> pdb=" O   ALA A 532 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLU A 549 " --> pdb=" O   GLU A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 611
      removed outlier: 3.747A  pdb=" N   VAL A 611 " --> pdb=" O   MET A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 663
      removed outlier: 3.628A  pdb=" N   GLU A 662 " --> pdb=" O   GLN A 658 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ARG A 663 " --> pdb=" O   LEU A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 717
      removed outlier: 3.884A  pdb=" N   VAL A 707 " --> pdb=" O   SER A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 731
    Processing helix  chain 'A' and resid 737 through 751
    Processing helix  chain 'A' and resid 777 through 813
    Processing helix  chain 'A' and resid 842 through 848
    Processing helix  chain 'A' and resid 857 through 873
    Processing helix  chain 'A' and resid 879 through 890
    Processing helix  chain 'A' and resid 890 through 900
    Processing helix  chain 'A' and resid 906 through 911
    Processing helix  chain 'A' and resid 913 through 930
    Processing helix  chain 'A' and resid 932 through 935
    Processing helix  chain 'A' and resid 948 through 959
      removed outlier: 3.703A  pdb=" N   ALA A 956 " --> pdb=" O   GLN A 952 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 960 through 967
    Processing helix  chain 'A' and resid 977 through 997
    Processing helix  chain 'A' and resid 998 through 1004
    Processing helix  chain 'A' and resid 1009 through 1021
      removed outlier: 3.729A  pdb=" N   VAL A1021 " --> pdb=" O   VAL A1017 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1025 through 1038
    Processing helix  chain 'A' and resid 1046 through 1066
      removed outlier: 4.435A  pdb=" N   PHE A1050 " --> pdb=" O   GLU A1046 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   TYR A1053 " --> pdb=" O   ASP A1049 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   HIS A1057 " --> pdb=" O   TYR A1053 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   SER A1060 " --> pdb=" O   LYS A1056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1067 through 1085
    Processing helix  chain 'A' and resid 1089 through 1094
      removed outlier: 4.066A  pdb=" N   LYS A1094 " --> pdb=" O   ASP A1090 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1149 through 1181
      Proline residue:  A1158  - end of helix
    Processing helix  chain 'A' and resid 1197 through 1213
    Processing helix  chain 'A' and resid 1216 through 1229
    Processing helix  chain 'A' and resid 1242 through 1244
      No H-bonds generated for 'chain 'A' and resid 1242 through 1244'
    Processing helix  chain 'A' and resid 1245 through 1260
    Processing helix  chain 'A' and resid 1264 through 1281
      removed outlier: 3.647A  pdb=" N   LEU A1279 " --> pdb=" O   ARG A1275 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   SER A1281 " --> pdb=" O   GLU A1277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1293
    Processing helix  chain 'A' and resid 1295 through 1301
      removed outlier: 3.774A  pdb=" N   LEU A1299 " --> pdb=" O   THR A1295 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   PHE A1300 " --> pdb=" O   THR A1296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1305 through 1310
    Processing helix  chain 'A' and resid 1339 through 1344
    Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 99
      removed outlier: 3.704A  pdb=" N   VAL B 135 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   MET B 247 " --> pdb=" O   MET B 168 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 206 through 207
      removed outlier: 3.953A  pdb=" N   ILE B 207 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 529 through 530
      removed outlier: 3.547A  pdb=" N   ALA A 635 " --> pdb=" O   LYS A 650 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 613 through 619
    Processing sheet with id=AA5, first strand: chain 'A' and resid 734 through 736
    Processing sheet with id=AA6, first strand: chain 'A' and resid 822 through 824
    Processing sheet with id=AA7, first strand: chain 'A' and resid 855 through 856
      removed outlier: 3.997A  pdb=" N   LYS A 855 " --> pdb=" O   SER A 938 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   SER A 938 " --> pdb=" O   LYS A 855 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 942 through 944
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1086 through 1087
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1109 through 1111
      removed outlier: 3.739A  pdb=" N   TRP A1110 " --> pdb=" O   ILE A1118 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1127 through 1131
      removed outlier: 3.610A  pdb=" N   ILE A1139 " --> pdb=" O   LYS A1128 " (cutoff:3.500A)

