Starting phenix.real_space_refine
on Wed Feb  4 12:43:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jbv_61327/02_2026/9jbv_61327.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jbv_61327/02_2026/9jbv_61327.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jbv_61327/02_2026/9jbv_61327.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jbv_61327/02_2026/9jbv_61327.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jbv_61327/02_2026/9jbv_61327.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jbv_61327/02_2026/9jbv_61327.cif"
  }
  resolution = 3.17
  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
-------------------------------------------------------------------------------
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=  -0.002 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      59      5.16       5
     C    6599      2.51       5
     N    1753      2.21       5
     O    1880      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10291
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 10291
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1276, 10291
          Classifications: {'peptide': 1276}
          Link IDs: {'PCIS': 3, 'PTRANS': 60, 'TRANS': 1212}
          Chain breaks: 5
  Time building chain proxies: 2.49, per 1000 atoms: 0.24
  Number of scatterers: 10291
  At special positions: 0
  Unit cell: (101.816, 100.71, 135.017, 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      59     16.00
     O    1880      8.00
     N    1753      7.00
     C    6599      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 172 " - pdb=" SG  CYS A 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 267 " - pdb=" SG  CYS A 348 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 547 " - pdb=" SG  CYS A 573 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 649 " - pdb=" SG  CYS A 730 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 957 " - pdb=" SG  CYS A 983 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1024 " - pdb=" SG  CYS A1028 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1146 " - pdb=" SG  CYS A1294 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1299 " - pdb=" SG  CYS A1451 " 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: 0.76
  Conformation dependent library (CDL) restraints added in 549.7 milliseconds
  

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2390

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 25 sheets defined
      10.8% alpha, 29.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 138 through 143
    Processing helix  chain 'A' and resid 160 through 164
    Processing helix  chain 'A' and resid 183 through 189
    Processing helix  chain 'A' and resid 201 through 209
      removed outlier: 3.588A  pdb=" N   LYS A 205 " --> pdb=" O   GLY A 201 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   THR A 208 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 234
      removed outlier: 3.696A  pdb=" N   ASN A 233 " --> pdb=" O   GLU A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 336
    Processing helix  chain 'A' and resid 425 through 431
    Processing helix  chain 'A' and resid 559 through 564
    Processing helix  chain 'A' and resid 601 through 603
      No H-bonds generated for 'chain 'A' and resid 601 through 603'
    Processing helix  chain 'A' and resid 606 through 614
      removed outlier: 3.650A  pdb=" N   LEU A 614 " --> pdb=" O   ILE A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 620
    Processing helix  chain 'A' and resid 624 through 631
    Processing helix  chain 'A' and resid 713 through 720
    Processing helix  chain 'A' and resid 878 through 882
      removed outlier: 3.730A  pdb=" N   GLY A 882 " --> pdb=" O   GLU A 879 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 917 through 923
      removed outlier: 3.586A  pdb=" N   GLN A 923 " --> pdb=" O   ASP A 920 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 967 through 975
    Processing helix  chain 'A' and resid 1011 through 1013
      No H-bonds generated for 'chain 'A' and resid 1011 through 1013'
    Processing helix  chain 'A' and resid 1015 through 1024
    Processing helix  chain 'A' and resid 1034 through 1041
    Processing helix  chain 'A' and resid 1128 through 1134
    Processing helix  chain 'A' and resid 1329 through 1333
    Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 24
    Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 24
    Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 97
      removed outlier: 6.671A  pdb=" N   ILE A  95 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   CYS A 198 " --> pdb=" O   ILE A  95 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   ALA A  97 " --> pdb=" O   CYS A 198 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA5, first strand: chain 'A' and resid 213 through 219
    Processing sheet with id=AA6, first strand: chain 'A' and resid 305 through 307
      removed outlier: 3.699A  pdb=" N   GLY A 323 " --> pdb=" O   VAL A 345 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 295 through 297
    Processing sheet with id=AA8, first strand: chain 'A' and resid 441 through 450
      removed outlier: 4.241A  pdb=" N   TYR A 404 " --> pdb=" O   TYR A 450 " (cutoff:3.500A)
      removed outlier: 6.077A  pdb=" N   HIS A 403 " --> pdb=" O   ILE A 483 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   LYS A 485 " --> pdb=" O   HIS A 403 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ILE A 405 " --> pdb=" O   LYS A 485 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 472 through 475
      removed outlier: 3.506A  pdb=" N   ILE A 572 " --> pdb=" O   LEU A 548 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 632 through 636
      removed outlier: 3.552A  pdb=" N   MET A 633 " --> pdb=" O   PHE A 598 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   ASN A 591 " --> pdb=" O   TYR A 657 " (cutoff:3.500A)
      removed outlier: 8.072A  pdb=" N   LEU A 659 " --> pdb=" O   ASN A 591 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   ILE A 593 " --> pdb=" O   LEU A 659 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER A 693 " --> pdb=" O   SER A 660 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 648 through 649
      removed outlier: 3.517A  pdb=" N   SER A 728 " --> pdb=" O   VAL A 648 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   TRP A 707 " --> pdb=" O   LEU A 725 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 677 through 679
    Processing sheet with id=AB4, first strand: chain 'A' and resid 855 through 862
      removed outlier: 3.616A  pdb=" N   ALA A 827 " --> pdb=" O   LYS A 901 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 911 through 912
    Processing sheet with id=AB6, first strand: chain 'A' and resid 957 through 958
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1042 through 1046
      removed outlier: 3.633A  pdb=" N   THR A1006 " --> pdb=" O   ALA A1045 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   GLN A 999 " --> pdb=" O   ARG A1066 " (cutoff:3.500A)
      removed outlier: 7.410A  pdb=" N   TYR A1068 " --> pdb=" O   GLN A 999 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   PHE A1001 " --> pdb=" O   TYR A1068 " (cutoff:3.500A)
      removed outlier: 7.682A  pdb=" N   LEU A1070 " --> pdb=" O   PHE A1001 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   LEU A1003 " --> pdb=" O   LEU A1070 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   SER A1071 " --> pdb=" O   VAL A1107 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   VAL A1107 " --> pdb=" O   SER A1071 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1058 through 1060
      removed outlier: 6.051A  pdb=" N   MET A1059 " --> pdb=" O   TYR A1142 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1095 through 1098
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1162 through 1164
      removed outlier: 13.045A  pdb=" N   VAL A1198 " --> pdb=" O   HIS A1277 " (cutoff:3.500A)
      removed outlier: 11.888A  pdb=" N   HIS A1277 " --> pdb=" O   VAL A1198 " (cutoff:3.500A)
      removed outlier: 11.851A  pdb=" N   LEU A1200 " --> pdb=" O   ARG A1275 " (cutoff:3.500A)
      removed outlier: 12.431A  pdb=" N   ARG A1275 " --> pdb=" O   LEU A1200 " (cutoff:3.500A)
      removed outlier: 9.511A  pdb=" N   ALA A1202 " --> pdb=" O   TYR A1273 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   TYR A1273 " --> pdb=" O   ALA A1202 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   MET A1204 " --> pdb=" O   ALA A1271 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ALA A1271 " --> pdb=" O   MET A1204 " (cutoff:3.500A)
      removed outlier: 7.554A  pdb=" N   GLY A1208 " --> pdb=" O   PRO A1267 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 1162 through 1164
      removed outlier: 5.041A  pdb=" N   ILE A1206 " --> pdb=" O   CYS A1294 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   CYS A1294 " --> pdb=" O   ILE A1206 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 1214 through 1215
      removed outlier: 4.064A  pdb=" N   ALA A1214 " --> pdb=" O   LEU A1221 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU A1221 " --> pdb=" O   ALA A1214 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC3
    Processing sheet with id=AC4, first strand: chain 'A' and resid 1397 through 1398
    Processing sheet with id=AC5, first strand: chain 'A' and resid 1397 through 1398
      removed outlier: 6.718A  pdb=" N   GLU A1384 " --> pdb=" O   GLN A1436 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   THR A1366 " --> pdb=" O   LEU A1422 " (cutoff:3.500A)
      removed outlier: 9.988A  pdb=" N   LYS A1364 " --> pdb=" O   PRO A1424 " (cutoff:3.500A)
      removed outlier: 10.201A  pdb=" N   LEU A1426 " --> pdb=" O   THR A1362 " (cutoff:3.500A)
      removed outlier: 8.987A  pdb=" N   THR A1362 " --> pdb=" O   LEU A1426 " (cutoff:3.500A)
      removed outlier: 10.499A  pdb=" N   THR A1428 " --> pdb=" O   GLN A1360 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   GLN A1360 " --> pdb=" O   THR A1428 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   TYR A1430 " --> pdb=" O   ASP A1358 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   ASP A1358 " --> pdb=" O   TYR A1430 " (cutoff:3.500A)
      removed outlier: 5.303A  pdb=" N   VAL A1365 " --> pdb=" O   CYS A1451 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   CYS A1451 " --> pdb=" O   VAL A1365 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLY A1367 " --> pdb=" O   LEU A1449 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'A' and resid 1373 through 1375
    Processing sheet with id=AC7, first strand: chain 'A' and resid 1400 through 1401

