Starting phenix.real_space_refine
on Thu Mar 13 18:30:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pcv_20308/03_2025/6pcv_20308.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pcv_20308/03_2025/6pcv_20308.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6pcv_20308/03_2025/6pcv_20308.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pcv_20308/03_2025/6pcv_20308.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pcv_20308/03_2025/6pcv_20308.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pcv_20308/03_2025/6pcv_20308.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
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      65      5.16       5
     C    5666      2.51       5
     N    1596      2.21       5
     O    1708      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 67 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9035
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 754, 5946
          Classifications: {'peptide': 754}
          Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 718}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 2607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2607
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 482
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 482
          Classifications: {'peptide': 62}
          Link IDs: {'PTRANS': 4, 'TRANS': 57}
  Time building chain proxies: 5.80, per 1000 atoms: 0.64
  Number of scatterers: 9035
  At special positions: 0
  Unit cell: (81, 105, 108, 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      65     16.00
     O    1708      8.00
     N    1596      7.00
     C    5666      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.34
  Conformation dependent library (CDL) restraints added in 968.2 milliseconds
  

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2170

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 13 sheets defined
      33.9% alpha, 21.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 509 through 522
    Processing helix  chain 'A' and resid 545 through 556
    Processing helix  chain 'A' and resid 560 through 574
    Processing helix  chain 'A' and resid 596 through 603
    Processing helix  chain 'A' and resid 655 through 661
    Processing helix  chain 'A' and resid 680 through 694
    Processing helix  chain 'A' and resid 738 through 744
    Processing helix  chain 'A' and resid 764 through 769
    Processing helix  chain 'A' and resid 791 through 803
    Processing helix  chain 'A' and resid 879 through 895
    Processing helix  chain 'A' and resid 933 through 947
      removed outlier: 4.166A  pdb=" N   ARG A 947 " --> pdb=" O   GLN A 943 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 964 through 968
      removed outlier: 3.622A  pdb=" N   PHE A 967 " --> pdb=" O   GLY A 964 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1319 through 1347
      removed outlier: 3.985A  pdb=" N   ALA A1333 " --> pdb=" O   GLN A1329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1359 through 1375
    Processing helix  chain 'A' and resid 1389 through 1407
    Processing helix  chain 'A' and resid 1444 through 1450
    Processing helix  chain 'A' and resid 1454 through 1458
      removed outlier: 3.598A  pdb=" N   GLY A1457 " --> pdb=" O   ARG A1454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1480 through 1518
      removed outlier: 4.311A  pdb=" N   ALA A1486 " --> pdb=" O   GLY A1482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1528 through 1551
      removed outlier: 5.080A  pdb=" N   ARG A1534 " --> pdb=" O   ASP A1530 " (cutoff:3.500A)
      Proline residue:  A1535  - end of helix
      removed outlier: 3.934A  pdb=" N   ALA A1538 " --> pdb=" O   ARG A1534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1563 through 1575
      removed outlier: 3.627A  pdb=" N   ILE A1567 " --> pdb=" O   GLY A1563 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   SER A1569 " --> pdb=" O   ILE A1565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1587 through 1605
    Processing helix  chain 'A' and resid 1612 through 1623
      removed outlier: 3.913A  pdb=" N   ARG A1621 " --> pdb=" O   THR A1617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1627 through 1634
    Processing helix  chain 'B' and resid 3 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 6 through 25
    Processing helix  chain 'G' and resid 29 through 44
    Processing sheet with id=AA1, first strand: chain 'A' and resid 532 through 534
    Processing sheet with id=AA2, first strand: chain 'A' and resid 542 through 544
    Processing sheet with id=AA3, first strand: chain 'A' and resid 668 through 671
      removed outlier: 6.446A  pdb=" N   LEU A 701 " --> pdb=" O   TYR A 669 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ILE A 671 " --> pdb=" O   ARG A 699 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   ARG A 699 " --> pdb=" O   ILE A 671 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   VAL A 702 " --> pdb=" O   LYS A 624 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   LEU A 617 " --> pdb=" O   GLU A 858 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   GLU A 858 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ARG A 866 " --> pdb=" O   PRO A 982 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   TYR A 981 " --> pdb=" O   SER A1016 " (cutoff:3.500A)
      removed outlier: 16.226A  pdb=" N   ALA A1577 " --> pdb=" O   TYR A1017 " (cutoff:3.500A)
      removed outlier: 11.943A  pdb=" N   GLN A1019 " --> pdb=" O   ALA A1577 " (cutoff:3.500A)
      removed outlier: 10.282A  pdb=" N   GLN A1579 " --> pdb=" O   GLN A1019 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   CYS A1021 " --> pdb=" O   GLN A1579 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   VAL A1581 " --> pdb=" O   CYS A1021 " (cutoff:3.500A)
      removed outlier: 5.999A  pdb=" N   THR A1023 " --> pdb=" O   VAL A1581 " (cutoff:3.500A)
      removed outlier: 7.641A  pdb=" N   CYS A1583 " --> pdb=" O   THR A1023 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   MET A1025 " --> pdb=" O   CYS A1583 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   LEU A1377 " --> pdb=" O   CYS A1578 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   MET A1580 " --> pdb=" O   LEU A1377 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   HIS A1379 " --> pdb=" O   MET A1580 " (cutoff:3.500A)
      removed outlier: 7.405A  pdb=" N   MET A1582 " --> pdb=" O   HIS A1379 " (cutoff:3.500A)
      removed outlier: 6.078A  pdb=" N   GLN A1381 " --> pdb=" O   MET A1582 " (cutoff:3.500A)
      removed outlier: 4.765A  pdb=" N   VAL A1409 " --> pdb=" O   LEU A1463 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   THR A1410 " --> pdb=" O   VAL A1439 " (cutoff:3.500A)
      removed outlier: 7.320A  pdb=" N   PHE A1441 " --> pdb=" O   THR A1410 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   SER A1412 " --> pdb=" O   PHE A1441 " (cutoff:3.500A)
      removed outlier: 8.157A  pdb=" N   LEU A1443 " --> pdb=" O   SER A1412 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   LYS A1414 " --> pdb=" O   LEU A1443 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 637 through 640
      removed outlier: 6.731A  pdb=" N   ASP A 638 " --> pdb=" O   LYS A 649 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 707 through 713
      removed outlier: 7.325A  pdb=" N   THR A 843 " --> pdb=" O   VAL A 754 " (cutoff:3.500A)
      removed outlier: 5.571A  pdb=" N   VAL A 754 " --> pdb=" O   THR A 843 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   THR A 845 " --> pdb=" O   LEU A 752 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 721 through 725
      removed outlier: 6.377A  pdb=" N   GLN A 722 " --> pdb=" O   TYR A 732 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.751A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.675A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.852A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.246A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.671A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 149 through 151
      removed outlier: 6.251A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.659A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.607A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 275 through 278
      removed outlier: 6.141A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    417 hydrogen bonds defined for protein.