    527 hydrogen bonds defined for protein.
    1524 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      59 hydrogen bonds
      118 hydrogen bond angles
      0 basepair planarities
      26 basepair parallelities
      47 stacking parallelities
  Total time for adding SS restraints: 2.63

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

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

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

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

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

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

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.730
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.0000

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

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

Rama-Z 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 (0.25), residues: 1232
  helix:  1.59 (0.21), residues: 666
  sheet: -1.19 (0.56), residues: 80
  loop : -1.01 (0.29), residues: 486

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

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

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

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 176
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  727 ASN cc_start: 0.7988 (m-40) cc_final: 0.7540 (m110)
REVERT: A  796 ASP cc_start: 0.8051 (m-30) cc_final: 0.7791 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 177
  average time/residue: 0.1035
  time to fit residues: 27.0191
Evaluate side-chains
  128 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:   40.0000
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:   20.0000
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   chunk 35 optimal weight:   20.0000
   overall best weight:    7.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN
A 628 HIS
A 642 ASN
** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.147415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.113764 restraints weight = 20709.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.117632 restraints weight = 11168.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.120189 restraints weight = 7736.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.121746 restraints weight = 6180.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.122781 restraints weight = 5413.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.1389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  11757  Z= 0.270
  Angle     :  0.721   9.484  16227  Z= 0.380
  Chirality :  0.045   0.156   1800
  Planarity :  0.005   0.103   1825
  Dihedral  : 19.617 173.647   2162
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  9.77 %
    Favored  : 88.73 %
  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:  0.22 (0.24), residues: 1232
  helix:  1.20 (0.20), residues: 677
  sheet: -1.07 (0.57), residues: 74
  loop : -1.16 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 800 
 TYR   0.032   0.002   TYR A 496 
 PHE   0.033   0.002   PHE A 754 
 TRP   0.030   0.003   TRP B 259 
 HIS   0.008   0.001   HIS A1188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00618 (11756)
  covalent geometry    : angle       0.72147 (16227)
  hydrogen bonds       : bond        0.05877 (  586)
  hydrogen bonds       : angle       5.00497 ( 1642)
  Misc. bond           : bond        0.00081 (    1)

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

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 153
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  533 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7198 (ptm160)
REVERT: A  656 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.9062 (tt)
REVERT: A  796 ASP cc_start: 0.8107 (m-30) cc_final: 0.7812 (m-30)
REVERT: A  856 LYS cc_start: 0.7392 (mmmt) cc_final: 0.7106 (mmmt)
REVERT: A 1128 LYS cc_start: 0.7778 (ptpt) cc_final: 0.7527 (ptmm)
REVERT: A 1160 ASN cc_start: 0.8924 (m-40) cc_final: 0.8493 (m110)
  outliers start: 16
  outliers final: 9
  residues processed: 160
  average time/residue: 0.1001
  time to fit residues: 23.6012
Evaluate side-chains
  154 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 143
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 37 optimal weight:    7.9990
   chunk 67 optimal weight:   50.0000
   chunk 58 optimal weight:   20.0000
   chunk 77 optimal weight:    9.9990
   chunk 76 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 63 optimal weight:    7.9990
   chunk 83 optimal weight:    8.9990
   chunk 38 optimal weight:    0.0060
   chunk 22 optimal weight:    9.9990
   overall best weight:    5.6004