    248 hydrogen bonds defined for protein.
    618 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: 2.21

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3290
        1.34 -     1.46: 2616
        1.46 -     1.58: 4570
        1.58 -     1.70: 0
        1.70 -     1.82: 99
  Bond restraints: 10575
  Sorted by residual:
  bond pdb=" CA  VAL A 343 "
       pdb=" CB  VAL A 343 "
    ideal  model  delta    sigma   weight residual
    1.540  1.526  0.014 1.36e-02 5.41e+03 1.12e+00
  bond pdb=" C   SER A 308 "
       pdb=" N   PRO A 309 "
    ideal  model  delta    sigma   weight residual
    1.334  1.359 -0.025 2.34e-02 1.83e+03 1.11e+00
  bond pdb=" N   SER A1285 "
       pdb=" CA  SER A1285 "
    ideal  model  delta    sigma   weight residual
    1.458  1.467 -0.009 9.00e-03 1.23e+04 9.59e-01
  bond pdb=" C   LEU A 523 "
       pdb=" N   PRO A 524 "
    ideal  model  delta    sigma   weight residual
    1.332  1.344 -0.013 1.30e-02 5.92e+03 9.59e-01
  bond pdb=" C   VAL A 147 "
       pdb=" N   PHE A 148 "
    ideal  model  delta    sigma   weight residual
    1.331  1.303  0.028 2.83e-02 1.25e+03 9.53e-01
  ... (remaining 10570 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 13936
        1.28 -     2.55: 310
        2.55 -     3.83: 77
        3.83 -     5.11: 9
        5.11 -     6.39: 4
  Bond angle restraints: 14336
  Sorted by residual:
  angle pdb=" CA  VAL A1255 "
        pdb=" C   VAL A1255 "
        pdb=" N   ASP A1256 "
      ideal   model   delta    sigma   weight residual
     116.60  121.57   -4.97 1.45e+00 4.76e-01 1.18e+01
  angle pdb=" C   ASP A 422 "
        pdb=" N   ASP A 423 "
        pdb=" CA  ASP A 423 "
      ideal   model   delta    sigma   weight residual
     121.54  126.67   -5.13 1.91e+00 2.74e-01 7.23e+00
  angle pdb=" C   VAL A1255 "
        pdb=" N   ASP A1256 "
        pdb=" CA  ASP A1256 "
      ideal   model   delta    sigma   weight residual
     121.54  116.58    4.96 1.91e+00 2.74e-01 6.75e+00
  angle pdb=" C   ILE A1283 "
        pdb=" N   ARG A1284 "
        pdb=" CA  ARG A1284 "
      ideal   model   delta    sigma   weight residual
     121.54  116.70    4.84 1.91e+00 2.74e-01 6.42e+00
  angle pdb=" O   VAL A1255 "
        pdb=" C   VAL A1255 "
        pdb=" N   ASP A1256 "
      ideal   model   delta    sigma   weight residual
     122.57  119.41    3.16 1.25e+00 6.40e-01 6.40e+00
  ... (remaining 14331 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 5607
       17.92 -    35.84: 536
       35.84 -    53.76: 93
       53.76 -    71.68: 29
       71.68 -    89.60: 6
  Dihedral angle restraints: 6271
    sinusoidal: 2551
      harmonic: 3720
  Sorted by residual:
  dihedral pdb=" CB  CYS A1146 "
           pdb=" SG  CYS A1146 "
           pdb=" SG  CYS A1294 "
           pdb=" CB  CYS A1294 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    2.29  -88.29     1      1.00e+01 1.00e-02 9.31e+01
  dihedral pdb=" CB  CYS A 649 "
           pdb=" SG  CYS A 649 "
           pdb=" SG  CYS A 730 "
           pdb=" CB  CYS A 730 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   26.13   66.87     1      1.00e+01 1.00e-02 5.83e+01
  dihedral pdb=" CA  SER A1257 "
           pdb=" C   SER A1257 "
           pdb=" N   SER A1258 "
           pdb=" CA  SER A1258 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.54  -19.46     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 6268 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1219
       0.048 -    0.096: 223
       0.096 -    0.144: 89
       0.144 -    0.192: 2
       0.192 -    0.240: 1
  Chirality restraints: 1534
  Sorted by residual:
  chirality pdb=" CG  LEU A1221 "
            pdb=" CB  LEU A1221 "
            pdb=" CD1 LEU A1221 "
            pdb=" CD2 LEU A1221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.35   -0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CB  ILE A 527 "
            pdb=" CA  ILE A 527 "
            pdb=" CG1 ILE A 527 "
            pdb=" CG2 ILE A 527 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.15 2.00e-01 2.50e+01 5.68e-01
  chirality pdb=" CA  PRO A 309 "
            pdb=" N   PRO A 309 "
            pdb=" C   PRO A 309 "
            pdb=" CB  PRO A 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.44e-01
  ... (remaining 1531 not shown)

  Planarity restraints: 1829
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 148 "   -0.025 5.00e-02 4.00e+02   3.77e-02 2.28e+00
        pdb=" N   PRO A 149 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 149 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 149 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 906 "   -0.022 5.00e-02 4.00e+02   3.39e-02 1.84e+00
        pdb=" N   PRO A 907 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 907 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 907 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 568 "   -0.019 5.00e-02 4.00e+02   2.92e-02 1.36e+00
        pdb=" N   PRO A 569 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A 569 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 569 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 1826 not shown)

  Histogram of nonbonded interaction distances:
        2.54 -     3.02: 5696
        3.02 -     3.49: 10464
        3.49 -     3.96: 17907
        3.96 -     4.43: 20979
        4.43 -     4.90: 33155
  Nonbonded interactions: 88201
  Sorted by model distance:
  nonbonded pdb=" O   ILE A1050 "
            pdb=" O   GLY A1134 "
     model   vdw
     2.545 3.040
  nonbonded pdb=" O   THR A 607 "
            pdb=" OE1 GLN A 611 "
     model   vdw
     2.562 3.040
  nonbonded pdb=" O   ASN A 895 "
            pdb=" OD1 ASN A 895 "
     model   vdw
     2.598 3.040
  nonbonded pdb=" O   VAL A1255 "
            pdb=" CA  ASP A1256 "
     model   vdw
     2.608 2.776
  nonbonded pdb=" N   GLU A1094 "
            pdb=" O   GLU A1094 "
     model   vdw
     2.617 2.496
  ... (remaining 88196 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:             0.250
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.180
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6759
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      :  0.003   0.028  10583  Z= 0.127
  Angle     :  0.504   6.385  14352  Z= 0.276
  Chirality :  0.043   0.240   1534
  Planarity :  0.003   0.038   1829
  Dihedral  : 14.398  89.600   3857
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.65 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.03 (0.24), residues: 1264
  helix: -1.36 (0.48), residues: 102
  sheet: -1.83 (0.29), residues: 310
  loop : -1.16 (0.22), residues: 852

