Starting phenix.real_space_refine
on Fri Oct 23 14:28:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/22fr_68246/10_2026/22fr_68246.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/22fr_68246/10_2026/22fr_68246.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/22fr_68246/10_2026/22fr_68246.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/22fr_68246/10_2026/22fr_68246.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/22fr_68246/10_2026/22fr_68246.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/22fr_68246/10_2026/22fr_68246.cif"
  }
  resolution = 2.74
  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=  -0.015 sd=   0.076
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: 4
    Type Number    sf(0)   Gaussians
     S      61      5.16       5
     C    6414      2.51       5
     N    1632      2.21       5
     O    1794      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 62 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9901
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1240, 9901
          Classifications: {'peptide': 1240}
          Link IDs: {'PTRANS': 53, 'TRANS': 1186}
          Chain breaks: 4
  Time building chain proxies: 2.21, per 1000 atoms: 0.22
  Number of scatterers: 9901
  At special positions: 0
  Unit cell: (73.209, 99.734, 144.296, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      61     16.00
     O    1794      8.00
     N    1632      7.00
     C    6414      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 712 " - pdb=" SG  CYS A 732 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1402 " - pdb=" SG  CYS A1444 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1418 " - pdb=" SG  CYS A1441 " distance=2.03

  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=0, symmetry=0
  Time building additional restraints: 0.88
  Conformation dependent library (CDL) restraints added in 418.8 milliseconds
  