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

Flipped N/Q/H residues before XYZ refinement:
A 459 ASN
A 628 HIS
** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.148530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.114686 restraints weight = 20776.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.118625 restraints weight = 11140.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.121200 restraints weight = 7679.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.122867 restraints weight = 6153.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.123776 restraints weight = 5356.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  11757  Z= 0.202
  Angle     :  0.644   8.668  16227  Z= 0.337
  Chirality :  0.042   0.150   1800
  Planarity :  0.004   0.059   1825
  Dihedral  : 19.338 168.670   2162
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.62 %
    Favored  : 84.23 %
  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:  0.33 (0.25), residues: 1232
  helix:  1.33 (0.20), residues: 678
  sheet: -1.29 (0.50), residues: 94
  loop : -1.10 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 827 
 TYR   0.029   0.002   TYR A 496 
 PHE   0.024   0.002   PHE A 936 
 TRP   0.024   0.002   TRP B 159 
 HIS   0.005   0.001   HIS A1188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (11756)
  covalent geometry    : angle       0.64403 (16227)
  hydrogen bonds       : bond        0.05176 (  586)
  hydrogen bonds       : angle       4.71881 ( 1642)
  Misc. bond           : bond        0.00072 (    1)

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

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 153
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  228 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7963 (tt)
REVERT: B  299 LEU cc_start: 0.8287 (tt) cc_final: 0.7708 (tp)
REVERT: B  321 TRP cc_start: 0.8083 (t60) cc_final: 0.7496 (t60)
REVERT: A  533 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7066 (ptm160)
REVERT: A  656 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9103 (tt)
REVERT: A  796 ASP cc_start: 0.8088 (m-30) cc_final: 0.7846 (m-30)
REVERT: A 1128 LYS cc_start: 0.7797 (ptpt) cc_final: 0.7549 (ptmm)
REVERT: A 1140 SER cc_start: 0.8692 (p) cc_final: 0.8484 (p)
REVERT: A 1157 LEU cc_start: 0.6723 (tp) cc_final: 0.6350 (tp)
REVERT: A 1160 ASN cc_start: 0.8955 (m-40) cc_final: 0.8521 (m110)
  outliers start: 23
  outliers final: 13
  residues processed: 166
  average time/residue: 0.0969
  time to fit residues: 24.1777
Evaluate side-chains
  156 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  628 HIS
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 35 optimal weight:   20.0000
   chunk 42 optimal weight:    8.9990
   chunk 62 optimal weight:   10.0000
   chunk 18 optimal weight:   50.0000
   chunk 69 optimal weight:    9.9990
   chunk 82 optimal weight:    9.9990
   chunk 114 optimal weight:    8.9990
   chunk 90 optimal weight:    5.9990
   chunk 65 optimal weight:    0.6980
   chunk 24 optimal weight:    9.9990
   overall best weight:    6.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 628 HIS
** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.146833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.112999 restraints weight = 20738.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.116841 restraints weight = 11177.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.119352 restraints weight = 7735.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.120940 restraints weight = 6199.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.121772 restraints weight = 5420.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  11757  Z= 0.232
  Angle     :  0.663   8.699  16227  Z= 0.347
  Chirality :  0.042   0.177   1800
  Planarity :  0.005   0.057   1825
  Dihedral  : 19.349 165.045   2162
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.15 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.25), residues: 1232
  helix:  1.22 (0.20), residues: 679
  sheet: -1.37 (0.51), residues: 84
  loop : -1.18 (0.30), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 827 
 TYR   0.025   0.002   TYR A 496 
 PHE   0.026   0.002   PHE B 132 
 TRP   0.031   0.002   TRP B 159 
 HIS   0.006   0.001   HIS A 628 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 (11756)
  covalent geometry    : angle       0.66339 (16227)
  hydrogen bonds       : bond        0.05308 (  586)
  hydrogen bonds       : angle       4.82565 ( 1642)
  Misc. bond           : bond        0.00065 (    1)