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 719 
 TYR   0.012   0.001   TYR A 675 
 PHE   0.009   0.001   PHE A1160 
 TRP   0.014   0.001   TRP A 125 
 HIS   0.003   0.001   HIS A 712 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (10575)
  covalent geometry    : angle       0.50381 (14336)
  SS BOND              : bond        0.00247 (    8)
  SS BOND              : angle       0.80819 (   16)
  hydrogen bonds       : bond        0.22956 (  240)
  hydrogen bonds       : angle      11.28829 (  618)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 291
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 THR cc_start: 0.8335 (m) cc_final: 0.7967 (p)
REVERT: A   75 ASP cc_start: 0.8455 (p0) cc_final: 0.7984 (p0)
REVERT: A  101 ASP cc_start: 0.8532 (m-30) cc_final: 0.7986 (m-30)
REVERT: A  110 MET cc_start: 0.7418 (mtp) cc_final: 0.6935 (mtm)
REVERT: A  140 ARG cc_start: 0.7922 (ttt-90) cc_final: 0.7530 (ttp80)
REVERT: A  141 GLU cc_start: 0.7493 (mp0) cc_final: 0.6667 (mp0)
REVERT: A  169 ASP cc_start: 0.7947 (m-30) cc_final: 0.7584 (m-30)
REVERT: A  432 ASN cc_start: 0.8205 (t0) cc_final: 0.7727 (m-40)
REVERT: A  598 PHE cc_start: 0.8260 (m-80) cc_final: 0.7345 (m-10)
REVERT: A  600 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7654 (mm-30)
REVERT: A  633 MET cc_start: 0.7984 (mmt) cc_final: 0.7751 (mmm)
REVERT: A  699 MET cc_start: 0.8624 (ptp) cc_final: 0.8366 (ptp)
REVERT: A  703 ASN cc_start: 0.5189 (t0) cc_final: 0.4987 (t0)
REVERT: A  718 ASN cc_start: 0.8795 (m-40) cc_final: 0.8583 (m-40)
REVERT: A  879 GLU cc_start: 0.8051 (tt0) cc_final: 0.7818 (tp30)
REVERT: A  897 MET cc_start: 0.7197 (ttt) cc_final: 0.6980 (ttm)
REVERT: A  917 TYR cc_start: 0.7187 (m-80) cc_final: 0.6211 (m-80)
REVERT: A  974 SER cc_start: 0.7482 (m) cc_final: 0.7269 (p)
REVERT: A 1020 MET cc_start: 0.8235 (tmm) cc_final: 0.8004 (ptm)
REVERT: A 1032 MET cc_start: 0.7758 (mpp) cc_final: 0.7556 (mmt)
REVERT: A 1037 PHE cc_start: 0.8131 (t80) cc_final: 0.7918 (t80)
REVERT: A 1072 MET cc_start: 0.6751 (mtm) cc_final: 0.6420 (mtm)
REVERT: A 1098 MET cc_start: 0.8525 (mtp) cc_final: 0.7787 (mtm)
REVERT: A 1226 PHE cc_start: 0.8780 (p90) cc_final: 0.8533 (p90)
REVERT: A 1229 MET cc_start: 0.8473 (mmt) cc_final: 0.7810 (mmt)
REVERT: A 1294 CYS cc_start: 0.6182 (p) cc_final: 0.5726 (p)
REVERT: A 1305 MET cc_start: 0.7917 (mmm) cc_final: 0.7293 (mmm)
REVERT: A 1316 THR cc_start: 0.7950 (t) cc_final: 0.7747 (p)
REVERT: A 1320 TYR cc_start: 0.9056 (p90) cc_final: 0.8319 (p90)
REVERT: A 1328 TRP cc_start: 0.7697 (m100) cc_final: 0.6111 (m100)
REVERT: A 1364 LYS cc_start: 0.7928 (tttt) cc_final: 0.7656 (ptmm)
REVERT: A 1380 MET cc_start: 0.8313 (mpp) cc_final: 0.7872 (mtm)
REVERT: A 1387 ILE cc_start: 0.8722 (mm) cc_final: 0.8455 (mm)
REVERT: A 1406 LYS cc_start: 0.8760 (tptm) cc_final: 0.8536 (tptp)
REVERT: A 1408 PHE cc_start: 0.7931 (m-80) cc_final: 0.7636 (m-80)
REVERT: A 1428 THR cc_start: 0.9062 (t) cc_final: 0.8759 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 291
  average time/residue: 0.1101
  time to fit residues: 44.4308
Evaluate side-chains
  170 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:   30.0000
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    9.9990
   chunk 53 optimal weight:    0.1980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:   10.0000
   chunk 123 optimal weight:    0.7980
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    0.0060
   chunk 51 optimal weight:    9.9990
   overall best weight:    2.4000

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

Flipped N/Q/H residues before XYZ refinement:
A  76 HIS
A 158 GLN
A 212 HIS
A 302 GLN
A 324 GLN
** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 436 GLN
A 463 HIS
A 487 GLN
A 497 HIS
A 631 ASN
** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 903 GLN
A 973 HIS
A 992 HIS
A1031 GLN
A1061 GLN
A1079 HIS
A1082 HIS
A1185 ASN
A1212 GLN
A1216 GLN
A1238 GLN
A1262 HIS
A1434 HIS
A1440 HIS

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.137746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.113088 restraints weight = 22911.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 4.12
r_work: 0.3615 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10583  Z= 0.153
  Angle     :  0.619  15.082  14352  Z= 0.318
  Chirality :  0.046   0.164   1534
  Planarity :  0.004   0.046   1829
  Dihedral  :  4.457  19.812   1388
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.17 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 12.12 %
    Favored  : 84.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.02 (0.24), residues: 1264
  helix: -1.42 (0.47), residues: 117
  sheet: -1.66 (0.30), residues: 305
  loop : -1.21 (0.22), residues: 842

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 458 
 TYR   0.013   0.001   TYR A 530 
 PHE   0.019   0.002   PHE A 148 
 TRP   0.013   0.002   TRP A1195 
 HIS   0.008   0.001   HIS A  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (10575)
  covalent geometry    : angle       0.61889 (14336)
  SS BOND              : bond        0.00273 (    8)
  SS BOND              : angle       0.69623 (   16)
  hydrogen bonds       : bond        0.03805 (  240)
  hydrogen bonds       : angle       8.01524 (  618)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 181
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.8525 (p0) cc_final: 0.7998 (p0)
REVERT: A  101 ASP cc_start: 0.8626 (m-30) cc_final: 0.8138 (m-30)
REVERT: A  110 MET cc_start: 0.7633 (mtp) cc_final: 0.7267 (mtm)
REVERT: A  140 ARG cc_start: 0.7677 (ttt-90) cc_final: 0.7435 (ttp80)
REVERT: A  141 GLU cc_start: 0.7380 (mp0) cc_final: 0.6974 (mp0)
REVERT: A  169 ASP cc_start: 0.8054 (m-30) cc_final: 0.7739 (m-30)
REVERT: A  274 TRP cc_start: 0.7426 (m100) cc_final: 0.6909 (m100)
REVERT: A  279 MET cc_start: 0.6579 (tmm) cc_final: 0.6048 (tmm)
REVERT: A  313 LEU cc_start: 0.7710 (pp) cc_final: 0.7228 (tp)
REVERT: A  586 MET cc_start: 0.3971 (tmm) cc_final: 0.3762 (tmm)
REVERT: A  608 GLU cc_start: 0.8061 (mp0) cc_final: 0.7693 (tm-30)
REVERT: A  612 ARG cc_start: 0.8376 (tmm-80) cc_final: 0.8166 (ptm-80)
REVERT: A  633 MET cc_start: 0.7519 (mmt) cc_final: 0.7292 (mmm)
REVERT: A  718 ASN cc_start: 0.8876 (m-40) cc_final: 0.8660 (m-40)
REVERT: A  917 TYR cc_start: 0.7375 (m-80) cc_final: 0.6535 (m-80)
REVERT: A 1031 GLN cc_start: 0.6376 (OUTLIER) cc_final: 0.6172 (mp10)
REVERT: A 1072 MET cc_start: 0.6910 (mtm) cc_final: 0.6573 (mtt)
REVERT: A 1098 MET cc_start: 0.8282 (mtp) cc_final: 0.7830 (mtm)
REVERT: A 1212 GLN cc_start: 0.6870 (OUTLIER) cc_final: 0.6563 (pm20)
REVERT: A 1217 LYS cc_start: 0.7390 (tptp) cc_final: 0.6472 (mttt)
REVERT: A 1227 ILE cc_start: 0.8650 (mm) cc_final: 0.8399 (mm)
REVERT: A 1229 MET cc_start: 0.8711 (mmt) cc_final: 0.8092 (mmt)
REVERT: A 1294 CYS cc_start: 0.6020 (p) cc_final: 0.5773 (p)
REVERT: A 1305 MET cc_start: 0.7975 (mmm) cc_final: 0.7765 (mmm)
REVERT: A 1320 TYR cc_start: 0.9074 (p90) cc_final: 0.8279 (p90)
REVERT: A 1328 TRP cc_start: 0.7764 (m100) cc_final: 0.6481 (m100)
REVERT: A 1364 LYS cc_start: 0.8166 (tttt) cc_final: 0.7807 (ptmm)
REVERT: A 1380 MET cc_start: 0.8460 (mpp) cc_final: 0.7806 (mtm)
REVERT: A 1406 LYS cc_start: 0.8948 (tptm) cc_final: 0.8656 (tppp)
REVERT: A 1408 PHE cc_start: 0.8139 (m-80) cc_final: 0.7934 (m-80)
  outliers start: 37
  outliers final: 20
  residues processed: 204
  average time/residue: 0.0995
  time to fit residues: 29.3000
Evaluate side-chains
  178 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 156
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  340 GLU
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  489 SER
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  543 SER
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  913 SER
Chi-restraints excluded: chain A residue  937 THR
Chi-restraints excluded: chain A residue 1031 GLN
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1212 GLN
Chi-restraints excluded: chain A residue 1216 GLN
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1280 HIS
Chi-restraints excluded: chain A residue 1287 LEU
Chi-restraints excluded: chain A residue 1301 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 120 optimal weight:    8.9990
   chunk 49 optimal weight:   30.0000
   chunk 91 optimal weight:    7.9990
   chunk 73 optimal weight:    4.9990
   chunk 36 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0070
   chunk 108 optimal weight:    5.9990
   chunk 71 optimal weight:   10.0000
   chunk 12 optimal weight:    0.8980
   overall best weight:    2.5804