    1194 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: 3.01

  Time building geometry restraints manager: 2.75 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: 3005
        1.34 -     1.46: 1648
        1.46 -     1.58: 4458
        1.58 -     1.69: 0
        1.69 -     1.81: 91
  Bond restraints: 9202
  Sorted by residual:
  bond pdb=" CB  VAL A 856 "
       pdb=" CG2 VAL A 856 "
    ideal  model  delta    sigma   weight residual
    1.521  1.462  0.059 3.30e-02 9.18e+02 3.16e+00
  bond pdb=" C   SER A 949 "
       pdb=" N   PRO A 950 "
    ideal  model  delta    sigma   weight residual
    1.329  1.349 -0.020 1.18e-02 7.18e+03 2.94e+00
  bond pdb=" CG  LEU A1383 "
       pdb=" CD1 LEU A1383 "
    ideal  model  delta    sigma   weight residual
    1.521  1.470  0.051 3.30e-02 9.18e+02 2.41e+00
  bond pdb=" C   PRO A 950 "
       pdb=" N   PRO A 951 "
    ideal  model  delta    sigma   weight residual
    1.338  1.365 -0.027 1.90e-02 2.77e+03 2.05e+00
  bond pdb=" C   ALA A 764 "
       pdb=" N   PRO A 765 "
    ideal  model  delta    sigma   weight residual
    1.336  1.353 -0.017 1.23e-02 6.61e+03 1.96e+00
  ... (remaining 9197 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.20: 12269
        3.20 -     6.40: 153
        6.40 -     9.60: 15
        9.60 -    12.81: 7
       12.81 -    16.01: 1
  Bond angle restraints: 12445
  Sorted by residual:
  angle pdb=" C   PRO A 950 "
        pdb=" N   PRO A 951 "
        pdb=" CA  PRO A 951 "
      ideal   model   delta    sigma   weight residual
     127.00  143.01  -16.01 2.40e+00 1.74e-01 4.45e+01
  angle pdb=" C   LEU A1564 "
        pdb=" N   ILE A1565 "
        pdb=" CA  ILE A1565 "
      ideal   model   delta    sigma   weight residual
     120.24  124.20   -3.96 6.30e-01 2.52e+00 3.95e+01
  angle pdb=" C   PRO A 950 "
        pdb=" N   PRO A 951 "
        pdb=" CD  PRO A 951 "
      ideal   model   delta    sigma   weight residual
     120.60  107.89   12.71 2.20e+00 2.07e-01 3.34e+01
  angle pdb=" N   PRO A 950 "
        pdb=" CA  PRO A 950 "
        pdb=" C   PRO A 950 "
      ideal   model   delta    sigma   weight residual
     110.70  115.12   -4.42 1.22e+00 6.72e-01 1.31e+01
  angle pdb=" N   SER A 949 "
        pdb=" CA  SER A 949 "
        pdb=" C   SER A 949 "
      ideal   model   delta    sigma   weight residual
     109.81  117.53   -7.72 2.21e+00 2.05e-01 1.22e+01
  ... (remaining 12440 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 5045
       17.84 -    35.69: 438
       35.69 -    53.53: 78
       53.53 -    71.38: 17
       71.38 -    89.22: 8
  Dihedral angle restraints: 5586
    sinusoidal: 2233
      harmonic: 3353
  Sorted by residual:
  dihedral pdb=" CA  TYR A1420 "
           pdb=" C   TYR A1420 "
           pdb=" N   VAL A1421 "
           pdb=" CA  VAL A1421 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.79   23.21     0      5.00e+00 4.00e-02 2.16e+01
  dihedral pdb=" CA  VAL A1421 "
           pdb=" C   VAL A1421 "
           pdb=" N   ALA A1422 "
           pdb=" CA  ALA A1422 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.26  -22.74     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CA  ARG A1626 "
           pdb=" C   ARG A1626 "
           pdb=" N   VAL A1627 "
           pdb=" CA  VAL A1627 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.69   22.31     0      5.00e+00 4.00e-02 1.99e+01
  ... (remaining 5583 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 918
       0.050 -    0.100: 345
       0.100 -    0.150: 99
       0.150 -    0.200: 24
       0.200 -    0.250: 6
  Chirality restraints: 1392
  Sorted by residual:
  chirality pdb=" CB  ILE A 529 "
            pdb=" CA  ILE A 529 "
            pdb=" CG1 ILE A 529 "
            pdb=" CG2 ILE A 529 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" CB  ILE B 157 "
            pdb=" CA  ILE B 157 "
            pdb=" CG1 ILE B 157 "
            pdb=" CG2 ILE B 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CB  ILE A 873 "
            pdb=" CA  ILE A 873 "
            pdb=" CG1 ILE A 873 "