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2314

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 8 sheets defined
      61.5% alpha, 9.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 192 through 201
    Processing helix  chain 'A' and resid 221 through 228
    Processing helix  chain 'A' and resid 229 through 231
      No H-bonds generated for 'chain 'A' and resid 229 through 231'
    Processing helix  chain 'A' and resid 247 through 258
      removed outlier: 3.645A  pdb=" N   ALA A 255 " --> pdb=" O   THR A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 285
    Processing helix  chain 'A' and resid 287 through 291
      removed outlier: 3.765A  pdb=" N   ARG A 291 " --> pdb=" O   SER A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 319
    Processing helix  chain 'A' and resid 334 through 351
      removed outlier: 3.565A  pdb=" N   GLU A 340 " --> pdb=" O   ALA A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 369
    Processing helix  chain 'A' and resid 388 through 399
      removed outlier: 4.593A  pdb=" N   LYS A 392 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   GLU A 393 " --> pdb=" O   THR A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 415
    Processing helix  chain 'A' and resid 434 through 444
      removed outlier: 3.535A  pdb=" N   ASN A 444 " --> pdb=" O   THR A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 460
    Processing helix  chain 'A' and resid 492 through 511
    Processing helix  chain 'A' and resid 512 through 533
      removed outlier: 3.618A  pdb=" N   ILE A 516 " --> pdb=" O   PRO A 512 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL A 532 " --> pdb=" O   ILE A 528 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   PHE A 533 " --> pdb=" O   LEU A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 541
      No H-bonds generated for 'chain 'A' and resid 539 through 541'
    Processing helix  chain 'A' and resid 542 through 560
    Processing helix  chain 'A' and resid 563 through 581
      removed outlier: 4.052A  pdb=" N   SER A 567 " --> pdb=" O   LEU A 563 " (cutoff:3.500A)
      Proline residue:  A 573  - end of helix
    Processing helix  chain 'A' and resid 585 through 617
      removed outlier: 3.538A  pdb=" N   ASP A 589 " --> pdb=" O   ARG A 585 " (cutoff:3.500A)
      Proline residue:  A 599  - end of helix
      removed outlier: 3.880A  pdb=" N   VAL A 611 " --> pdb=" O   SER A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 649
      removed outlier: 3.725A  pdb=" N   VAL A 649 " --> pdb=" O   SER A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 670
      removed outlier: 3.733A  pdb=" N   MET A 657 " --> pdb=" O   ILE A 653 " (cutoff:3.500A)
      Proline residue:  A 659  - end of helix
      removed outlier: 3.808A  pdb=" N   VAL A 662 " --> pdb=" O   THR A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 680
    Processing helix  chain 'A' and resid 681 through 683
      No H-bonds generated for 'chain 'A' and resid 681 through 683'
    Processing helix  chain 'A' and resid 684 through 690
    Processing helix  chain 'A' and resid 691 through 706
    Processing helix  chain 'A' and resid 726 through 730
    Processing helix  chain 'A' and resid 746 through 754
    Processing helix  chain 'A' and resid 757 through 759
      No H-bonds generated for 'chain 'A' and resid 757 through 759'
    Processing helix  chain 'A' and resid 760 through 785
    Processing helix  chain 'A' and resid 900 through 909
    Processing helix  chain 'A' and resid 933 through 935
      No H-bonds generated for 'chain 'A' and resid 933 through 935'
    Processing helix  chain 'A' and resid 951 through 964
    Processing helix  chain 'A' and resid 969 through 985
    Processing helix  chain 'A' and resid 1002 through 1016
      removed outlier: 3.585A  pdb=" N   GLU A1014 " --> pdb=" O   THR A1010 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1033 through 1050
    Processing helix  chain 'A' and resid 1062 through 1067
      removed outlier: 3.595A  pdb=" N   ALA A1067 " --> pdb=" O   ALA A1063 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1077 through 1079
      No H-bonds generated for 'chain 'A' and resid 1077 through 1079'
    Processing helix  chain 'A' and resid 1088 through 1090
      No H-bonds generated for 'chain 'A' and resid 1088 through 1090'
    Processing helix  chain 'A' and resid 1091 through 1101
      removed outlier: 3.586A  pdb=" N   TYR A1101 " --> pdb=" O   TYR A1097 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1111 through 1120
    Processing helix  chain 'A' and resid 1131 through 1138
    Processing helix  chain 'A' and resid 1139 through 1157
      removed outlier: 3.511A  pdb=" N   GLN A1143 " --> pdb=" O   SER A1139 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   SER A1157 " --> pdb=" O   GLU A1153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1174 through 1193
    Processing helix  chain 'A' and resid 1196 through 1215
    Processing helix  chain 'A' and resid 1221 through 1235
      removed outlier: 3.690A  pdb=" N   GLN A1226 " --> pdb=" O   MET A1222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1238 through 1260
      Proline residue:  A1248  - end of helix
    Processing helix  chain 'A' and resid 1268 through 1300
      removed outlier: 3.771A  pdb=" N   GLU A1280 " --> pdb=" O   GLN A1276 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ILE A1281 " --> pdb=" O   ILE A1277 " (cutoff:3.500A)
      Proline residue:  A1282  - end of helix
      removed outlier: 4.081A  pdb=" N   TYR A1297 " --> pdb=" O   PHE A1293 " (cutoff:3.500A)
      Proline residue:  A1298  - end of helix
    Processing helix  chain 'A' and resid 1301 through 1305
    Processing helix  chain 'A' and resid 1310 through 1339
      removed outlier: 4.239A  pdb=" N   PHE A1339 " --> pdb=" O   LEU A1335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1342 through 1360
    Processing helix  chain 'A' and resid 1371 through 1374
    Processing helix  chain 'A' and resid 1375 through 1380
    Processing helix  chain 'A' and resid 1381 through 1396
      removed outlier: 3.898A  pdb=" N   TYR A1385 " --> pdb=" O   ASN A1381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1417 through 1430
      Proline residue:  A1424  - end of helix
      removed outlier: 3.719A  pdb=" N   PHE A1428 " --> pdb=" O   PRO A1424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1448 through 1456
      removed outlier: 4.034A  pdb=" N   PHE A1452 " --> pdb=" O   SER A1448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1459 through 1461
      No H-bonds generated for 'chain 'A' and resid 1459 through 1461'
    Processing helix  chain 'A' and resid 1462 through 1489
    Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 177
      removed outlier: 5.399A  pdb=" N   MET A 173 " --> pdb=" O   ASN A 127 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 130 through 131
    Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 236
      removed outlier: 6.963A  pdb=" N   ILE A 234 " --> pdb=" O   CYS A 325 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   ASP A 327 " --> pdb=" O   ILE A 234 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   SER A 236 " --> pdb=" O   ASP A 327 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   GLN A 324 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 7.876A  pdb=" N   ALA A 359 " --> pdb=" O   GLN A 324 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   TRP A 326 " --> pdb=" O   ALA A 359 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   VAL A 374 " --> pdb=" O   PHE A 385 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   PHE A 385 " --> pdb=" O   VAL A 374 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   VAL A 376 " --> pdb=" O   ILE A 383 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 709 through 711
    Processing sheet with id=AA5, first strand: chain 'A' and resid 874 through 885
      removed outlier: 6.382A  pdb=" N   TYR A 866 " --> pdb=" O   ILE A 877 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   ASP A 879 " --> pdb=" O   LEU A 864 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   LEU A 864 " --> pdb=" O   ASP A 879 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   VAL A 881 " --> pdb=" O   ARG A 862 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   ARG A 862 " --> pdb=" O   VAL A 881 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   GLY A 883 " --> pdb=" O   PHE A 860 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   PHE A 860 " --> pdb=" O   GLY A 883 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 874 through 885
      removed outlier: 6.382A  pdb=" N   TYR A 866 " --> pdb=" O   ILE A 877 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   ASP A 879 " --> pdb=" O   LEU A 864 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   LEU A 864 " --> pdb=" O   ASP A 879 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   VAL A 881 " --> pdb=" O   ARG A 862 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   ARG A 862 " --> pdb=" O   VAL A 881 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   GLY A 883 " --> pdb=" O   PHE A 860 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   PHE A 860 " --> pdb=" O   GLY A 883 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 937 through 940
      removed outlier: 6.182A  pdb=" N   GLY A 938 " --> pdb=" O   PHE A1024 " (cutoff:3.500A)
      removed outlier: 7.647A  pdb=" N   ASP A1026 " --> pdb=" O   GLY A 938 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   VAL A 940 " --> pdb=" O   ASP A1026 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   LEU A1023 " --> pdb=" O   LEU A1055 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   THR A1057 " --> pdb=" O   LEU A1023 " (cutoff:3.500A)
      removed outlier: 7.443A  pdb=" N   LEU A1025 " --> pdb=" O   THR A1057 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   ILE A 890 " --> pdb=" O   ARG A1071 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   LEU A1073 " --> pdb=" O   ILE A 890 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ALA A 892 " --> pdb=" O   LEU A1073 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   LEU A1075 " --> pdb=" O   ALA A 892 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   MET A 894 " --> pdb=" O   LEU A1075 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   LEU A1072 " --> pdb=" O   PHE A1084 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   PHE A1084 " --> pdb=" O   LEU A1072 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   PHE A1074 " --> pdb=" O   ALA A1082 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1408 through 1410