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

Flipped N/Q/H residues before XYZ refinement:
A 228 HIS
A 258 ASN
** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 822 HIS
** A1079 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1102 ASN
** A1216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1434 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.134902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.110667 restraints weight = 23394.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3711 rms_B_bonded: 4.02
r_work: 0.3579 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10583  Z= 0.155
  Angle     :  0.599  12.595  14352  Z= 0.307
  Chirality :  0.046   0.225   1534
  Planarity :  0.004   0.045   1829
  Dihedral  :  4.503  24.837   1388
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.57 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 15.75 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.13 (0.23), residues: 1264
  helix: -1.27 (0.48), residues: 117
  sheet: -1.79 (0.27), residues: 342
  loop : -1.25 (0.22), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 424 
 TYR   0.012   0.001   TYR A 962 
 PHE   0.022   0.002   PHE A1252 
 TRP   0.015   0.002   TRP A 401 
 HIS   0.004   0.001   HIS A 880 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (10575)
  covalent geometry    : angle       0.59876 (14336)
  SS BOND              : bond        0.00450 (    8)
  SS BOND              : angle       0.63095 (   16)
  hydrogen bonds       : bond        0.03546 (  240)
  hydrogen bonds       : angle       7.33234 (  618)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 169
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.8551 (p0) cc_final: 0.8108 (p0)
REVERT: A  101 ASP cc_start: 0.8550 (m-30) cc_final: 0.8132 (m-30)
REVERT: A  110 MET cc_start: 0.7607 (mtp) cc_final: 0.7387 (mtm)
REVERT: A  140 ARG cc_start: 0.7770 (ttt-90) cc_final: 0.7552 (ttp80)
REVERT: A  141 GLU cc_start: 0.7259 (mp0) cc_final: 0.6553 (mp0)
REVERT: A  169 ASP cc_start: 0.8085 (m-30) cc_final: 0.7818 (m-30)
REVERT: A  274 TRP cc_start: 0.7573 (m100) cc_final: 0.7074 (m100)
REVERT: A  279 MET cc_start: 0.6984 (tmm) cc_final: 0.6322 (tmm)
REVERT: A  313 LEU cc_start: 0.7728 (pp) cc_final: 0.7266 (tp)
REVERT: A  339 MET cc_start: 0.7366 (ttm) cc_final: 0.6827 (tpp)
REVERT: A  478 ASP cc_start: 0.7503 (t0) cc_final: 0.7273 (t0)
REVERT: A  585 MET cc_start: 0.4209 (ppp) cc_final: 0.3956 (ppp)
REVERT: A  605 TYR cc_start: 0.7104 (m-80) cc_final: 0.6569 (m-80)
REVERT: A  608 GLU cc_start: 0.8201 (mp0) cc_final: 0.7825 (tm-30)
REVERT: A  612 ARG cc_start: 0.8483 (tmm-80) cc_final: 0.7994 (ptm160)
REVERT: A  718 ASN cc_start: 0.8938 (m-40) cc_final: 0.8710 (m110)
REVERT: A  917 TYR cc_start: 0.7497 (m-80) cc_final: 0.6745 (m-80)
REVERT: A 1020 MET cc_start: 0.7914 (ptm) cc_final: 0.7558 (ptm)
REVERT: A 1098 MET cc_start: 0.8414 (mtp) cc_final: 0.8093 (mtm)
REVERT: A 1205 ILE cc_start: 0.8435 (mp) cc_final: 0.8191 (tp)
REVERT: A 1217 LYS cc_start: 0.7267 (tptp) cc_final: 0.6500 (mptt)
REVERT: A 1229 MET cc_start: 0.8817 (mmt) cc_final: 0.8216 (mmt)
REVERT: A 1294 CYS cc_start: 0.6625 (p) cc_final: 0.6256 (p)
REVERT: A 1320 TYR cc_start: 0.9017 (p90) cc_final: 0.8247 (p90)
REVERT: A 1328 TRP cc_start: 0.7645 (m100) cc_final: 0.6379 (m100)
REVERT: A 1364 LYS cc_start: 0.8305 (tttt) cc_final: 0.7892 (ptmm)
REVERT: A 1380 MET cc_start: 0.8456 (mpp) cc_final: 0.7955 (mtm)
REVERT: A 1406 LYS cc_start: 0.8941 (tptm) cc_final: 0.8664 (tppp)
REVERT: A 1411 ASN cc_start: 0.6591 (m-40) cc_final: 0.6283 (m-40)
  outliers start: 30
  outliers final: 22
  residues processed: 189
  average time/residue: 0.0982
  time to fit residues: 26.7555
Evaluate side-chains
  172 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 150
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  340 GLU
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  489 SER
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  543 SER
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  696 THR
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  913 SER
Chi-restraints excluded: chain A residue  937 THR
Chi-restraints excluded: chain A residue 1125 CYS
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1280 HIS
Chi-restraints excluded: chain A residue 1287 LEU
Chi-restraints excluded: chain A residue 1301 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   chunk 92 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 97 optimal weight:    0.0270
   chunk 119 optimal weight:   40.0000
   chunk 33 optimal weight:    9.9990
   chunk 83 optimal weight:    3.9990
   chunk 9 optimal weight:    8.9990
   chunk 96 optimal weight:    8.9990
   overall best weight:    3.6046

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

Flipped N/Q/H residues before XYZ refinement:
A 293 HIS
** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 591 ASN
A 601 ASN
A 631 ASN
A 713 ASN
A1023 ASN
** A1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1212 GLN
** A1336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1434 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.132081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.108391 restraints weight = 23734.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 3.99
r_work: 0.3540 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7180
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10583  Z= 0.190
  Angle     :  0.626  10.184  14352  Z= 0.320
  Chirality :  0.046   0.174   1534
  Planarity :  0.004   0.047   1829
  Dihedral  :  4.688  18.994   1388
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.88 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 16.28 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.33 (0.23), residues: 1264
  helix: -1.64 (0.44), residues: 123
  sheet: -1.78 (0.27), residues: 354
  loop : -1.40 (0.22), residues: 787

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 424 
 TYR   0.015   0.002   TYR A 962 
 PHE   0.018   0.002   PHE A1252 
 TRP   0.018   0.002   TRP A1237 
 HIS   0.004   0.001   HIS A 880 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 (10575)
  covalent geometry    : angle       0.62408 (14336)
  SS BOND              : bond        0.00467 (    8)
  SS BOND              : angle       1.40726 (   16)
  hydrogen bonds       : bond        0.03672 (  240)
  hydrogen bonds       : angle       7.01624 (  618)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 169
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.8507 (p0) cc_final: 0.8027 (p0)
REVERT: A  101 ASP cc_start: 0.8585 (m-30) cc_final: 0.8186 (m-30)
REVERT: A  110 MET cc_start: 0.7698 (mtp) cc_final: 0.7393 (mtm)
REVERT: A  140 ARG cc_start: 0.7894 (ttt-90) cc_final: 0.7684 (ttp80)
REVERT: A  141 GLU cc_start: 0.7637 (mp0) cc_final: 0.7234 (mp0)
REVERT: A  169 ASP cc_start: 0.8154 (m-30) cc_final: 0.7865 (m-30)
REVERT: A  274 TRP cc_start: 0.7704 (m100) cc_final: 0.7062 (m100)
REVERT: A  279 MET cc_start: 0.7144 (tmm) cc_final: 0.6350 (tmm)
REVERT: A  448 MET cc_start: 0.7884 (mtp) cc_final: 0.7423 (mtp)
REVERT: A  478 ASP cc_start: 0.7255 (t0) cc_final: 0.6981 (t0)
REVERT: A  608 GLU cc_start: 0.8213 (mp0) cc_final: 0.7795 (tm-30)
REVERT: A  612 ARG cc_start: 0.8540 (tmm-80) cc_final: 0.8185 (ptm160)
REVERT: A  633 MET cc_start: 0.7544 (mmm) cc_final: 0.7338 (mmm)
REVERT: A  718 ASN cc_start: 0.8959 (m-40) cc_final: 0.8739 (m110)
REVERT: A  917 TYR cc_start: 0.7696 (m-80) cc_final: 0.7036 (m-80)
REVERT: A 1020 MET cc_start: 0.7804 (ptm) cc_final: 0.7569 (ptm)
REVERT: A 1032 MET cc_start: 0.7297 (mmt) cc_final: 0.6901 (mmt)
REVERT: A 1072 MET cc_start: 0.7374 (mtm) cc_final: 0.6948 (mtm)
REVERT: A 1098 MET cc_start: 0.8500 (mtp) cc_final: 0.8153 (mtm)
REVERT: A 1210 MET cc_start: 0.7000 (mmm) cc_final: 0.6767 (mmm)
REVERT: A 1212 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.7165 (pm20)
REVERT: A 1217 LYS cc_start: 0.7549 (tptp) cc_final: 0.6924 (mttt)
REVERT: A 1229 MET cc_start: 0.8759 (mmt) cc_final: 0.8129 (mmt)
REVERT: A 1294 CYS cc_start: 0.6582 (p) cc_final: 0.6211 (p)
REVERT: A 1295 ASP cc_start: 0.6632 (t0) cc_final: 0.6416 (t0)
REVERT: A 1320 TYR cc_start: 0.9060 (p90) cc_final: 0.8306 (p90)
REVERT: A 1328 TRP cc_start: 0.7626 (m100) cc_final: 0.6086 (m100)
REVERT: A 1363 MET cc_start: 0.7533 (tpp) cc_final: 0.7197 (mtt)
REVERT: A 1364 LYS cc_start: 0.8408 (tttt) cc_final: 0.7829 (ptmm)
REVERT: A 1380 MET cc_start: 0.8648 (mpp) cc_final: 0.7934 (mtt)
REVERT: A 1406 LYS cc_start: 0.8843 (tptm) cc_final: 0.8583 (tptt)
REVERT: A 1447 GLU cc_start: 0.8110 (tp30) cc_final: 0.7808 (tp30)
  outliers start: 41
  outliers final: 25
  residues processed: 197
  average time/residue: 0.0858
  time to fit residues: 24.5777
Evaluate side-chains
  186 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 160
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  340 GLU
Chi-restraints excluded: chain A residue  489 SER
Chi-restraints excluded: chain A residue  543 SER
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  696 THR
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  913 SER
Chi-restraints excluded: chain A residue  937 THR
Chi-restraints excluded: chain A residue 1017 THR
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1163 THR
Chi-restraints excluded: chain A residue 1212 GLN
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1280 HIS
Chi-restraints excluded: chain A residue 1287 LEU
Chi-restraints excluded: chain A residue 1301 MET
Chi-restraints excluded: chain A residue 1400 LEU
Chi-restraints excluded: chain A residue 1449 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 100 optimal weight:    0.0170
   chunk 68 optimal weight:    0.6980
   chunk 74 optimal weight:    9.9990
   chunk 126 optimal weight:    7.9990
   chunk 40 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 43 optimal weight:    8.9990
   chunk 36 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   chunk 24 optimal weight:    7.9990
   chunk 97 optimal weight:    9.9990
   overall best weight:    4.1424