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

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 145
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  133 LEU cc_start: 0.7334 (tp) cc_final: 0.7039 (mt)
REVERT: B  159 TRP cc_start: 0.7936 (t60) cc_final: 0.7288 (t60)
REVERT: B  228 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7984 (tt)
REVERT: B  299 LEU cc_start: 0.8329 (tt) cc_final: 0.7762 (tp)
REVERT: A  533 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7078 (ptm160)
REVERT: A  796 ASP cc_start: 0.8087 (m-30) cc_final: 0.7857 (m-30)
REVERT: A  865 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9031 (tt)
REVERT: A 1128 LYS cc_start: 0.7857 (ptpt) cc_final: 0.7556 (ptmm)
REVERT: A 1140 SER cc_start: 0.8724 (p) cc_final: 0.8516 (p)
REVERT: A 1157 LEU cc_start: 0.6782 (tp) cc_final: 0.6339 (tp)
REVERT: A 1160 ASN cc_start: 0.8960 (m-40) cc_final: 0.8532 (m110)
  outliers start: 34
  outliers final: 21
  residues processed: 168
  average time/residue: 0.0927
  time to fit residues: 23.2262
Evaluate side-chains
  161 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  736 VAL
Chi-restraints excluded: chain A residue  865 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue  912 ASP
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1193 THR
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 48 optimal weight:    0.0980
   chunk 113 optimal weight:    8.9990
   chunk 104 optimal weight:   10.0000
   chunk 88 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 76 optimal weight:    0.0010
   chunk 94 optimal weight:    6.9990
   chunk 62 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 77 optimal weight:   20.0000
   chunk 101 optimal weight:    1.9990
   overall best weight:    1.4192

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.152869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.119450 restraints weight = 20379.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.123568 restraints weight = 10783.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.126237 restraints weight = 7353.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.127833 restraints weight = 5839.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.128993 restraints weight = 5102.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7185
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  11757  Z= 0.128
  Angle     :  0.610   9.562  16227  Z= 0.315
  Chirality :  0.039   0.143   1800
  Planarity :  0.004   0.062   1825
  Dihedral  : 19.103 162.237   2162
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.53 %
    Favored  : 80.75 %
  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:  0.72 (0.25), residues: 1232
  helix:  1.65 (0.21), residues: 674
  sheet: -0.78 (0.58), residues: 74
  loop : -1.01 (0.29), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 827 
 TYR   0.032   0.002   TYR B  29 
 PHE   0.022   0.001   PHE B 132 
 TRP   0.026   0.002   TRP B 159 
 HIS   0.006   0.001   HIS B  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (11756)
  covalent geometry    : angle       0.60976 (16227)
  hydrogen bonds       : bond        0.04228 (  586)
  hydrogen bonds       : angle       4.33138 ( 1642)
  Misc. bond           : bond        0.00065 (    1)

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

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 171
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  150 TRP cc_start: 0.7080 (m-10) cc_final: 0.6810 (m-10)
REVERT: B  228 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7956 (tt)
REVERT: B  321 TRP cc_start: 0.7907 (t60) cc_final: 0.7477 (t60)
REVERT: A  533 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7004 (ptm160)
REVERT: A  796 ASP cc_start: 0.7958 (m-30) cc_final: 0.7739 (m-30)
REVERT: A  865 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8919 (tt)
REVERT: A 1140 SER cc_start: 0.8710 (p) cc_final: 0.8488 (p)
REVERT: A 1157 LEU cc_start: 0.6426 (tp) cc_final: 0.6203 (tp)
REVERT: A 1201 MET cc_start: 0.7672 (ttp) cc_final: 0.7385 (ttp)
  outliers start: 29
  outliers final: 17
  residues processed: 186
  average time/residue: 0.0919
  time to fit residues: 25.9476
Evaluate side-chains
  173 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue  172 MET
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  628 HIS
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  865 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 7 optimal weight:   20.0000
   chunk 74 optimal weight:   10.0000
   chunk 94 optimal weight:    8.9990
   chunk 23 optimal weight:   20.0000
   chunk 98 optimal weight:    0.5980
   chunk 117 optimal weight:    0.0980
   chunk 99 optimal weight:   20.0000
   chunk 3 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 48 optimal weight:    0.5980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
B  44 HIS
** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 943 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.155445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.123830 restraints weight = 20472.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.127834 restraints weight = 11022.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.130493 restraints weight = 7570.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.132253 restraints weight = 5990.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.132970 restraints weight = 5172.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073  11757  Z= 0.126
  Angle     :  0.599   9.367  16227  Z= 0.311
  Chirality :  0.040   0.234   1800
  Planarity :  0.004   0.058   1825
  Dihedral  : 18.942 164.271   2162
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 18.59 %
    Favored  : 78.97 %
  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:  0.79 (0.25), residues: 1232
  helix:  1.63 (0.21), residues: 677
  sheet: -0.61 (0.55), residues: 84
  loop : -0.89 (0.30), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1250 
 TYR   0.032   0.002   TYR B  29 
 PHE   0.026   0.001   PHE B 132 
 TRP   0.042   0.001   TRP B 159 
 HIS   0.005   0.001   HIS A 943 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (11756)
  covalent geometry    : angle       0.59895 (16227)
  hydrogen bonds       : bond        0.04045 (  586)
  hydrogen bonds       : angle       4.24490 ( 1642)
  Misc. bond           : bond        0.00056 (    1)