    547 hydrogen bonds defined for protein.
    1587 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.13

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2329
        1.33 -     1.45: 2282
        1.45 -     1.57: 5452
        1.57 -     1.69: 0
        1.69 -     1.81: 100
  Bond restraints: 10163
  Sorted by residual:
  bond pdb=" CA  LEU A 562 "
       pdb=" C   LEU A 562 "
    ideal  model  delta    sigma   weight residual
    1.522  1.552 -0.030 1.43e-02 4.89e+03 4.37e+00
  bond pdb=" CB  THR A1355 "
       pdb=" OG1 THR A1355 "
    ideal  model  delta    sigma   weight residual
    1.433  1.400  0.033 1.60e-02 3.91e+03 4.18e+00
  bond pdb=" CB  THR A 661 "
       pdb=" OG1 THR A 661 "
    ideal  model  delta    sigma   weight residual
    1.433  1.401  0.032 1.60e-02 3.91e+03 4.07e+00
  bond pdb=" CB  THR A 636 "
       pdb=" OG1 THR A 636 "
    ideal  model  delta    sigma   weight residual
    1.433  1.403  0.030 1.60e-02 3.91e+03 3.46e+00
  bond pdb=" CB  THR A 671 "
       pdb=" OG1 THR A 671 "
    ideal  model  delta    sigma   weight residual
    1.433  1.404  0.029 1.60e-02 3.91e+03 3.35e+00
  ... (remaining 10158 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 13351
        1.56 -     3.11: 323
        3.11 -     4.67: 93
        4.67 -     6.23: 15
        6.23 -     7.79: 6
  Bond angle restraints: 13788
  Sorted by residual:
  angle pdb=" N   THR A 636 "
        pdb=" CA  THR A 636 "
        pdb=" CB  THR A 636 "
      ideal   model   delta    sigma   weight residual
     110.12  116.41   -6.29 1.47e+00 4.63e-01 1.83e+01
  angle pdb=" OE1 GLN A 522 "
        pdb=" CD  GLN A 522 "
        pdb=" NE2 GLN A 522 "
      ideal   model   delta    sigma   weight residual
     122.60  118.42    4.18 1.00e+00 1.00e+00 1.74e+01
  angle pdb=" CA  PHE A 556 "
        pdb=" CB  PHE A 556 "
        pdb=" CG  PHE A 556 "
      ideal   model   delta    sigma   weight residual
     113.80  109.64    4.16 1.00e+00 1.00e+00 1.73e+01
  angle pdb=" CA  PHE A 643 "
        pdb=" CB  PHE A 643 "
        pdb=" CG  PHE A 643 "
      ideal   model   delta    sigma   weight residual
     113.80  117.87   -4.07 1.00e+00 1.00e+00 1.66e+01
  angle pdb=" CA  SER A 605 "
        pdb=" C   SER A 605 "
        pdb=" O   SER A 605 "
      ideal   model   delta    sigma   weight residual
     120.70  116.82    3.88 1.03e+00 9.43e-01 1.42e+01
  ... (remaining 13783 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 5252
       17.13 -    34.26: 509
       34.26 -    51.39: 153
       51.39 -    68.52: 39
       68.52 -    85.65: 12
  Dihedral angle restraints: 5965
    sinusoidal: 2347
      harmonic: 3618
  Sorted by residual:
  dihedral pdb=" C   THR A 661 "
           pdb=" N   THR A 661 "
           pdb=" CA  THR A 661 "
           pdb=" CB  THR A 661 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.71    9.71     0      2.50e+00 1.60e-01 1.51e+01
  dihedral pdb=" N   THR A 661 "
           pdb=" C   THR A 661 "
           pdb=" CA  THR A 661 "
           pdb=" CB  THR A 661 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  132.34   -8.94     0      2.50e+00 1.60e-01 1.28e+01
  dihedral pdb=" CA  PRO A 403 "
           pdb=" C   PRO A 403 "
           pdb=" N   GLN A 404 "
           pdb=" CA  GLN A 404 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.93  -17.07     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 5962 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 1382
       0.080 -    0.159: 105
       0.159 -    0.239: 7
       0.239 -    0.318: 2
       0.318 -    0.398: 1
  Chirality restraints: 1497
  Sorted by residual:
  chirality pdb=" CA  THR A 661 "
            pdb=" N   THR A 661 "
            pdb=" C   THR A 661 "
            pdb=" CB  THR A 661 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.13    0.40 2.00e-01 2.50e+01 3.95e+00
  chirality pdb=" CB  THR A 636 "
            pdb=" CA  THR A 636 "
            pdb=" OG1 THR A 636 "
            pdb=" CG2 THR A 636 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.25    0.31 2.00e-01 2.50e+01 2.34e+00
  chirality pdb=" CA  PHE A 556 "
            pdb=" N   PHE A 556 "
            pdb=" C   PHE A 556 "
            pdb=" CB  PHE A 556 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.52e+00
  ... (remaining 1494 not shown)