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

Flipped N/Q/H residues before XYZ refinement:
A 228 HIS
** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1212 GLN
** A1336 HIS ** 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 = 0.4059 r_free = 0.4059 target = 0.130706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.107082 restraints weight = 23900.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 4.00
r_work: 0.3515 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.3561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  10583  Z= 0.210
  Angle     :  0.660  15.514  14352  Z= 0.333
  Chirality :  0.047   0.231   1534
  Planarity :  0.004   0.046   1829
  Dihedral  :  4.801  19.065   1388
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.99 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 16.11 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.37 (0.23), residues: 1264
  helix: -1.63 (0.44), residues: 128
  sheet: -1.74 (0.26), residues: 363
  loop : -1.47 (0.22), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 424 
 TYR   0.013   0.002   TYR A 530 
 PHE   0.016   0.002   PHE A1108 
 TRP   0.020   0.002   TRP A1237 
 HIS   0.005   0.001   HIS A 880 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 (10575)
  covalent geometry    : angle       0.65939 (14336)
  SS BOND              : bond        0.00335 (    8)
  SS BOND              : angle       1.08385 (   16)
  hydrogen bonds       : bond        0.03602 (  240)
  hydrogen bonds       : angle       6.93709 (  618)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 159
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.8502 (p0) cc_final: 0.8021 (p0)
REVERT: A  101 ASP cc_start: 0.8629 (m-30) cc_final: 0.8242 (m-30)
REVERT: A  110 MET cc_start: 0.7640 (mtp) cc_final: 0.7325 (mtm)
REVERT: A  140 ARG cc_start: 0.7947 (ttt-90) cc_final: 0.7729 (ttp80)
REVERT: A  141 GLU cc_start: 0.7703 (mp0) cc_final: 0.7283 (mp0)
REVERT: A  169 ASP cc_start: 0.8112 (m-30) cc_final: 0.7840 (m-30)
REVERT: A  274 TRP cc_start: 0.7690 (m100) cc_final: 0.7051 (m100)
REVERT: A  279 MET cc_start: 0.7237 (tmm) cc_final: 0.6456 (tmm)
REVERT: A  339 MET cc_start: 0.7551 (ttm) cc_final: 0.7077 (tpp)
REVERT: A  448 MET cc_start: 0.7830 (mtp) cc_final: 0.7294 (mtp)
REVERT: A  478 ASP cc_start: 0.7116 (t0) cc_final: 0.6833 (t0)
REVERT: A  487 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8314 (mt0)
REVERT: A  526 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7569 (mt-10)
REVERT: A  608 GLU cc_start: 0.8202 (mp0) cc_final: 0.7784 (tm-30)
REVERT: A  612 ARG cc_start: 0.8582 (tmm-80) cc_final: 0.8251 (ptm160)
REVERT: A  713 ASN cc_start: 0.8172 (m-40) cc_final: 0.7704 (m110)
REVERT: A  718 ASN cc_start: 0.8993 (m-40) cc_final: 0.8774 (m110)
REVERT: A 1020 MET cc_start: 0.7839 (ptm) cc_final: 0.7502 (ptm)
REVERT: A 1032 MET cc_start: 0.7334 (mmt) cc_final: 0.6898 (mmt)
REVERT: A 1070 LEU cc_start: 0.3992 (OUTLIER) cc_final: 0.3603 (pp)
REVERT: A 1072 MET cc_start: 0.7439 (mtm) cc_final: 0.7067 (mtm)
REVERT: A 1098 MET cc_start: 0.8543 (mtp) cc_final: 0.8200 (mtm)
REVERT: A 1212 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8062 (pm20)
REVERT: A 1217 LYS cc_start: 0.7486 (tptp) cc_final: 0.6817 (mttp)
REVERT: A 1229 MET cc_start: 0.8806 (mmt) cc_final: 0.8184 (mmt)
REVERT: A 1233 ASP cc_start: 0.8255 (t0) cc_final: 0.7579 (p0)
REVERT: A 1249 MET cc_start: 0.6603 (tpt) cc_final: 0.6373 (tpt)
REVERT: A 1294 CYS cc_start: 0.6771 (p) cc_final: 0.6438 (p)
REVERT: A 1320 TYR cc_start: 0.9108 (p90) cc_final: 0.8345 (p90)
REVERT: A 1328 TRP cc_start: 0.7507 (m100) cc_final: 0.5875 (m100)
REVERT: A 1363 MET cc_start: 0.7552 (tpp) cc_final: 0.7261 (mtt)
REVERT: A 1364 LYS cc_start: 0.8439 (tttt) cc_final: 0.7820 (ptmm)
REVERT: A 1380 MET cc_start: 0.8628 (mpp) cc_final: 0.7890 (mtt)
REVERT: A 1447 GLU cc_start: 0.8068 (tp30) cc_final: 0.7757 (tp30)
REVERT: A 1449 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8651 (mm)
  outliers start: 53
  outliers final: 32
  residues processed: 198
  average time/residue: 0.0793
  time to fit residues: 22.7289
Evaluate side-chains
  188 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 152
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  340 GLU
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  433 ASN
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  489 SER
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  543 SER
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  696 THR
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  913 SER
Chi-restraints excluded: chain A residue  937 THR
Chi-restraints excluded: chain A residue 1017 THR
Chi-restraints excluded: chain A residue 1070 LEU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1125 CYS
Chi-restraints excluded: chain A residue 1135 MET
Chi-restraints excluded: chain A residue 1163 THR
Chi-restraints excluded: chain A residue 1196 ILE
Chi-restraints excluded: chain A residue 1212 GLN
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1280 HIS
Chi-restraints excluded: chain A residue 1287 LEU
Chi-restraints excluded: chain A residue 1301 MET
Chi-restraints excluded: chain A residue 1400 LEU
Chi-restraints excluded: chain A residue 1449 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 58 optimal weight:    7.9990
   chunk 66 optimal weight:   10.0000
   chunk 108 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 83 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9980
   chunk 61 optimal weight:   10.0000
   chunk 96 optimal weight:    1.9990
   chunk 92 optimal weight:    8.9990
   chunk 97 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 228 HIS
** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 973 HIS
** A1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1075 ASN
A1212 GLN
A1336 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.131402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.107616 restraints weight = 24109.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 4.08
r_work: 0.3523 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.3794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10583  Z= 0.164
  Angle     :  0.625  13.584  14352  Z= 0.314
  Chirality :  0.046   0.231   1534
  Planarity :  0.004   0.044   1829
  Dihedral  :  4.690  19.513   1388
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.12 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 17.96 %
    Favored  : 78.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.29 (0.23), residues: 1264
  helix: -1.62 (0.44), residues: 122
  sheet: -1.62 (0.27), residues: 354
  loop : -1.45 (0.22), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 424 
 TYR   0.011   0.001   TYR A 605 
 PHE   0.012   0.001   PHE A1252 
 TRP   0.021   0.002   TRP A1195 
 HIS   0.004   0.001   HIS A 973 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (10575)
  covalent geometry    : angle       0.62444 (14336)
  SS BOND              : bond        0.00194 (    8)
  SS BOND              : angle       0.72855 (   16)
  hydrogen bonds       : bond        0.03285 (  240)
  hydrogen bonds       : angle       6.70788 (  618)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 159
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.7643 (mtp) cc_final: 0.7317 (mtm)
REVERT: A  141 GLU cc_start: 0.7719 (mp0) cc_final: 0.7180 (mp0)
REVERT: A  169 ASP cc_start: 0.8101 (m-30) cc_final: 0.7804 (m-30)
REVERT: A  274 TRP cc_start: 0.7634 (m100) cc_final: 0.7089 (m100)
REVERT: A  279 MET cc_start: 0.7178 (tmm) cc_final: 0.6393 (tmm)
REVERT: A  339 MET cc_start: 0.7479 (ttm) cc_final: 0.6858 (tpp)
REVERT: A  448 MET cc_start: 0.7819 (mtp) cc_final: 0.7240 (mtp)
REVERT: A  526 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7534 (mt-10)
REVERT: A  593 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8171 (pt)
REVERT: A  608 GLU cc_start: 0.8103 (mp0) cc_final: 0.7725 (tm-30)
REVERT: A  612 ARG cc_start: 0.8356 (tmm-80) cc_final: 0.8044 (ptm160)
REVERT: A  713 ASN cc_start: 0.8121 (m-40) cc_final: 0.7731 (m110)
REVERT: A  718 ASN cc_start: 0.9012 (m-40) cc_final: 0.8774 (m110)
REVERT: A 1020 MET cc_start: 0.7910 (ptm) cc_final: 0.7535 (ptm)
REVERT: A 1032 MET cc_start: 0.7439 (mmt) cc_final: 0.6869 (mmt)
REVERT: A 1072 MET cc_start: 0.7483 (mtm) cc_final: 0.7111 (mtm)
REVERT: A 1098 MET cc_start: 0.8518 (mtp) cc_final: 0.8176 (mtm)
REVERT: A 1217 LYS cc_start: 0.7515 (tptp) cc_final: 0.6941 (mttp)
REVERT: A 1229 MET cc_start: 0.8820 (mmt) cc_final: 0.8216 (mmt)
REVERT: A 1294 CYS cc_start: 0.6836 (p) cc_final: 0.6578 (p)
REVERT: A 1320 TYR cc_start: 0.9059 (p90) cc_final: 0.8217 (p90)
REVERT: A 1363 MET cc_start: 0.7516 (tpp) cc_final: 0.7278 (mtt)
REVERT: A 1364 LYS cc_start: 0.8354 (tttt) cc_final: 0.7747 (ptmm)
REVERT: A 1380 MET cc_start: 0.8737 (mpp) cc_final: 0.8269 (mtt)
REVERT: A 1447 GLU cc_start: 0.8255 (tp30) cc_final: 0.7965 (tp30)
  outliers start: 40
  outliers final: 28
  residues processed: 187
  average time/residue: 0.0814
  time to fit residues: 22.6048
Evaluate side-chains
  180 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 151
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  340 GLU
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  543 SER
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  696 THR
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  913 SER
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  937 THR
Chi-restraints excluded: chain A residue 1017 THR
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1114 LEU
Chi-restraints excluded: chain A residue 1135 MET
Chi-restraints excluded: chain A residue 1163 THR
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1287 LEU
Chi-restraints excluded: chain A residue 1301 MET
Chi-restraints excluded: chain A residue 1400 LEU
Chi-restraints excluded: chain A residue 1449 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 111 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 89 optimal weight:   10.0000
   chunk 122 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 78 optimal weight:    9.9990
   chunk 86 optimal weight:    9.9990
   chunk 81 optimal weight:    7.9990
   chunk 76 optimal weight:    0.7980
   chunk 97 optimal weight:    0.0980
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 228 HIS
** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1075 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.133355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.109688 restraints weight = 23409.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 4.00
r_work: 0.3565 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7194
moved from start:          0.3955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10583  Z= 0.118
  Angle     :  0.601  11.986  14352  Z= 0.302
  Chirality :  0.045   0.264   1534
  Planarity :  0.004   0.048   1829
  Dihedral  :  4.498  19.652   1388
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.93 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 19.56 %
    Favored  : 77.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.04 (0.23), residues: 1264
  helix: -1.46 (0.45), residues: 123
  sheet: -1.35 (0.28), residues: 344
  loop : -1.34 (0.22), residues: 797