            pdb=" CG2 ILE A 873 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.32e+00
  ... (remaining 1389 not shown)

  Planarity restraints: 1621
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 712 "    0.043 5.00e-02 4.00e+02   6.55e-02 6.86e+00
        pdb=" N   PRO A 713 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 713 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 713 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A1480 "    0.042 5.00e-02 4.00e+02   6.40e-02 6.56e+00
        pdb=" N   PRO A1481 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A1481 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A1481 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.042 5.00e-02 4.00e+02   6.30e-02 6.34e+00
        pdb=" N   PRO B 236 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.035 5.00e-02 4.00e+02
  ... (remaining 1618 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1680
        2.77 -     3.30: 8280
        3.30 -     3.83: 15757
        3.83 -     4.37: 18379
        4.37 -     4.90: 31956
  Nonbonded interactions: 76052
  Sorted by model distance:
  nonbonded pdb=" OG  SER A1359 "
            pdb=" OD1 ASP A1362 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OG1 THR B  34 "
            pdb=" O   LEU B 300 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   ASP A1398 "
            pdb=" OG1 THR A1402 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   SER B  67 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.302 3.040
  ... (remaining 76047 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.610
  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:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.870
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7032
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      :  0.006   0.061   9202  Z= 0.386
  Angle     :  0.978  16.008  12445  Z= 0.530
  Chirality :  0.059   0.250   1392
  Planarity :  0.007   0.065   1621
  Dihedral  : 14.309  89.224   3416
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  8.97 %
    Favored  : 90.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.37 (0.20), residues: 1137
  helix: -2.19 (0.19), residues: 383
  sheet: -2.10 (0.28), residues: 249
  loop : -2.20 (0.25), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP A1367 
 HIS   0.010   0.002   HIS A1379 
 PHE   0.020   0.002   PHE B 253 
 TYR   0.012   0.002   TYR A 859 
 ARG   0.013   0.001   ARG B  96 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  342 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 335
  time to evaluate  : 1.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  530 LYS cc_start: 0.8435 (pttt) cc_final: 0.8053 (ptpp)
REVERT: A  531 ASP cc_start: 0.7104 (p0) cc_final: 0.6448 (p0)
REVERT: A  547 LYS cc_start: 0.7394 (tptm) cc_final: 0.6827 (tppt)
REVERT: A  563 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7053 (mt-10)
REVERT: A  565 VAL cc_start: 0.8498 (m) cc_final: 0.8281 (p)
REVERT: A  574 ASN cc_start: 0.7512 (m110) cc_final: 0.7108 (m110)
REVERT: A  577 MET cc_start: 0.7258 (ptp) cc_final: 0.6969 (ptt)
REVERT: A  580 VAL cc_start: 0.8366 (m) cc_final: 0.8146 (t)
REVERT: A  619 GLU cc_start: 0.7001 (tt0) cc_final: 0.6760 (tt0)
REVERT: A  639 ILE cc_start: 0.8629 (pt) cc_final: 0.8325 (pt)
REVERT: A  644 LYS cc_start: 0.8835 (mptt) cc_final: 0.8605 (mmtm)
REVERT: A  696 ARG cc_start: 0.7382 (mtt-85) cc_final: 0.7109 (mtt-85)
REVERT: A  709 ILE cc_start: 0.8468 (pt) cc_final: 0.8051 (pt)
REVERT: A  723 ILE cc_start: 0.8377 (mt) cc_final: 0.8097 (mm)
REVERT: A  754 VAL cc_start: 0.8084 (t) cc_final: 0.7834 (p)
REVERT: A  759 VAL cc_start: 0.9192 (m) cc_final: 0.8618 (p)
REVERT: A  777 ARG cc_start: 0.7635 (ptp-170) cc_final: 0.7403 (ptp-170)
REVERT: A  858 GLU cc_start: 0.7048 (pp20) cc_final: 0.6663 (pt0)
REVERT: A  872 LYS cc_start: 0.7800 (mtmm) cc_final: 0.7516 (mtpp)
REVERT: A  882 LEU cc_start: 0.8091 (tp) cc_final: 0.7858 (tp)
REVERT: A 1019 GLN cc_start: 0.7469 (tt0) cc_final: 0.7008 (tm-30)