  Planarity restraints: 1753
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 629 "    0.178 2.00e-02 2.50e+03   9.61e-02 2.31e+02
        pdb=" CG  TRP A 629 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 629 "   -0.068 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 629 "   -0.072 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 629 "   -0.075 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 629 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 629 "   -0.123 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 629 "    0.134 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 629 "   -0.060 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 629 "    0.092 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 628 "   -0.053 2.00e-02 2.50e+03   3.23e-02 2.08e+01
        pdb=" CG  TYR A 628 "    0.004 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 628 "    0.040 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 628 "    0.018 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 628 "    0.012 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 628 "    0.035 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 628 "   -0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR A 628 "   -0.047 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 552 "    0.048 2.00e-02 2.50e+03   2.95e-02 1.52e+01
        pdb=" CG  PHE A 552 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 552 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 552 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 552 "    0.011 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 552 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 552 "    0.025 2.00e-02 2.50e+03
  ... (remaining 1750 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 121
        2.65 -     3.21: 9318
        3.21 -     3.77: 15955
        3.77 -     4.34: 22943
        4.34 -     4.90: 36984
  Nonbonded interactions: 85321
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 304 "
            pdb=" OE1 GLU A 307 "
     model   vdw
     2.082 3.040
  nonbonded pdb=" O   ALA A 734 "
            pdb=" OG  SER A 737 "
     model   vdw
     2.124 3.040
  nonbonded pdb=" N   GLU A1109 "
            pdb=" OE1 GLU A1109 "
     model   vdw
     2.144 3.120
  nonbonded pdb=" N   GLU A 723 "
            pdb=" OE1 GLU A 723 "
     model   vdw
     2.179 3.120
  nonbonded pdb=" O   TYR A 670 "
            pdb=" ND2 ASN A 688 "
     model   vdw
     2.205 3.120
  ... (remaining 85316 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
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:             2.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.380
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9233
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      :  0.004   0.042  10166  Z= 0.182
  Angle     :  0.649   7.787  13794  Z= 0.386
  Chirality :  0.045   0.398   1497
  Planarity :  0.006   0.096   1753
  Dihedral  : 15.890  85.653   3642
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 16.54 %
    Favored  : 82.33 %
  Cbeta Deviations :  0.09 %
  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 are not related in a simple way.
  whole:  0.84 (0.24), residues: 1230
  helix:  1.26 (0.19), residues: 679
  sheet: -0.15 (0.47), residues: 95
  loop : -0.23 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 126 
 TYR   0.053   0.002   TYR A 628 
 PHE   0.048   0.003   PHE A 552 
 TRP   0.178   0.005   TRP A 629 
 HIS   0.002   0.001   HIS A1127 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.18 (10163)
  covalent geometry    : angle       0.64875 /  0.39 (13788)
  SS BOND              : bond        0.00111 /  0.05 (    3)
  SS BOND              : angle       0.37000 /  0.23 (    6)
  hydrogen bonds       : bond        0.12834 /  8.61 (  544)
  hydrogen bonds       : angle       5.55903 /  3.79 ( 1587)

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.245 
Fit side-chains
  outliers start: 12
  outliers final: 11
  residues processed: 118
  average time/residue: 0.6169
  time to fit residues: 77.8031
Evaluate side-chains
  115 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 SER
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  699 SER
Chi-restraints excluded: chain A residue  727 ARG
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  965 SER
Chi-restraints excluded: chain A residue 1164 ASP
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1461 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks: [108, 49, 97, 113, 53, 5, 33, 123, 65, 62, 51]
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 123 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 724 ASN
A 729 ASN
A1414 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2574 r_free = 0.2574 target = 0.045478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2436 r_free = 0.2436 target = 0.040874 restraints weight = 27092.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.2436 rms_B_bonded: 1.46
r_work: 0.2348 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2261 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.2261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9228
moved from start:          0.0783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10166  Z= 0.161
  Angle     :  0.564   7.827  13794  Z= 0.300
  Chirality :  0.043   0.134   1497
  Planarity :  0.004   0.053   1753
  Dihedral  :  5.406  47.344   1381
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 15.22 %
    Favored  : 82.42 %
  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 are not related in a simple way.
  whole:  1.09 (0.24), residues: 1230
  helix:  1.50 (0.19), residues: 688
  sheet: -0.18 (0.47), residues: 95
  loop : -0.19 (0.31), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 126 
 TYR   0.014   0.002   TYR A 285 
 PHE   0.016   0.002   PHE A 556 
 TRP   0.016   0.001   TRP A 629 
 HIS   0.003   0.001   HIS A 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00376 /  0.16 (10163)
  covalent geometry    : angle       0.56440 /  0.30 (13788)
  SS BOND              : bond        0.00341 /  0.17 (    3)
  SS BOND              : angle       0.72136 /  0.46 (    6)
  hydrogen bonds       : bond        0.04699 /  3.09 (  544)
  hydrogen bonds       : angle       4.42158 /  3.01 ( 1587)