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 424 
 TYR   0.009   0.001   TYR A 605 
 PHE   0.012   0.001   PHE A1325 
 TRP   0.023   0.001   TRP A1195 
 HIS   0.006   0.001   HIS A1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (10575)
  covalent geometry    : angle       0.60143 (14336)
  SS BOND              : bond        0.00115 (    8)
  SS BOND              : angle       0.55151 (   16)
  hydrogen bonds       : bond        0.02918 (  240)
  hydrogen bonds       : angle       6.39310 (  618)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 153
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.8652 (p0) cc_final: 0.8075 (p0)
REVERT: A  110 MET cc_start: 0.7626 (mtp) cc_final: 0.7333 (mtm)
REVERT: A  141 GLU cc_start: 0.7759 (mp0) cc_final: 0.7519 (mp0)
REVERT: A  169 ASP cc_start: 0.8066 (m-30) cc_final: 0.7751 (m-30)
REVERT: A  279 MET cc_start: 0.7231 (tmm) cc_final: 0.6524 (tmm)
REVERT: A  339 MET cc_start: 0.7289 (ttm) cc_final: 0.6916 (tpp)
REVERT: A  448 MET cc_start: 0.7876 (mtp) cc_final: 0.7354 (mtp)
REVERT: A  478 ASP cc_start: 0.6207 (t0) cc_final: 0.5961 (t70)
REVERT: A  487 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8296 (mt0)
REVERT: A  526 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7665 (mt-10)
REVERT: A  687 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7272 (tt)
REVERT: A  713 ASN cc_start: 0.8105 (m-40) cc_final: 0.7758 (m110)
REVERT: A  917 TYR cc_start: 0.7627 (m-80) cc_final: 0.6961 (m-80)
REVERT: A  918 GLU cc_start: 0.7216 (tm-30) cc_final: 0.6992 (tp30)
REVERT: A  936 GLU cc_start: 0.8297 (tp30) cc_final: 0.8030 (tp30)
REVERT: A 1020 MET cc_start: 0.7999 (ptm) cc_final: 0.7538 (ptm)
REVERT: A 1032 MET cc_start: 0.7563 (mmt) cc_final: 0.7235 (mmt)
REVERT: A 1070 LEU cc_start: 0.4577 (OUTLIER) cc_final: 0.4316 (pp)
REVERT: A 1072 MET cc_start: 0.7477 (mtm) cc_final: 0.7067 (mtm)
REVERT: A 1098 MET cc_start: 0.8489 (mtp) cc_final: 0.7952 (mtm)
REVERT: A 1217 LYS cc_start: 0.7452 (tptp) cc_final: 0.7029 (mttt)
REVERT: A 1229 MET cc_start: 0.8798 (mmt) cc_final: 0.8181 (mmt)
REVERT: A 1275 ARG cc_start: 0.8032 (ttp-170) cc_final: 0.7710 (ttp-110)
REVERT: A 1294 CYS cc_start: 0.6698 (p) cc_final: 0.6321 (p)
REVERT: A 1320 TYR cc_start: 0.9040 (p90) cc_final: 0.8090 (p90)
REVERT: A 1363 MET cc_start: 0.7481 (tpp) cc_final: 0.7251 (mtt)
REVERT: A 1364 LYS cc_start: 0.8445 (tttt) cc_final: 0.7817 (ptmm)
REVERT: A 1447 GLU cc_start: 0.8223 (tp30) cc_final: 0.7925 (tp30)
  outliers start: 32
  outliers final: 21
  residues processed: 177
  average time/residue: 0.0836
  time to fit residues: 21.9337
Evaluate side-chains
  169 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  543 SER
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  913 SER
Chi-restraints excluded: chain A residue 1017 THR
Chi-restraints excluded: chain A residue 1070 LEU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1135 MET
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1280 HIS
Chi-restraints excluded: chain A residue 1366 THR
Chi-restraints excluded: chain A residue 1400 LEU
Chi-restraints excluded: chain A residue 1449 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 106 optimal weight:   10.0000
   chunk 54 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 91 optimal weight:    9.9990
   chunk 42 optimal weight:    0.1980
   chunk 0 optimal weight:   10.0000
   chunk 87 optimal weight:    8.9990
   chunk 45 optimal weight:    8.9990
   chunk 123 optimal weight:    0.0030
   chunk 58 optimal weight:    5.9990
   overall best weight:    3.0396