REVERT: A 1320 GLN cc_start: 0.6942 (mm-40) cc_final: 0.6422 (mm-40)
REVERT: A 1322 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7677 (ptm-80)
REVERT: A 1353 ASN cc_start: 0.7315 (m-40) cc_final: 0.6903 (m-40)
REVERT: A 1366 LYS cc_start: 0.8362 (pttp) cc_final: 0.8074 (pttp)
REVERT: A 1405 GLU cc_start: 0.6598 (tp30) cc_final: 0.6197 (tp30)
REVERT: A 1443 LEU cc_start: 0.8578 (mp) cc_final: 0.8349 (mm)
REVERT: A 1450 LYS cc_start: 0.8176 (mmtp) cc_final: 0.7802 (mtpp)
REVERT: A 1507 LYS cc_start: 0.8233 (mttt) cc_final: 0.7822 (mttp)
REVERT: A 1580 MET cc_start: 0.6530 (mtp) cc_final: 0.6263 (mtp)
REVERT: A 1614 MET cc_start: 0.7973 (tpt) cc_final: 0.7764 (tpt)
REVERT: A 1632 LYS cc_start: 0.8002 (mtmt) cc_final: 0.7680 (mttp)
REVERT: A 1648 TYR cc_start: 0.7379 (m-80) cc_final: 0.7156 (m-80)
REVERT: B    4 LEU cc_start: 0.8304 (mm) cc_final: 0.8100 (mt)
REVERT: B   15 LYS cc_start: 0.8756 (mttp) cc_final: 0.8439 (mttp)
REVERT: B   97 SER cc_start: 0.8223 (p) cc_final: 0.7966 (m)
REVERT: B  102 THR cc_start: 0.7819 (t) cc_final: 0.7604 (t)
REVERT: B  118 ASP cc_start: 0.6668 (t0) cc_final: 0.6395 (t0)
REVERT: B  123 ILE cc_start: 0.8038 (mm) cc_final: 0.7791 (mm)
REVERT: B  188 MET cc_start: 0.6764 (mmm) cc_final: 0.6559 (mmm)
REVERT: B  196 THR cc_start: 0.8193 (p) cc_final: 0.7535 (t)
REVERT: B  247 ASP cc_start: 0.7002 (t70) cc_final: 0.6302 (t0)
REVERT: B  250 CYS cc_start: 0.6716 (m) cc_final: 0.6247 (m)
REVERT: B  251 ARG cc_start: 0.7561 (mtt-85) cc_final: 0.6986 (mmm-85)
REVERT: B  279 SER cc_start: 0.8579 (m) cc_final: 0.8348 (t)
REVERT: B  289 TYR cc_start: 0.8270 (m-80) cc_final: 0.8068 (m-80)
REVERT: B  336 LEU cc_start: 0.7633 (mt) cc_final: 0.7368 (mm)
REVERT: B  338 ILE cc_start: 0.8451 (mm) cc_final: 0.8125 (mm)
REVERT: G   15 LEU cc_start: 0.8784 (mt) cc_final: 0.8412 (mt)
REVERT: G   17 GLU cc_start: 0.8276 (pt0) cc_final: 0.7960 (mt-10)
REVERT: G   18 GLN cc_start: 0.8144 (tp40) cc_final: 0.7345 (tp40)
REVERT: G   19 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8652 (mp)
REVERT: G   20 LYS cc_start: 0.8599 (ptmt) cc_final: 0.8188 (ptpp)
REVERT: G   22 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7247 (mt-10)
REVERT: G   38 MET cc_start: 0.7271 (ttp) cc_final: 0.6990 (tmm)
  outliers start: 7
  outliers final: 3
  residues processed: 339
  average time/residue: 0.2860
  time to fit residues: 123.7720
Evaluate side-chains
  280 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 276
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  671 ILE
Chi-restraints excluded: chain A residue  970 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.0770
   chunk 86 optimal weight:    0.3980
   chunk 47 optimal weight:    0.6980
   chunk 29 optimal weight:    5.9990
   chunk 58 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 54 optimal weight:    0.5980
   chunk 66 optimal weight:    0.5980
   chunk 103 optimal weight:    0.7980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
A 535 HIS
A 643 ASN
A 802 GLN
A 975 ASN
A1329 GLN
A1415 GLN
A1490 GLN
A1588 GLN
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
B  35 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.157331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.135278 restraints weight = 11746.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3793 rms_B_bonded: 2.67
r_work: 0.3648 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   9202  Z= 0.214
  Angle     :  0.648   8.760  12445  Z= 0.338
  Chirality :  0.043   0.151   1392
  Planarity :  0.005   0.055   1621
  Dihedral  :  5.399  40.628   1261
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 14.78 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.23), residues: 1137
  helix:  0.03 (0.25), residues: 384
  sheet: -1.78 (0.28), residues: 264
  loop : -1.69 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 297 
 HIS   0.004   0.001   HIS A 790 
 PHE   0.020   0.001   PHE A 637 
 TYR   0.017   0.001   TYR A 534 
 ARG   0.008   0.001   ARG A1361 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 282