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
REVERT: A  270 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7454 (ptm-80)
REVERT: A  523 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8616 (tp)
REVERT: A  525 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.8002 (tmm)
REVERT: A 1229 MET cc_start: 0.9357 (OUTLIER) cc_final: 0.9055 (ttm)
  outliers start: 25
  outliers final: 11
  residues processed: 119
  average time/residue: 0.5717
  time to fit residues: 72.9421
Evaluate side-chains
  118 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  270 ARG
Chi-restraints excluded: chain A residue  387 LYS
Chi-restraints excluded: chain A residue  518 SER
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  699 SER
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain A residue  965 SER
Chi-restraints excluded: chain A residue 1229 MET
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1320 MET
Chi-restraints excluded: chain A residue 1402 CYS
Chi-restraints excluded: chain A residue 1414 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks: [56, 67, 13, 50, 107, 48, 37, 42, 72, 84, 108]
   chunk 56 optimal weight:    5.9990
   chunk 67 optimal weight:    0.7980
   chunk 13 optimal weight:    0.4980
   chunk 50 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 84 optimal weight:    3.9990
   chunk 108 optimal weight:    2.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1414 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.046396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2466 r_free = 0.2466 target = 0.041837 restraints weight = 26719.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.2465 rms_B_bonded: 1.40
r_work: 0.2379 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.2292 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.2292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9211
moved from start:          0.0947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10166  Z= 0.139
  Angle     :  0.527   7.069  13794  Z= 0.279
  Chirality :  0.041   0.171   1497
  Planarity :  0.004   0.050   1753
  Dihedral  :  4.693  44.400   1370
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 15.31 %
    Favored  : 81.76 %
  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 are not related in a simple way.
  whole:  1.24 (0.24), residues: 1230
  helix:  1.62 (0.19), residues: 687
  sheet: -0.19 (0.47), residues: 95
  loop : -0.10 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 126 
 TYR   0.012   0.001   TYR A1132 
 PHE   0.014   0.002   PHE A 625 
 TRP   0.013   0.001   TRP A 629 
 HIS   0.002   0.001   HIS A 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.14 (10163)
  covalent geometry    : angle       0.52738 /  0.28 (13788)
  SS BOND              : bond        0.00279 /  0.14 (    3)
  SS BOND              : angle       0.63301 /  0.41 (    6)
  hydrogen bonds       : bond        0.04299 /  2.83 (  544)
  hydrogen bonds       : angle       4.25172 /  2.90 ( 1587)

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 105
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A  270 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7387 (ptm-80)
REVERT: A  523 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8633 (tp)
REVERT: A  525 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7989 (tmm)
  outliers start: 31
  outliers final: 12
  residues processed: 126
  average time/residue: 0.5762
  time to fit residues: 78.0078
Evaluate side-chains
  116 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 ARG
Chi-restraints excluded: chain A residue  387 LYS
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  699 SER
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  965 SER
Chi-restraints excluded: chain A residue 1164 ASP
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1320 MET
Chi-restraints excluded: chain A residue 1368 ASP
Chi-restraints excluded: chain A residue 1402 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks: [73, 6, 92, 69, 65, 19, 54, 71, 25, 58, 88]
   chunk 73 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0980
   chunk 92 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0770
   chunk 71 optimal weight:    0.0970
   chunk 25 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 88 optimal weight:    4.9990
   overall best weight:    0.6540

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 436 GLN
A1414 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.046911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2480 r_free = 0.2480 target = 0.042354 restraints weight = 26961.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.2480 rms_B_bonded: 1.41
r_work: 0.2395 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.2309 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.2309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9201
moved from start:          0.1113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10166  Z= 0.128
  Angle     :  0.511   7.077  13794  Z= 0.270
  Chirality :  0.041   0.144   1497
  Planarity :  0.004   0.048   1753
  Dihedral  :  4.536  44.291   1370
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.97 %
    Favored  : 81.47 %
  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 are not related in a simple way.
  whole:  1.37 (0.24), residues: 1230
  helix:  1.74 (0.19), residues: 688
  sheet: -0.21 (0.47), residues: 95
  loop : -0.06 (0.31), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 126 
 TYR   0.012   0.001   TYR A 394 
 PHE   0.016   0.001   PHE A 556 
 TRP   0.011   0.001   TRP A 629 
 HIS   0.002   0.001   HIS A 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 (10163)
  covalent geometry    : angle       0.51127 /  0.27 (13788)
  SS BOND              : bond        0.00250 /  0.12 (    3)
  SS BOND              : angle       0.63446 /  0.41 (    6)
  hydrogen bonds       : bond        0.04077 /  2.69 (  544)
  hydrogen bonds       : angle       4.14777 /  2.84 ( 1587)

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
REVERT: A  270 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7462 (ptm-80)
REVERT: A  523 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8611 (tp)
REVERT: A  525 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.8088 (tmm)
REVERT: A  566 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8067 (mmt)
  outliers start: 27
  outliers final: 12
  residues processed: 117
  average time/residue: 0.5849
  time to fit residues: 73.2948
Evaluate side-chains
  119 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  270 ARG
Chi-restraints excluded: chain A residue  387 LYS
Chi-restraints excluded: chain A residue  518 SER
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue 1164 ASP
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1320 MET
Chi-restraints excluded: chain A residue 1368 ASP
Chi-restraints excluded: chain A residue 1402 CYS
Chi-restraints excluded: chain A residue 1414 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks: [94, 29, 17, 1, 16, 75, 7, 37, 87, 71, 45]
   chunk 94 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0870
   chunk 71 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.6158