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

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 159
  time to evaluate  : 0.432 
Fit side-chains
REVERT: B   79 ARG cc_start: 0.6649 (mpp80) cc_final: 0.6245 (mmt180)
REVERT: B  228 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8015 (tt)
REVERT: B  296 LYS cc_start: 0.7965 (mmtm) cc_final: 0.7541 (mmmt)
REVERT: B  321 TRP cc_start: 0.7901 (t60) cc_final: 0.7294 (t60)
REVERT: A  727 ASN cc_start: 0.7638 (m-40) cc_final: 0.7258 (m110)
REVERT: A  865 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8890 (tt)
REVERT: A 1140 SER cc_start: 0.8716 (p) cc_final: 0.8494 (p)
REVERT: A 1157 LEU cc_start: 0.6375 (tp) cc_final: 0.6166 (tp)
REVERT: A 1201 MET cc_start: 0.7703 (ttp) cc_final: 0.7171 (ttp)
  outliers start: 26
  outliers final: 19
  residues processed: 173
  average time/residue: 0.0983
  time to fit residues: 25.1977
Evaluate side-chains
  164 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  628 HIS
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  736 VAL
Chi-restraints excluded: chain A residue  848 LEU
Chi-restraints excluded: chain A residue  865 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  954 TYR
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1351 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 21 optimal weight:    8.9990
   chunk 125 optimal weight:   20.0000
   chunk 111 optimal weight:    3.9990
   chunk 43 optimal weight:    7.9990
   chunk 3 optimal weight:   10.0000
   chunk 112 optimal weight:    8.9990
   chunk 105 optimal weight:    1.9990
   chunk 118 optimal weight:   30.0000
   chunk 109 optimal weight:    9.9990
   chunk 45 optimal weight:    0.4980
   overall best weight:    3.0786

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.153563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.121846 restraints weight = 20467.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.125789 restraints weight = 11132.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.128410 restraints weight = 7664.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.130064 restraints weight = 6083.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.131017 restraints weight = 5281.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081  11757  Z= 0.149
  Angle     :  0.619   9.123  16227  Z= 0.319
  Chirality :  0.041   0.368   1800
  Planarity :  0.004   0.054   1825
  Dihedral  : 18.937 166.802   2162
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.87 %
    Favored  : 77.93 %
  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:  0.89 (0.25), residues: 1232
  helix:  1.68 (0.21), residues: 671
  sheet: -0.60 (0.55), residues: 84
  loop : -0.74 (0.30), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 189 
 TYR   0.028   0.002   TYR B  29 
 PHE   0.035   0.002   PHE A 936 
 TRP   0.053   0.002   TRP B 159 
 HIS   0.003   0.001   HIS A1163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (11756)
  covalent geometry    : angle       0.61902 (16227)
  hydrogen bonds       : bond        0.04184 (  586)
  hydrogen bonds       : angle       4.32007 ( 1642)
  Misc. bond           : bond        0.00044 (    1)