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  530 LYS cc_start: 0.8619 (pttt) cc_final: 0.8276 (ptpp)
REVERT: A  547 LYS cc_start: 0.7665 (tptm) cc_final: 0.7065 (tppt)
REVERT: A  550 ASP cc_start: 0.7436 (t0) cc_final: 0.7026 (t0)
REVERT: A  563 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7423 (mt-10)
REVERT: A  565 VAL cc_start: 0.8500 (m) cc_final: 0.8273 (p)
REVERT: A  587 ARG cc_start: 0.8148 (ttp-110) cc_final: 0.7673 (ttp-110)
REVERT: A  593 PHE cc_start: 0.6927 (m-10) cc_final: 0.6567 (m-10)
REVERT: A  625 ARG cc_start: 0.7315 (ptp90) cc_final: 0.7085 (ptp90)
REVERT: A  638 ASP cc_start: 0.6861 (p0) cc_final: 0.6660 (p0)
REVERT: A  644 LYS cc_start: 0.8888 (mptt) cc_final: 0.8597 (mmtm)
REVERT: A  663 GLN cc_start: 0.7867 (mt0) cc_final: 0.7640 (mt0)
REVERT: A  683 GLU cc_start: 0.7489 (tt0) cc_final: 0.7109 (tt0)
REVERT: A  696 ARG cc_start: 0.7821 (mtt-85) cc_final: 0.7321 (mtt-85)
REVERT: A  699 ARG cc_start: 0.7612 (mtt90) cc_final: 0.7318 (mpp80)
REVERT: A  701 LEU cc_start: 0.8226 (mt) cc_final: 0.6151 (mt)
REVERT: A  705 LYS cc_start: 0.8198 (mtmm) cc_final: 0.7839 (mttm)
REVERT: A  715 GLN cc_start: 0.8451 (mt0) cc_final: 0.8181 (mp10)
REVERT: A  723 ILE cc_start: 0.8565 (mt) cc_final: 0.8332 (mm)
REVERT: A  754 VAL cc_start: 0.8338 (t) cc_final: 0.8040 (p)
REVERT: A  777 ARG cc_start: 0.8027 (ptp-170) cc_final: 0.7621 (ptp90)
REVERT: A  802 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.7046 (pp30)
REVERT: A  872 LYS cc_start: 0.8346 (mtmm) cc_final: 0.7841 (mtpp)
REVERT: A  939 GLU cc_start: 0.8243 (tp30) cc_final: 0.7891 (tp30)
REVERT: A 1019 GLN cc_start: 0.8051 (tt0) cc_final: 0.7602 (tm-30)
REVERT: A 1025 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8194 (ttt)
REVERT: A 1322 ARG cc_start: 0.8376 (ttp80) cc_final: 0.8148 (ptm-80)
REVERT: A 1326 ILE cc_start: 0.8424 (pt) cc_final: 0.8143 (tt)
REVERT: A 1327 PHE cc_start: 0.7956 (t80) cc_final: 0.7676 (t80)
REVERT: A 1340 GLU cc_start: 0.6951 (tp30) cc_final: 0.6524 (tp30)
REVERT: A 1343 LEU cc_start: 0.8354 (mp) cc_final: 0.8135 (mm)
REVERT: A 1353 ASN cc_start: 0.7585 (m-40) cc_final: 0.7190 (m-40)
REVERT: A 1366 LYS cc_start: 0.8592 (pttp) cc_final: 0.8238 (ttpp)
REVERT: A 1405 GLU cc_start: 0.6882 (tp30) cc_final: 0.6311 (tp30)
REVERT: A 1431 GLU cc_start: 0.7511 (tm-30) cc_final: 0.6978 (tm-30)
REVERT: A 1443 LEU cc_start: 0.8785 (mp) cc_final: 0.8502 (mm)
REVERT: A 1491 GLN cc_start: 0.7702 (tp-100) cc_final: 0.7148 (tm-30)
REVERT: A 1507 LYS cc_start: 0.8432 (mttt) cc_final: 0.8060 (mttp)
REVERT: A 1597 GLU cc_start: 0.7344 (tt0) cc_final: 0.7088 (tt0)
REVERT: A 1632 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7709 (mtmm)
REVERT: B    8 ARG cc_start: 0.8339 (mtt90) cc_final: 0.8004 (mtt90)
REVERT: B   15 LYS cc_start: 0.8918 (mttp) cc_final: 0.8609 (mttp)
REVERT: B   61 MET cc_start: 0.7794 (ppp) cc_final: 0.7321 (ptm)
REVERT: B  168 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8106 (tt)
REVERT: B  188 MET cc_start: 0.7148 (mmm) cc_final: 0.6352 (mmm)
REVERT: B  279 SER cc_start: 0.8773 (m) cc_final: 0.8445 (t)
REVERT: B  286 LEU cc_start: 0.8324 (mp) cc_final: 0.8097 (mp)
REVERT: B  289 TYR cc_start: 0.8580 (m-80) cc_final: 0.8289 (m-80)
REVERT: B  336 LEU cc_start: 0.7970 (mt) cc_final: 0.7667 (mm)
REVERT: G   15 LEU cc_start: 0.8723 (mt) cc_final: 0.8356 (mt)
REVERT: G   17 GLU cc_start: 0.8671 (pt0) cc_final: 0.8427 (mt-10)
REVERT: G   18 GLN cc_start: 0.8180 (tp40) cc_final: 0.7345 (tp40)
REVERT: G   20 LYS cc_start: 0.8694 (ptmt) cc_final: 0.8285 (ptpp)
REVERT: G   21 MET cc_start: 0.7512 (mmm) cc_final: 0.7266 (mmm)
REVERT: G   22 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7356 (mt-10)
REVERT: G   38 MET cc_start: 0.8008 (ttp) cc_final: 0.7481 (tmm)
  outliers start: 34
  outliers final: 7
  residues processed: 304
  average time/residue: 0.2786
  time to fit residues: 108.5611
Evaluate side-chains
  279 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 269
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  802 GLN
Chi-restraints excluded: chain A residue  970 THR