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 729 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2632 r_free = 0.2632 target = 0.047284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2494 r_free = 0.2494 target = 0.042619 restraints weight = 26885.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.2493 rms_B_bonded: 1.46
r_work: 0.2407 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2319 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9204
moved from start:          0.1198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10166  Z= 0.123
  Angle     :  0.512   7.082  13794  Z= 0.270
  Chirality :  0.041   0.182   1497
  Planarity :  0.004   0.044   1753
  Dihedral  :  4.253  44.271   1367
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 16.54 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.24), residues: 1230
  helix:  1.80 (0.19), residues: 688
  sheet: -0.20 (0.48), residues: 95
  loop : -0.05 (0.31), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 126 
 TYR   0.016   0.001   TYR A 285 
 PHE   0.015   0.001   PHE A 556 
 TRP   0.014   0.001   TRP A 629 
 HIS   0.002   0.001   HIS A 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.12 (10163)
  covalent geometry    : angle       0.51199 /  0.27 (13788)
  SS BOND              : bond        0.00168 /  0.08 (    3)
  SS BOND              : angle       0.68721 /  0.45 (    6)
  hydrogen bonds       : bond        0.03960 /  2.61 (  544)
  hydrogen bonds       : angle       4.11335 /  2.82 ( 1587)

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A  270 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7539 (ptm-80)
REVERT: A  523 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8632 (tp)
REVERT: A  566 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8069 (mmt)
  outliers start: 27
  outliers final: 12
  residues processed: 119
  average time/residue: 0.5879
  time to fit residues: 75.2209
Evaluate side-chains
  116 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  270 ARG
Chi-restraints excluded: chain A residue  387 LYS
Chi-restraints excluded: chain A residue  518 SER
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue 1164 ASP
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1320 MET
Chi-restraints excluded: chain A residue 1368 ASP
Chi-restraints excluded: chain A residue 1402 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks: [43, 54, 119, 47, 61, 100, 99, 34, 92, 58, 46]
   chunk 43 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 119 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0870
   chunk 61 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 46 optimal weight:    6.9990
   overall best weight:    0.9762

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2608 r_free = 0.2608 target = 0.046562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2472 r_free = 0.2472 target = 0.041991 restraints weight = 26928.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.2471 rms_B_bonded: 1.42
r_work: 0.2385 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.2299 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.2299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9203
moved from start:          0.1227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10166  Z= 0.149
  Angle     :  0.530   7.103  13794  Z= 0.279
  Chirality :  0.042   0.162   1497
  Planarity :  0.004   0.044   1753
  Dihedral  :  4.306  44.344   1367
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 15.88 %
    Favored  : 81.29 %
  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 are not related in a simple way.
  whole:  1.38 (0.24), residues: 1230
  helix:  1.74 (0.19), residues: 688
  sheet: -0.21 (0.48), residues: 95
  loop : -0.03 (0.31), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 126 
 TYR   0.015   0.002   TYR A 285 
 PHE   0.030   0.002   PHE A 556 
 TRP   0.017   0.001   TRP A 629 
 HIS   0.002   0.001   HIS A 760 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.15 (10163)
  covalent geometry    : angle       0.52974 /  0.28 (13788)
  SS BOND              : bond        0.00221 /  0.11 (    3)
  SS BOND              : angle       0.64108 /  0.42 (    6)
  hydrogen bonds       : bond        0.04197 /  2.75 (  544)
  hydrogen bonds       : angle       4.11896 /  2.82 ( 1587)

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 106
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: A  177 MET cc_start: 0.9122 (mpt) cc_final: 0.8811 (mpt)
REVERT: A  202 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8846 (t)
REVERT: A  270 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7560 (ptm-80)
REVERT: A  429 ASP cc_start: 0.8561 (p0) cc_final: 0.8332 (p0)
REVERT: A  523 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8600 (tp)
REVERT: A  525 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7949 (tmm)
REVERT: A  566 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8069 (mmt)
REVERT: A 1086 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8243 (mm-30)
REVERT: A 1229 MET cc_start: 0.9385 (OUTLIER) cc_final: 0.9129 (ttm)
  outliers start: 30
  outliers final: 13
  residues processed: 125
  average time/residue: 0.5758
  time to fit residues: 77.3112
Evaluate side-chains
  122 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  270 ARG
Chi-restraints excluded: chain A residue  387 LYS
Chi-restraints excluded: chain A residue  518 SER
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue 1164 ASP
Chi-restraints excluded: chain A residue 1229 MET
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1320 MET
Chi-restraints excluded: chain A residue 1368 ASP
Chi-restraints excluded: chain A residue 1402 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks: [6, 103, 0, 2, 4, 76, 87, 105, 11, 56, 32]
   chunk 6 optimal weight:    0.6980
   chunk 103 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.5386

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2574 r_free = 0.2574 target = 0.045357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2437 r_free = 0.2437 target = 0.040821 restraints weight = 26985.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.2432 rms_B_bonded: 1.41
r_work: 0.2348 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2262 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.2262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9220
moved from start:          0.1199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  10166  Z= 0.201
  Angle     :  0.571   7.162  13794  Z= 0.302
  Chirality :  0.044   0.139   1497
  Planarity :  0.004   0.048   1753
  Dihedral  :  4.472  44.764   1367
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 16.16 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.23), residues: 1230
  helix:  1.52 (0.19), residues: 689
  sheet: -0.27 (0.48), residues: 95
  loop : -0.22 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 331 
 TYR   0.016   0.002   TYR A 285 
 PHE   0.030   0.002   PHE A 556 
 TRP   0.011   0.001   TRP A 629 
 HIS   0.004   0.001   HIS A 760 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00485 /  0.20 (10163)
  covalent geometry    : angle       0.57083 /  0.30 (13788)
  SS BOND              : bond        0.00288 /  0.15 (    3)
  SS BOND              : angle       0.70278 /  0.46 (    6)
  hydrogen bonds       : bond        0.04661 /  3.05 (  544)
  hydrogen bonds       : angle       4.22815 /  2.88 ( 1587)