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

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 152
  time to evaluate  : 0.417 
Fit side-chains
REVERT: B  228 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8008 (tt)
REVERT: B  296 LYS cc_start: 0.7961 (mmtm) cc_final: 0.7603 (mmmt)
REVERT: B  321 TRP cc_start: 0.7898 (t60) cc_final: 0.7296 (t60)
REVERT: A  533 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7026 (ptm160)
REVERT: A  727 ASN cc_start: 0.7670 (m-40) cc_final: 0.7280 (m110)
REVERT: A  796 ASP cc_start: 0.7838 (m-30) cc_final: 0.7635 (t0)
REVERT: A  865 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8908 (tt)
REVERT: A 1140 SER cc_start: 0.8720 (p) cc_final: 0.8499 (p)
REVERT: A 1201 MET cc_start: 0.7724 (ttp) cc_final: 0.7173 (ttp)
  outliers start: 34
  outliers final: 22
  residues processed: 172
  average time/residue: 0.0967
  time to fit residues: 24.8508
Evaluate side-chains
  168 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 TYR
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  496 TYR
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  736 VAL
Chi-restraints excluded: chain A residue  865 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1193 THR
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1350 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 78 optimal weight:   20.0000
   chunk 70 optimal weight:   10.0000
   chunk 126 optimal weight:   20.0000
   chunk 76 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 30 optimal weight:   10.0000
   chunk 62 optimal weight:    9.9990
   chunk 77 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    3.5786

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

Flipped N/Q/H residues before XYZ refinement:
B  44 HIS
** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1160 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.151712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.118214 restraints weight = 20418.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.122254 restraints weight = 10873.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.124882 restraints weight = 7465.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.126532 restraints weight = 5953.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.127582 restraints weight = 5178.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076  11757  Z= 0.157
  Angle     :  0.634   9.866  16227  Z= 0.326
  Chirality :  0.042   0.317   1800
  Planarity :  0.004   0.051   1825
  Dihedral  : 18.938 168.251   2162
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 18.78 %
    Favored  : 77.84 %
  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:  0.86 (0.25), residues: 1232
  helix:  1.66 (0.21), residues: 668
  sheet: -0.65 (0.55), residues: 86
  loop : -0.73 (0.30), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 189 
 TYR   0.024   0.002   TYR A 954 
 PHE   0.033   0.002   PHE B 132 
 TRP   0.061   0.002   TRP B 159 
 HIS   0.003   0.001   HIS A 943 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (11756)
  covalent geometry    : angle       0.63353 (16227)
  hydrogen bonds       : bond        0.04333 (  586)
  hydrogen bonds       : angle       4.41884 ( 1642)
  Misc. bond           : bond        0.00039 (    1)

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

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 145
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: B  150 TRP cc_start: 0.7255 (m-10) cc_final: 0.6956 (m-10)
REVERT: B  159 TRP cc_start: 0.7752 (t60) cc_final: 0.7064 (t60)
REVERT: B  228 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7988 (tt)
REVERT: B  292 ARG cc_start: 0.7630 (mmm-85) cc_final: 0.7371 (mmm-85)
REVERT: B  296 LYS cc_start: 0.8112 (mmtm) cc_final: 0.7735 (mmmt)
REVERT: B  321 TRP cc_start: 0.7901 (t60) cc_final: 0.7323 (t60)
REVERT: A  533 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7013 (ptm160)
REVERT: A  727 ASN cc_start: 0.7757 (m-40) cc_final: 0.7354 (m110)
REVERT: A  865 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8953 (tt)
REVERT: A 1140 SER cc_start: 0.8722 (p) cc_final: 0.8491 (p)
REVERT: A 1160 ASN cc_start: 0.8936 (m110) cc_final: 0.8576 (m110)
REVERT: A 1201 MET cc_start: 0.7761 (ttp) cc_final: 0.7053 (ttp)
  outliers start: 36
  outliers final: 26
  residues processed: 163
  average time/residue: 0.1012
  time to fit residues: 24.2095
Evaluate side-chains
  171 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 142
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 TYR
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  628 HIS
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  736 VAL
Chi-restraints excluded: chain A residue  865 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue  954 TYR
Chi-restraints excluded: chain A residue 1036 GLN
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1193 THR
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1350 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 89 optimal weight:   30.0000
   chunk 123 optimal weight:   10.0000
   chunk 81 optimal weight:    3.9990
   chunk 91 optimal weight:    7.9990
   chunk 86 optimal weight:    0.0980
   chunk 60 optimal weight:    9.9990
   chunk 109 optimal weight:    8.9990
   chunk 0 optimal weight:   30.0000
   chunk 36 optimal weight:    9.9990
   chunk 100 optimal weight:    7.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    5.0188