Chi-restraints excluded: chain A residue 1025 MET
Chi-restraints excluded: chain A residue 1369 GLU
Chi-restraints excluded: chain A residue 1384 LEU
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1514 GLU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 93 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 104 optimal weight:    0.0270
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1019 GLN
A1370 GLN
A1381 GLN
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.156564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.134848 restraints weight = 12012.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 2.66
r_work: 0.3619 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9202  Z= 0.237
  Angle     :  0.644   8.940  12445  Z= 0.333
  Chirality :  0.044   0.256   1392
  Planarity :  0.005   0.050   1621
  Dihedral  :  5.050  37.714   1257
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 18.76 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.25), residues: 1137
  helix:  0.86 (0.27), residues: 381
  sheet: -1.55 (0.28), residues: 266
  loop : -1.38 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 297 
 HIS   0.005   0.001   HIS B 311 
 PHE   0.024   0.002   PHE A 637 
 TYR   0.018   0.001   TYR B 111 
 ARG   0.007   0.001   ARG B  96 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 288
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  511 MET cc_start: 0.7240 (tpp) cc_final: 0.6852 (mmm)
REVERT: A  530 LYS cc_start: 0.8561 (pttt) cc_final: 0.8194 (ptpp)
REVERT: A  540 LYS cc_start: 0.8098 (tptp) cc_final: 0.7741 (tptp)
REVERT: A  547 LYS cc_start: 0.7839 (tptm) cc_final: 0.7246 (tppt)
REVERT: A  550 ASP cc_start: 0.7435 (t0) cc_final: 0.7056 (t0)
REVERT: A  563 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7401 (mt-10)
REVERT: A  565 VAL cc_start: 0.8542 (m) cc_final: 0.8318 (p)
REVERT: A  577 MET cc_start: 0.7778 (ptp) cc_final: 0.6946 (mtt)
REVERT: A  618 VAL cc_start: 0.8263 (p) cc_final: 0.8044 (t)
REVERT: A  644 LYS cc_start: 0.8849 (mptt) cc_final: 0.8558 (mmtm)
REVERT: A  683 GLU cc_start: 0.7504 (tt0) cc_final: 0.7097 (tt0)
REVERT: A  687 ILE cc_start: 0.7996 (mt) cc_final: 0.7651 (mm)
REVERT: A  696 ARG cc_start: 0.7873 (mtt-85) cc_final: 0.7517 (mtt-85)
REVERT: A  705 LYS cc_start: 0.8147 (mtmm) cc_final: 0.7789 (mttm)
REVERT: A  715 GLN cc_start: 0.8410 (mt0) cc_final: 0.8098 (mp10)
REVERT: A  723 ILE cc_start: 0.8624 (mt) cc_final: 0.8363 (mm)
REVERT: A  777 ARG cc_start: 0.8056 (ptp-170) cc_final: 0.7702 (mtm180)
REVERT: A  796 GLN cc_start: 0.7982 (pt0) cc_final: 0.7357 (pt0)
REVERT: A  852 GLU cc_start: 0.7462 (pt0) cc_final: 0.6997 (pp20)
REVERT: A  872 LYS cc_start: 0.8387 (mtmm) cc_final: 0.7948 (mtpp)
REVERT: A  874 VAL cc_start: 0.8726 (t) cc_final: 0.8483 (m)
REVERT: A  882 LEU cc_start: 0.8496 (tp) cc_final: 0.8129 (tp)
REVERT: A  939 GLU cc_start: 0.8278 (tp30) cc_final: 0.7872 (tp30)
REVERT: A 1019 GLN cc_start: 0.8049 (tt0) cc_final: 0.7318 (tm-30)
REVERT: A 1020 HIS cc_start: 0.7891 (m-70) cc_final: 0.7621 (m-70)
REVERT: A 1322 ARG cc_start: 0.8462 (ttp80) cc_final: 0.8187 (ptm-80)
REVERT: A 1326 ILE cc_start: 0.8380 (pt) cc_final: 0.8082 (tt)
REVERT: A 1327 PHE cc_start: 0.8048 (t80) cc_final: 0.7733 (t80)
REVERT: A 1340 GLU cc_start: 0.6986 (tp30) cc_final: 0.6532 (tp30)
REVERT: A 1353 ASN cc_start: 0.7708 (m-40) cc_final: 0.7199 (m-40)
REVERT: A 1361 ARG cc_start: 0.7771 (ttt-90) cc_final: 0.7559 (ttt180)
REVERT: A 1366 LYS cc_start: 0.8635 (pttp) cc_final: 0.8254 (ttpp)
REVERT: A 1370 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7920 (tm130)
REVERT: A 1405 GLU cc_start: 0.6938 (tp30) cc_final: 0.6319 (tp30)
REVERT: A 1412 SER cc_start: 0.8100 (m) cc_final: 0.7894 (p)
REVERT: A 1428 TYR cc_start: 0.8342 (m-10) cc_final: 0.7986 (m-10)
REVERT: A 1431 GLU cc_start: 0.7468 (tm-30) cc_final: 0.6916 (tm-30)
REVERT: A 1491 GLN cc_start: 0.7685 (tp-100) cc_final: 0.7150 (tm-30)
REVERT: A 1503 GLN cc_start: 0.8277 (tp40) cc_final: 0.7680 (mm-40)
REVERT: A 1507 LYS cc_start: 0.8439 (mttt) cc_final: 0.8081 (mttp)