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 105
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
REVERT: A  177 MET cc_start: 0.9135 (mpt) cc_final: 0.8783 (mpt)
REVERT: A  202 VAL cc_start: 0.9117 (OUTLIER) cc_final: 0.8905 (t)
REVERT: A  270 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7641 (ptm-80)
REVERT: A  523 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8621 (tp)
REVERT: A  525 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8000 (tmm)
REVERT: A  566 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8133 (mmt)
REVERT: A 1086 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8276 (mm-30)
REVERT: A 1229 MET cc_start: 0.9384 (OUTLIER) cc_final: 0.9145 (ttm)
  outliers start: 31
  outliers final: 14
  residues processed: 124
  average time/residue: 0.5684
  time to fit residues: 75.9739
Evaluate side-chains
  124 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  236 SER
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  270 ARG
Chi-restraints excluded: chain A residue  387 LYS
Chi-restraints excluded: chain A residue  518 SER
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  699 SER
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue 1164 ASP
Chi-restraints excluded: chain A residue 1229 MET
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1320 MET
Chi-restraints excluded: chain A residue 1368 ASP
Chi-restraints excluded: chain A residue 1402 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks: [96, 28, 26, 29, 95, 122, 117, 7, 17, 18, 12]
   chunk 96 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0270
   chunk 29 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 122 optimal weight:    0.5980
   chunk 117 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.7242

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2617 r_free = 0.2617 target = 0.046899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2482 r_free = 0.2482 target = 0.042334 restraints weight = 26747.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.2481 rms_B_bonded: 1.41
r_work: 0.2395 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.2308 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9198
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10166  Z= 0.131
  Angle     :  0.538   7.191  13794  Z= 0.282
  Chirality :  0.041   0.158   1497
  Planarity :  0.004   0.044   1753
  Dihedral  :  4.303  44.820   1367
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 17.30 %
    Favored  : 80.15 %
  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 are not related in a simple way.
  whole:  1.28 (0.24), residues: 1230
  helix:  1.68 (0.19), residues: 689
  sheet: -0.05 (0.49), residues: 88
  loop : -0.17 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 433 
 TYR   0.012   0.001   TYR A 285 
 PHE   0.022   0.002   PHE A 625 
 TRP   0.009   0.001   TRP A 634 
 HIS   0.002   0.001   HIS A 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 (10163)
  covalent geometry    : angle       0.53800 /  0.28 (13788)
  SS BOND              : bond        0.00176 /  0.09 (    3)
  SS BOND              : angle       0.60508 /  0.39 (    6)
  hydrogen bonds       : bond        0.04054 /  2.67 (  544)
  hydrogen bonds       : angle       4.12300 /  2.82 ( 1587)

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A  177 MET cc_start: 0.9144 (mpt) cc_final: 0.8830 (mpt)
REVERT: A  202 VAL cc_start: 0.9045 (OUTLIER) cc_final: 0.8825 (t)
REVERT: A  270 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7582 (ptm-80)
REVERT: A  523 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8575 (tp)
REVERT: A  525 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7978 (tmm)
REVERT: A  566 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8054 (mmt)
REVERT: A 1086 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8254 (mm-30)
REVERT: A 1229 MET cc_start: 0.9394 (OUTLIER) cc_final: 0.9118 (ttm)
  outliers start: 27
  outliers final: 11
  residues processed: 121
  average time/residue: 0.5628
  time to fit residues: 73.2780
Evaluate side-chains
  119 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  270 ARG
Chi-restraints excluded: chain A residue  518 SER
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  699 SER
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue 1164 ASP
Chi-restraints excluded: chain A residue 1229 MET
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1320 MET
Chi-restraints excluded: chain A residue 1368 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks: [25, 24, 96, 110, 45, 58, 0, 52, 32, 40, 92]
   chunk 25 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0010
   chunk 96 optimal weight:    3.9990
   chunk 110 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 58 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.5186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.047828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2506 r_free = 0.2506 target = 0.043219 restraints weight = 26731.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.2500 rms_B_bonded: 1.43
r_work: 0.2417 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.2333 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.2333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9177
moved from start:          0.1493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10166  Z= 0.118
  Angle     :  0.539  13.032  13794  Z= 0.279
  Chirality :  0.041   0.160   1497
  Planarity :  0.004   0.051   1753
  Dihedral  :  4.182  44.189   1367
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 17.86 %
    Favored  : 79.68 %
  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 are not related in a simple way.
  whole:  1.38 (0.24), residues: 1230
  helix:  1.78 (0.19), residues: 688
  sheet:  0.03 (0.51), residues: 88
  loop : -0.17 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 685 
 TYR   0.019   0.001   TYR A 285 
 PHE   0.023   0.001   PHE A 556 
 TRP   0.022   0.001   TRP A 629 
 HIS   0.002   0.001   HIS A1050 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.12 (10163)
  covalent geometry    : angle       0.53901 /  0.28 (13788)
  SS BOND              : bond        0.00154 /  0.08 (    3)
  SS BOND              : angle       0.55857 /  0.36 (    6)
  hydrogen bonds       : bond        0.03842 /  2.53 (  544)
  hydrogen bonds       : angle       4.05135 /  2.78 ( 1587)