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.150100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.116704 restraints weight = 20159.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.120621 restraints weight = 10841.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.123192 restraints weight = 7493.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.124655 restraints weight = 5976.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.125785 restraints weight = 5259.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  11757  Z= 0.188
  Angle     :  0.655  10.201  16227  Z= 0.338
  Chirality :  0.042   0.318   1800
  Planarity :  0.004   0.050   1825
  Dihedral  : 19.002 169.382   2162
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 19.06 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.25), residues: 1232
  helix:  1.52 (0.20), residues: 668
  sheet: -0.81 (0.55), residues: 84
  loop : -0.78 (0.30), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 829 
 TYR   0.028   0.002   TYR A 954 
 PHE   0.034   0.002   PHE B 132 
 TRP   0.053   0.002   TRP B 159 
 HIS   0.005   0.001   HIS B  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (11756)
  covalent geometry    : angle       0.65533 (16227)
  hydrogen bonds       : bond        0.04634 (  586)
  hydrogen bonds       : angle       4.58334 ( 1642)
  Misc. bond           : bond        0.00037 (    1)

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

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 141
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  150 TRP cc_start: 0.7315 (m-10) cc_final: 0.7009 (m-10)
REVERT: B  159 TRP cc_start: 0.7694 (t60) cc_final: 0.6902 (t60)
REVERT: B  228 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7986 (tt)
REVERT: B  296 LYS cc_start: 0.8186 (mmtm) cc_final: 0.7710 (mmmt)
REVERT: B  321 TRP cc_start: 0.7895 (t60) cc_final: 0.7414 (t60)
REVERT: A  533 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7123 (ptm160)
REVERT: A  865 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8975 (tt)
REVERT: A  926 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7691 (tm-30)
REVERT: A  936 PHE cc_start: 0.7588 (t80) cc_final: 0.7236 (t80)
REVERT: A 1140 SER cc_start: 0.8749 (p) cc_final: 0.8498 (p)
REVERT: A 1160 ASN cc_start: 0.8875 (m110) cc_final: 0.8634 (m-40)
REVERT: A 1201 MET cc_start: 0.7758 (ttp) cc_final: 0.7116 (ttp)
  outliers start: 36
  outliers final: 27
  residues processed: 161
  average time/residue: 0.1024
  time to fit residues: 24.3905
Evaluate side-chains
  170 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 140
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  628 HIS
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  736 VAL
Chi-restraints excluded: chain A residue  865 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue  951 LEU
Chi-restraints excluded: chain A residue  954 TYR
Chi-restraints excluded: chain A residue 1036 GLN
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1193 THR
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1350 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 125 optimal weight:   20.0000
   chunk 124 optimal weight:   10.0000
   chunk 117 optimal weight:    6.9990
   chunk 4 optimal weight:    0.0170
   chunk 84 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 94 optimal weight:    7.9990
   chunk 115 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    2.2026

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

Flipped N/Q/H residues before XYZ refinement:
A 691 HIS
** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.152926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.119382 restraints weight = 20222.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.123448 restraints weight = 10774.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.126155 restraints weight = 7392.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.127899 restraints weight = 5863.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.128794 restraints weight = 5077.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.2558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  11757  Z= 0.140
  Angle     :  0.636  10.774  16227  Z= 0.325
  Chirality :  0.041   0.276   1800
  Planarity :  0.004   0.054   1825
  Dihedral  : 18.887 170.794   2162
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 19.62 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.25), residues: 1232
  helix:  1.60 (0.20), residues: 670
  sheet: -0.66 (0.55), residues: 86
  loop : -0.74 (0.30), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 189 
 TYR   0.024   0.002   TYR A 496 
 PHE   0.028   0.002   PHE B 132 
 TRP   0.049   0.002   TRP B 159 
 HIS   0.005   0.001   HIS B  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (11756)
  covalent geometry    : angle       0.63570 (16227)
  hydrogen bonds       : bond        0.04234 (  586)
  hydrogen bonds       : angle       4.44040 ( 1642)
  Misc. bond           : bond        0.00039 (    1)