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

Flipped N/Q/H residues before XYZ refinement:
A 228 HIS
** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1075 ASN
** A1079 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1420 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.131421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.107702 restraints weight = 23588.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 4.00
r_work: 0.3533 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.4185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10583  Z= 0.169
  Angle     :  0.650  13.179  14352  Z= 0.326
  Chirality :  0.047   0.326   1534
  Planarity :  0.004   0.050   1829
  Dihedral  :  4.647  19.204   1388
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.20 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 19.65 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.07 (0.24), residues: 1264
  helix: -1.45 (0.44), residues: 129
  sheet: -1.30 (0.29), residues: 342
  loop : -1.40 (0.22), residues: 793

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 424 
 TYR   0.013   0.001   TYR A 962 
 PHE   0.016   0.002   PHE A1408 
 TRP   0.036   0.002   TRP A1237 
 HIS   0.006   0.001   HIS A1441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (10575)
  covalent geometry    : angle       0.64965 (14336)
  SS BOND              : bond        0.00206 (    8)
  SS BOND              : angle       0.80861 (   16)
  hydrogen bonds       : bond        0.03234 (  240)
  hydrogen bonds       : angle       6.41947 (  618)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 146
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.8635 (p0) cc_final: 0.8108 (p0)
REVERT: A  110 MET cc_start: 0.7565 (mtp) cc_final: 0.7258 (mtm)
REVERT: A  141 GLU cc_start: 0.7643 (mp0) cc_final: 0.7428 (mp0)
REVERT: A  169 ASP cc_start: 0.8068 (m-30) cc_final: 0.7759 (m-30)
REVERT: A  279 MET cc_start: 0.7354 (tmm) cc_final: 0.6557 (tmm)
REVERT: A  339 MET cc_start: 0.7310 (ttm) cc_final: 0.6772 (tpp)
REVERT: A  448 MET cc_start: 0.7885 (mtp) cc_final: 0.7281 (mtp)
REVERT: A  478 ASP cc_start: 0.6400 (t0) cc_final: 0.6199 (t70)
REVERT: A  487 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8289 (mt0)
REVERT: A  520 MET cc_start: 0.7945 (ttm) cc_final: 0.7646 (ttp)
REVERT: A  526 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7511 (mt-10)
REVERT: A  687 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7559 (tt)
REVERT: A  713 ASN cc_start: 0.8148 (m-40) cc_final: 0.7811 (m110)
REVERT: A  718 ASN cc_start: 0.9024 (m-40) cc_final: 0.8796 (m110)
REVERT: A  865 ASP cc_start: 0.6655 (p0) cc_final: 0.6382 (p0)
REVERT: A  906 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.7059 (ttp80)
REVERT: A  918 GLU cc_start: 0.7247 (tm-30) cc_final: 0.7005 (tp30)
REVERT: A  936 GLU cc_start: 0.8320 (tp30) cc_final: 0.8053 (tp30)
REVERT: A  973 HIS cc_start: 0.7880 (OUTLIER) cc_final: 0.7388 (m90)
REVERT: A 1020 MET cc_start: 0.8019 (ptm) cc_final: 0.7619 (ptm)
REVERT: A 1032 MET cc_start: 0.7540 (mmt) cc_final: 0.7004 (mmt)
REVERT: A 1070 LEU cc_start: 0.3941 (OUTLIER) cc_final: 0.3644 (pp)
REVERT: A 1072 MET cc_start: 0.7528 (mtm) cc_final: 0.7142 (mtm)
REVERT: A 1098 MET cc_start: 0.8567 (mtp) cc_final: 0.7965 (mtm)
REVERT: A 1217 LYS cc_start: 0.7581 (tptp) cc_final: 0.7041 (mttp)
REVERT: A 1229 MET cc_start: 0.8754 (mmt) cc_final: 0.8096 (mmt)
REVERT: A 1320 TYR cc_start: 0.9126 (p90) cc_final: 0.8560 (p90)
REVERT: A 1363 MET cc_start: 0.7502 (tpp) cc_final: 0.7285 (mtt)
REVERT: A 1364 LYS cc_start: 0.8391 (tttt) cc_final: 0.7738 (ptmm)
REVERT: A 1384 GLU cc_start: 0.7898 (tt0) cc_final: 0.7258 (tp30)
REVERT: A 1411 ASN cc_start: 0.6796 (m-40) cc_final: 0.6545 (m-40)
  outliers start: 38
  outliers final: 28
  residues processed: 173
  average time/residue: 0.0898
  time to fit residues: 23.1859
Evaluate side-chains
  177 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 144
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  489 SER
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  543 SER
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  696 THR
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  906 ARG
Chi-restraints excluded: chain A residue  913 SER
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  973 HIS
Chi-restraints excluded: chain A residue 1017 THR
Chi-restraints excluded: chain A residue 1070 LEU
Chi-restraints excluded: chain A residue 1093 LYS
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1135 MET
Chi-restraints excluded: chain A residue 1163 THR
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1280 HIS
Chi-restraints excluded: chain A residue 1287 LEU
Chi-restraints excluded: chain A residue 1301 MET
Chi-restraints excluded: chain A residue 1366 THR
Chi-restraints excluded: chain A residue 1400 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 105 optimal weight:   10.0000
   chunk 57 optimal weight:    6.9990
   chunk 85 optimal weight:    0.0870
   chunk 113 optimal weight:   10.0000
   chunk 25 optimal weight:    0.0170
   chunk 88 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0000
   chunk 37 optimal weight:    9.9990
   chunk 77 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 81 optimal weight:    0.5980
   overall best weight:    0.7402

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

Flipped N/Q/H residues before XYZ refinement:
A 228 HIS
** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1075 ASN
** A1349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1441 HIS ** 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 = 0.4116 r_free = 0.4116 target = 0.134519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.110768 restraints weight = 23660.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 4.06
r_work: 0.3588 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7139
moved from start:          0.4290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  10583  Z= 0.106
  Angle     :  0.625  16.006  14352  Z= 0.309
  Chirality :  0.046   0.278   1534
  Planarity :  0.004   0.052   1829
  Dihedral  :  4.420  19.187   1388
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.62 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 20.44 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.86 (0.24), residues: 1264
  helix: -1.25 (0.46), residues: 123
  sheet: -1.16 (0.29), residues: 351
  loop : -1.26 (0.23), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 424 
 TYR   0.008   0.001   TYR A 552 
 PHE   0.017   0.001   PHE A1408 
 TRP   0.036   0.002   TRP A1237 
 HIS   0.003   0.001   HIS A1079 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (10575)
  covalent geometry    : angle       0.62452 (14336)
  SS BOND              : bond        0.00141 (    8)
  SS BOND              : angle       0.79635 (   16)
  hydrogen bonds       : bond        0.02792 (  240)
  hydrogen bonds       : angle       6.10989 (  618)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 156
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.8672 (p0) cc_final: 0.8144 (p0)
REVERT: A  110 MET cc_start: 0.7519 (mtp) cc_final: 0.7251 (mtm)
REVERT: A  144 ASP cc_start: 0.4819 (OUTLIER) cc_final: 0.4410 (p0)
REVERT: A  169 ASP cc_start: 0.8143 (m-30) cc_final: 0.7807 (m-30)
REVERT: A  279 MET cc_start: 0.7168 (tmm) cc_final: 0.6420 (tmm)
REVERT: A  339 MET cc_start: 0.7375 (ttm) cc_final: 0.6757 (tpp)
REVERT: A  448 MET cc_start: 0.7932 (mtp) cc_final: 0.7368 (mtp)
REVERT: A  487 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8282 (mt0)
REVERT: A  520 MET cc_start: 0.7831 (ttm) cc_final: 0.7626 (ttp)
REVERT: A  526 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7685 (mt-10)
REVERT: A  713 ASN cc_start: 0.8112 (m-40) cc_final: 0.7781 (m110)
REVERT: A  865 ASP cc_start: 0.6655 (p0) cc_final: 0.6340 (p0)
REVERT: A  906 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6963 (ttp80)
REVERT: A  917 TYR cc_start: 0.7652 (m-80) cc_final: 0.6936 (m-80)
REVERT: A  918 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6886 (tp30)
REVERT: A  936 GLU cc_start: 0.8331 (tp30) cc_final: 0.8107 (tp30)
REVERT: A 1020 MET cc_start: 0.8074 (ptm) cc_final: 0.7628 (ptm)
REVERT: A 1032 MET cc_start: 0.7558 (mmt) cc_final: 0.7227 (mmt)
REVERT: A 1070 LEU cc_start: 0.4456 (OUTLIER) cc_final: 0.4191 (pp)
REVERT: A 1072 MET cc_start: 0.7451 (mtm) cc_final: 0.7026 (mtm)
REVERT: A 1075 ASN cc_start: 0.8199 (m-40) cc_final: 0.7977 (m-40)
REVERT: A 1098 MET cc_start: 0.8424 (mtp) cc_final: 0.7838 (mtm)
REVERT: A 1210 MET cc_start: 0.7138 (mmm) cc_final: 0.6302 (mmm)
REVERT: A 1217 LYS cc_start: 0.7501 (tptp) cc_final: 0.7066 (mttp)
REVERT: A 1229 MET cc_start: 0.8709 (mmt) cc_final: 0.7933 (mmm)
REVERT: A 1305 MET cc_start: 0.7828 (mmm) cc_final: 0.7235 (mmm)
REVERT: A 1320 TYR cc_start: 0.9104 (p90) cc_final: 0.8112 (p90)
REVERT: A 1336 HIS cc_start: 0.8989 (t70) cc_final: 0.8516 (m170)
REVERT: A 1363 MET cc_start: 0.7406 (tpp) cc_final: 0.7204 (mtt)
REVERT: A 1364 LYS cc_start: 0.8417 (tttt) cc_final: 0.7830 (ptmm)
REVERT: A 1384 GLU cc_start: 0.7833 (tt0) cc_final: 0.7228 (tp30)
REVERT: A 1411 ASN cc_start: 0.6779 (m-40) cc_final: 0.6475 (m-40)
REVERT: A 1447 GLU cc_start: 0.8226 (tp30) cc_final: 0.7900 (tp30)
  outliers start: 29
  outliers final: 20
  residues processed: 178
  average time/residue: 0.0919
  time to fit residues: 24.4785
Evaluate side-chains
  171 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 147
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  906 ARG
Chi-restraints excluded: chain A residue 1017 THR
Chi-restraints excluded: chain A residue 1070 LEU
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1114 LEU
Chi-restraints excluded: chain A residue 1135 MET
Chi-restraints excluded: chain A residue 1163 THR
Chi-restraints excluded: chain A residue 1280 HIS
Chi-restraints excluded: chain A residue 1287 LEU
Chi-restraints excluded: chain A residue 1301 MET
Chi-restraints excluded: chain A residue 1366 THR
Chi-restraints excluded: chain A residue 1400 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 62 optimal weight:    0.0870
   chunk 113 optimal weight:    0.4980
   chunk 11 optimal weight:    2.9990
   chunk 54 optimal weight:   10.0000
   chunk 64 optimal weight:    6.9990
   chunk 3 optimal weight:    7.9990
   chunk 36 optimal weight:    9.9990
   chunk 89 optimal weight:    7.9990
   chunk 114 optimal weight:    0.0670
   chunk 42 optimal weight:    6.9990
   chunk 123 optimal weight:    6.9990
   overall best weight:    2.1300