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 TYR cc_start: 0.5881 (t80) cc_final: 0.5561 (t80)
REVERT: A  202 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8740 (t)
REVERT: A  430 LYS cc_start: 0.8895 (mtmm) cc_final: 0.8660 (mmmm)
REVERT: A  523 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8526 (tp)
REVERT: A  525 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7935 (tmm)
REVERT: A  566 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8006 (mmt)
REVERT: A  614 PHE cc_start: 0.8215 (t80) cc_final: 0.7976 (t80)
REVERT: A 1086 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8247 (mm-30)
  outliers start: 26
  outliers final: 13
  residues processed: 121
  average time/residue: 0.5752
  time to fit residues: 74.9041
Evaluate side-chains
  120 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  236 SER
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  518 SER
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  699 SER
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  965 SER
Chi-restraints excluded: chain A residue 1164 ASP
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1320 MET
Chi-restraints excluded: chain A residue 1402 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks: [32, 76, 96, 37, 46, 98, 92, 112, 38, 79, 119]
   chunk 32 optimal weight:    2.9990
   chunk 76 optimal weight:    0.2980
   chunk 96 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 98 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9980
   chunk 112 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0570
   chunk 79 optimal weight:    0.8980
   chunk 119 optimal weight:    3.9990
   overall best weight:    0.6098

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.047794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2506 r_free = 0.2506 target = 0.043219 restraints weight = 26585.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.2501 rms_B_bonded: 1.41
r_work: 0.2419 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.2335 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.2335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9179
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10166  Z= 0.122
  Angle     :  0.543  12.852  13794  Z= 0.280
  Chirality :  0.041   0.177   1497
  Planarity :  0.004   0.046   1753
  Dihedral  :  4.172  44.094   1367
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 19.19 %
    Favored  : 79.21 %
  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 are not related in a simple way.
  whole:  1.39 (0.24), residues: 1230
  helix:  1.77 (0.19), residues: 688
  sheet:  0.08 (0.51), residues: 88
  loop : -0.15 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 685 
 TYR   0.018   0.001   TYR A 722 
 PHE   0.015   0.001   PHE A 625 
 TRP   0.031   0.001   TRP A 629 
 HIS   0.002   0.001   HIS A 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.12 (10163)
  covalent geometry    : angle       0.54295 /  0.28 (13788)
  SS BOND              : bond        0.00159 /  0.08 (    3)
  SS BOND              : angle       0.55690 /  0.36 (    6)
  hydrogen bonds       : bond        0.03857 /  2.54 (  544)
  hydrogen bonds       : angle       4.05013 /  2.78 ( 1587)

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 TYR cc_start: 0.5887 (t80) cc_final: 0.5577 (t80)
REVERT: A  202 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8759 (t)
REVERT: A  523 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8527 (tp)
REVERT: A  525 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7918 (tmm)
REVERT: A  566 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.7996 (mmt)
REVERT: A  614 PHE cc_start: 0.8211 (t80) cc_final: 0.7982 (t80)
REVERT: A 1086 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8186 (mm-30)
  outliers start: 17
  outliers final: 12
  residues processed: 115
  average time/residue: 0.5730
  time to fit residues: 70.8083
Evaluate side-chains
  119 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  518 SER
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  699 SER
Chi-restraints excluded: chain A residue  885 VAL
Chi-restraints excluded: chain A residue  965 SER
Chi-restraints excluded: chain A residue 1164 ASP
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1320 MET
Chi-restraints excluded: chain A residue 1402 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks: [122, 94, 112, 61, 119, 68, 87, 34, 36, 29, 73]
   chunk 122 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 112 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 119 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 73 optimal weight:    4.9990
   overall best weight:    1.3186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2593 r_free = 0.2593 target = 0.046082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2456 r_free = 0.2456 target = 0.041506 restraints weight = 26911.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.2451 rms_B_bonded: 1.40
r_work: 0.2367 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2283 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.2283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9209
moved from start:          0.1393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10166  Z= 0.180
  Angle     :  0.585  12.722  13794  Z= 0.306
  Chirality :  0.044   0.241   1497
  Planarity :  0.004   0.045   1753
  Dihedral  :  4.399  44.596   1367
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 19.28 %
    Favored  : 79.02 %
  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 are not related in a simple way.
  whole:  1.03 (0.23), residues: 1230
  helix:  1.52 (0.19), residues: 689
  sheet: -0.35 (0.50), residues: 90
  loop : -0.32 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 685 
 TYR   0.021   0.002   TYR A 285 
 PHE   0.030   0.002   PHE A 556 
 TRP   0.043   0.002   TRP A 629 
 HIS   0.003   0.001   HIS A 760 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00428 /  0.18 (10163)
  covalent geometry    : angle       0.58478 /  0.31 (13788)
  SS BOND              : bond        0.00271 /  0.14 (    3)
  SS BOND              : angle       0.61962 /  0.41 (    6)
  hydrogen bonds       : bond        0.04487 /  2.93 (  544)
  hydrogen bonds       : angle       4.17540 /  2.85 ( 1587)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2881.32 seconds
wall clock time: 50 minutes 0.99 seconds (3000.99 seconds total)