REVERT: A 1515 ARG cc_start: 0.7525 (mtp-110) cc_final: 0.7313 (mtp-110)
REVERT: A 1565 ILE cc_start: 0.8505 (mt) cc_final: 0.8183 (mm)
REVERT: A 1596 LEU cc_start: 0.7312 (mt) cc_final: 0.6921 (mt)
REVERT: A 1614 MET cc_start: 0.8252 (tpt) cc_final: 0.7688 (tpt)
REVERT: A 1632 LYS cc_start: 0.8249 (mtmt) cc_final: 0.7675 (mtmm)
REVERT: A 1640 MET cc_start: 0.6629 (mmt) cc_final: 0.6386 (mmm)
REVERT: B    8 ARG cc_start: 0.8287 (mtt90) cc_final: 0.7988 (mtt90)
REVERT: B   15 LYS cc_start: 0.8949 (mttp) cc_final: 0.8665 (mttp)
REVERT: B   61 MET cc_start: 0.7841 (ppp) cc_final: 0.7424 (ptm)
REVERT: B   97 SER cc_start: 0.8360 (p) cc_final: 0.8135 (m)
REVERT: B  118 ASP cc_start: 0.7281 (t0) cc_final: 0.6982 (t0)
REVERT: B  145 TYR cc_start: 0.8394 (p90) cc_final: 0.7913 (p90)
REVERT: B  168 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8072 (tt)
REVERT: B  188 MET cc_start: 0.7415 (mmm) cc_final: 0.6822 (mmm)
REVERT: B  251 ARG cc_start: 0.7961 (mtt-85) cc_final: 0.7450 (tpp80)
REVERT: B  260 GLU cc_start: 0.7102 (tt0) cc_final: 0.6704 (tt0)
REVERT: B  279 SER cc_start: 0.8714 (m) cc_final: 0.8400 (t)
REVERT: B  289 TYR cc_start: 0.8658 (m-80) cc_final: 0.8313 (m-80)
REVERT: B  336 LEU cc_start: 0.7958 (mt) cc_final: 0.7657 (mm)
REVERT: G   15 LEU cc_start: 0.8765 (mt) cc_final: 0.8438 (mt)
REVERT: G   18 GLN cc_start: 0.8190 (tp40) cc_final: 0.6716 (tp40)
REVERT: G   19 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8855 (mp)
REVERT: G   20 LYS cc_start: 0.8708 (ptmt) cc_final: 0.8300 (ptpp)
REVERT: G   22 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7238 (mt-10)
REVERT: G   38 MET cc_start: 0.7978 (ttp) cc_final: 0.7443 (tmm)
  outliers start: 30
  outliers final: 18
  residues processed: 306
  average time/residue: 0.2771
  time to fit residues: 109.3609
Evaluate side-chains
  292 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 271
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  671 ILE
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  970 THR
Chi-restraints excluded: chain A residue 1021 CYS
Chi-restraints excluded: chain A residue 1329 GLN
Chi-restraints excluded: chain A residue 1369 GLU
Chi-restraints excluded: chain A residue 1370 GLN
Chi-restraints excluded: chain A residue 1384 LEU
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1451 LEU
Chi-restraints excluded: chain A residue 1514 GLU
Chi-restraints excluded: chain A residue 1582 MET
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   30 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0570
   chunk 2 optimal weight:    3.9990
   chunk 49 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 802 GLN
** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1381 GLN
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** 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 = 0.4032 r_free = 0.4032 target = 0.156812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.134962 restraints weight = 11859.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 2.64
r_work: 0.3623 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.2881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9202  Z= 0.219
  Angle     :  0.627   8.729  12445  Z= 0.323
  Chirality :  0.044   0.171   1392
  Planarity :  0.004   0.048   1621
  Dihedral  :  4.940  40.260   1257
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 19.98 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.25), residues: 1137
  helix:  1.03 (0.27), residues: 388
  sheet: -1.41 (0.29), residues: 264
  loop : -1.25 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 297 
 HIS   0.003   0.001   HIS A 790 
 PHE   0.028   0.002   PHE A 637 
 TYR   0.015   0.001   TYR B 111 
 ARG   0.006   0.001   ARG B  19 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 290
  time to evaluate  : 1.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  510 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7545 (tt)
REVERT: A  511 MET cc_start: 0.7221 (tpp) cc_final: 0.6900 (mmm)
REVERT: A  516 ARG cc_start: 0.7739 (ttm110) cc_final: 0.7196 (ttm110)