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

Flipped N/Q/H residues before XYZ refinement:
** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1079 HIS
** A1277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.132677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.108866 restraints weight = 23554.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 4.07
r_work: 0.3555 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.4417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10583  Z= 0.138
  Angle     :  0.654  13.647  14352  Z= 0.326
  Chirality :  0.046   0.322   1534
  Planarity :  0.004   0.052   1829
  Dihedral  :  4.518  23.857   1388
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.49 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 20.88 %
    Favored  : 76.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.91 (0.24), residues: 1264
  helix: -1.29 (0.45), residues: 130
  sheet: -1.10 (0.29), residues: 340
  loop : -1.35 (0.22), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 424 
 TYR   0.013   0.001   TYR A1273 
 PHE   0.016   0.001   PHE A1325 
 TRP   0.046   0.002   TRP A1237 
 HIS   0.004   0.001   HIS A1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (10575)
  covalent geometry    : angle       0.65416 (14336)
  SS BOND              : bond        0.00163 (    8)
  SS BOND              : angle       0.86643 (   16)
  hydrogen bonds       : bond        0.02968 (  240)
  hydrogen bonds       : angle       6.11762 (  618)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 143
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.8648 (p0) cc_final: 0.8091 (p0)
REVERT: A  110 MET cc_start: 0.7577 (mtp) cc_final: 0.7306 (mtm)
REVERT: A  144 ASP cc_start: 0.4957 (OUTLIER) cc_final: 0.4535 (p0)
REVERT: A  169 ASP cc_start: 0.8012 (m-30) cc_final: 0.7715 (m-30)
REVERT: A  279 MET cc_start: 0.7353 (tmm) cc_final: 0.6613 (tmm)
REVERT: A  339 MET cc_start: 0.7443 (ttm) cc_final: 0.6758 (tpp)
REVERT: A  448 MET cc_start: 0.8006 (mtp) cc_final: 0.7404 (mtp)
REVERT: A  487 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8300 (mt0)
REVERT: A  526 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7658 (mt-10)
REVERT: A  699 MET cc_start: 0.8242 (ptp) cc_final: 0.7850 (ptt)
REVERT: A  713 ASN cc_start: 0.8141 (m-40) cc_final: 0.7891 (m110)
REVERT: A  719 ARG cc_start: 0.8301 (mpt-90) cc_final: 0.7957 (mpp80)
REVERT: A  865 ASP cc_start: 0.6654 (p0) cc_final: 0.6375 (p0)
REVERT: A  906 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.7081 (ttp80)
REVERT: A  918 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6896 (tp30)
REVERT: A  936 GLU cc_start: 0.8342 (tp30) cc_final: 0.8121 (tp30)
REVERT: A  973 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.7479 (m90)
REVERT: A 1020 MET cc_start: 0.8144 (ptm) cc_final: 0.7775 (ptm)
REVERT: A 1032 MET cc_start: 0.7560 (mmt) cc_final: 0.7354 (mmt)
REVERT: A 1070 LEU cc_start: 0.3921 (OUTLIER) cc_final: 0.3598 (pp)
REVERT: A 1072 MET cc_start: 0.7542 (mtm) cc_final: 0.7149 (mtm)
REVERT: A 1075 ASN cc_start: 0.8218 (m-40) cc_final: 0.8005 (m-40)
REVERT: A 1098 MET cc_start: 0.8506 (mtp) cc_final: 0.7948 (mtm)
REVERT: A 1210 MET cc_start: 0.7094 (mmm) cc_final: 0.6199 (mmm)
REVERT: A 1217 LYS cc_start: 0.7603 (tptp) cc_final: 0.7078 (mttp)
REVERT: A 1229 MET cc_start: 0.8762 (mmt) cc_final: 0.8175 (mmt)
REVERT: A 1275 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.8069 (mtm110)
REVERT: A 1320 TYR cc_start: 0.9165 (p90) cc_final: 0.8838 (p90)
REVERT: A 1364 LYS cc_start: 0.8423 (tttt) cc_final: 0.7829 (ptmm)
REVERT: A 1447 GLU cc_start: 0.8274 (tp30) cc_final: 0.7962 (tp30)
  outliers start: 29
  outliers final: 21
  residues processed: 164
  average time/residue: 0.0925
  time to fit residues: 22.6455
Evaluate side-chains
  168 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 141
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  144 ASP
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  906 ARG
Chi-restraints excluded: chain A residue  973 HIS
Chi-restraints excluded: chain A residue 1017 THR
Chi-restraints excluded: chain A residue 1070 LEU
Chi-restraints excluded: chain A residue 1093 LYS
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1114 LEU
Chi-restraints excluded: chain A residue 1135 MET
Chi-restraints excluded: chain A residue 1163 THR
Chi-restraints excluded: chain A residue 1275 ARG
Chi-restraints excluded: chain A residue 1280 HIS
Chi-restraints excluded: chain A residue 1287 LEU
Chi-restraints excluded: chain A residue 1301 MET
Chi-restraints excluded: chain A residue 1366 THR
Chi-restraints excluded: chain A residue 1400 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 117 optimal weight:    0.0010
   chunk 99 optimal weight:   10.0000
   chunk 46 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   chunk 105 optimal weight:    9.9990
   chunk 126 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 88 optimal weight:    5.9990
   chunk 51 optimal weight:   20.0000
   overall best weight:    3.9994

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

Flipped N/Q/H residues before XYZ refinement:
A 228 HIS
** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1079 HIS
** A1207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1411 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.130826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.107024 restraints weight = 24066.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 4.06
r_work: 0.3517 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.4543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10583  Z= 0.208
  Angle     :  0.707  16.946  14352  Z= 0.352
  Chirality :  0.048   0.333   1534
  Planarity :  0.004   0.049   1829
  Dihedral  :  4.793  21.376   1388
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.07 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 20.00 %
    Favored  : 76.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.11 (0.24), residues: 1264
  helix: -1.42 (0.44), residues: 129
  sheet: -1.35 (0.28), residues: 359
  loop : -1.42 (0.22), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 424 
 TYR   0.015   0.002   TYR A 962 
 PHE   0.015   0.002   PHE A1325 
 TRP   0.048   0.002   TRP A1237 
 HIS   0.007   0.001   HIS A1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 (10575)
  covalent geometry    : angle       0.70673 (14336)
  SS BOND              : bond        0.00217 (    8)
  SS BOND              : angle       1.09300 (   16)
  hydrogen bonds       : bond        0.03389 (  240)
  hydrogen bonds       : angle       6.35905 (  618)

===============================================================================
Job complete
usr+sys time: 2885.70 seconds
wall clock time: 50 minutes 9.98 seconds (3009.98 seconds total)