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

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 148
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  137 ASN cc_start: 0.8110 (t0) cc_final: 0.7799 (t0)
REVERT: B  150 TRP cc_start: 0.7227 (m-10) cc_final: 0.6958 (m-10)
REVERT: B  159 TRP cc_start: 0.7763 (t60) cc_final: 0.7136 (t60)
REVERT: B  228 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7949 (tt)
REVERT: B  296 LYS cc_start: 0.7924 (mmtm) cc_final: 0.7480 (mmmt)
REVERT: B  321 TRP cc_start: 0.7823 (t60) cc_final: 0.7320 (t60)
REVERT: A  533 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7063 (ptm160)
REVERT: A  865 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8935 (tt)
REVERT: A  926 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7709 (tm-30)
REVERT: A  936 PHE cc_start: 0.7575 (t80) cc_final: 0.7365 (t80)
REVERT: A 1140 SER cc_start: 0.8706 (p) cc_final: 0.8481 (p)
REVERT: A 1201 MET cc_start: 0.7721 (ttp) cc_final: 0.7019 (ttp)
  outliers start: 31
  outliers final: 27
  residues processed: 164
  average time/residue: 0.1009
  time to fit residues: 24.4818
Evaluate side-chains
  172 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 142
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  496 TYR
Chi-restraints excluded: chain A residue  533 ARG
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain A residue  628 HIS
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  709 TYR
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  736 VAL
Chi-restraints excluded: chain A residue  865 LEU
Chi-restraints excluded: chain A residue  869 LEU
Chi-restraints excluded: chain A residue  896 ASP
Chi-restraints excluded: chain A residue  951 LEU
Chi-restraints excluded: chain A residue  954 TYR
Chi-restraints excluded: chain A residue 1036 GLN
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1170 MET
Chi-restraints excluded: chain A residue 1193 THR
Chi-restraints excluded: chain A residue 1217 LEU
Chi-restraints excluded: chain A residue 1223 GLU
Chi-restraints excluded: chain A residue 1342 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1350 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 56 optimal weight:    0.0470
   chunk 79 optimal weight:   30.0000
   chunk 51 optimal weight:    2.9990
   chunk 85 optimal weight:    8.9990
   chunk 113 optimal weight:   40.0000
   chunk 119 optimal weight:    0.0970
   chunk 54 optimal weight:    9.9990
   chunk 86 optimal weight:    7.9990
   chunk 102 optimal weight:    5.9990
   chunk 31 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    3.0282

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.152274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.118652 restraints weight = 20471.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.122702 restraints weight = 10940.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.125334 restraints weight = 7504.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.127113 restraints weight = 5961.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.128197 restraints weight = 5161.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.2644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  11757  Z= 0.150
  Angle     :  0.648  12.699  16227  Z= 0.329
  Chirality :  0.041   0.286   1800
  Planarity :  0.004   0.061   1825
  Dihedral  : 18.864 169.297   2162
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 19.72 %
    Favored  : 77.37 %
  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 (0.25), residues: 1232
  helix:  1.58 (0.20), residues: 670
  sheet: -0.57 (0.56), residues: 84
  loop : -0.75 (0.30), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 189 
 TYR   0.025   0.002   TYR A 496 
 PHE   0.030   0.002   PHE B 132 
 TRP   0.045   0.002   TRP B 159 
 HIS   0.003   0.001   HIS A1163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (11756)
  covalent geometry    : angle       0.64763 (16227)
  hydrogen bonds       : bond        0.04262 (  586)
  hydrogen bonds       : angle       4.43970 ( 1642)
  Misc. bond           : bond        0.00036 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2005.24 seconds
wall clock time: 35 minutes 25.52 seconds (2125.52 seconds total)