REVERT: A  530 LYS cc_start: 0.8538 (pttt) cc_final: 0.8185 (ptpp)
REVERT: A  540 LYS cc_start: 0.8053 (tptp) cc_final: 0.7700 (tptp)
REVERT: A  547 LYS cc_start: 0.7840 (tptm) cc_final: 0.7117 (tppt)
REVERT: A  553 LEU cc_start: 0.8613 (mp) cc_final: 0.8265 (mm)
REVERT: A  561 ARG cc_start: 0.8411 (mtp85) cc_final: 0.8143 (mtp85)
REVERT: A  563 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7365 (mt-10)
REVERT: A  565 VAL cc_start: 0.8541 (m) cc_final: 0.8320 (p)
REVERT: A  574 ASN cc_start: 0.7739 (m110) cc_final: 0.7505 (m110)
REVERT: A  577 MET cc_start: 0.7739 (ptp) cc_final: 0.6909 (mtt)
REVERT: A  587 ARG cc_start: 0.8080 (ttp-110) cc_final: 0.7712 (ttp-110)
REVERT: A  618 VAL cc_start: 0.8246 (p) cc_final: 0.7997 (m)
REVERT: A  644 LYS cc_start: 0.8838 (mptt) cc_final: 0.8509 (mmtm)
REVERT: A  696 ARG cc_start: 0.7823 (mtt-85) cc_final: 0.7466 (mtt-85)
REVERT: A  699 ARG cc_start: 0.7556 (mtt90) cc_final: 0.6839 (mtm-85)
REVERT: A  701 LEU cc_start: 0.7927 (mp) cc_final: 0.7633 (mt)
REVERT: A  705 LYS cc_start: 0.8119 (mtmm) cc_final: 0.7897 (mptt)
REVERT: A  715 GLN cc_start: 0.8369 (mt0) cc_final: 0.8131 (mp10)
REVERT: A  723 ILE cc_start: 0.8621 (mt) cc_final: 0.8344 (mm)
REVERT: A  796 GLN cc_start: 0.7912 (pt0) cc_final: 0.7292 (pt0)
REVERT: A  799 ARG cc_start: 0.7587 (mpt180) cc_final: 0.7219 (mmt180)
REVERT: A  802 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7234 (pp30)
REVERT: A  852 GLU cc_start: 0.7486 (pt0) cc_final: 0.7055 (pp20)
REVERT: A  872 LYS cc_start: 0.8367 (mtmm) cc_final: 0.7957 (mtpp)
REVERT: A  882 LEU cc_start: 0.8508 (tp) cc_final: 0.8223 (tp)
REVERT: A  939 GLU cc_start: 0.8279 (tp30) cc_final: 0.7857 (tp30)
REVERT: A 1019 GLN cc_start: 0.8026 (tt0) cc_final: 0.7572 (tt0)
REVERT: A 1020 HIS cc_start: 0.7862 (m-70) cc_final: 0.7493 (m-70)
REVERT: A 1322 ARG cc_start: 0.8440 (ttp80) cc_final: 0.8182 (ptm-80)
REVERT: A 1326 ILE cc_start: 0.8371 (pt) cc_final: 0.8070 (tt)
REVERT: A 1327 PHE cc_start: 0.8034 (t80) cc_final: 0.7741 (t80)
REVERT: A 1338 PHE cc_start: 0.7837 (t80) cc_final: 0.7571 (t80)
REVERT: A 1340 GLU cc_start: 0.6934 (tp30) cc_final: 0.6582 (tp30)
REVERT: A 1343 LEU cc_start: 0.8393 (mm) cc_final: 0.8057 (mp)
REVERT: A 1353 ASN cc_start: 0.7790 (m-40) cc_final: 0.7413 (m-40)
REVERT: A 1366 LYS cc_start: 0.8554 (pttp) cc_final: 0.8130 (ttpp)
REVERT: A 1405 GLU cc_start: 0.6957 (tp30) cc_final: 0.6335 (tp30)
REVERT: A 1412 SER cc_start: 0.8173 (m) cc_final: 0.7955 (p)
REVERT: A 1428 TYR cc_start: 0.8304 (m-10) cc_final: 0.8038 (m-10)
REVERT: A 1431 GLU cc_start: 0.7428 (tm-30) cc_final: 0.6882 (tm-30)
REVERT: A 1469 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8827 (p)
REVERT: A 1491 GLN cc_start: 0.7672 (tp-100) cc_final: 0.7175 (tm-30)
REVERT: A 1503 GLN cc_start: 0.8162 (tp40) cc_final: 0.7596 (mm-40)
REVERT: A 1507 LYS cc_start: 0.8462 (mttt) cc_final: 0.8090 (mttp)
REVERT: A 1546 MET cc_start: 0.7987 (tpp) cc_final: 0.7654 (tpp)
REVERT: A 1565 ILE cc_start: 0.8501 (mt) cc_final: 0.8208 (mm)
REVERT: A 1614 MET cc_start: 0.8233 (tpt) cc_final: 0.7652 (tpt)
REVERT: A 1622 LYS cc_start: 0.8302 (mttp) cc_final: 0.7825 (mmtm)
REVERT: A 1632 LYS cc_start: 0.8257 (mtmt) cc_final: 0.7634 (mtmm)
REVERT: B    8 ARG cc_start: 0.8308 (mtt90) cc_final: 0.7970 (mtt90)
REVERT: B   15 LYS cc_start: 0.8950 (mttp) cc_final: 0.8683 (mttp)
REVERT: B   61 MET cc_start: 0.7906 (ppp) cc_final: 0.7489 (ptm)
REVERT: B  118 ASP cc_start: 0.7335 (t0) cc_final: 0.7025 (t0)
REVERT: B  145 TYR cc_start: 0.8377 (p90) cc_final: 0.7784 (p90)
REVERT: B  156 GLN cc_start: 0.8106 (mt0) cc_final: 0.7894 (mt0)
REVERT: B  158 VAL cc_start: 0.8039 (OUTLIER) cc_final: 0.7838 (m)
REVERT: B  168 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8063 (tt)
REVERT: B  188 MET cc_start: 0.7332 (mmm) cc_final: 0.6613 (mmm)
REVERT: B  230 ASN cc_start: 0.8629 (m-40) cc_final: 0.8221 (m-40)
REVERT: B  279 SER cc_start: 0.8648 (m) cc_final: 0.8348 (t)
REVERT: B  289 TYR cc_start: 0.8647 (m-80) cc_final: 0.8321 (m-80)
REVERT: B  336 LEU cc_start: 0.7960 (mt) cc_final: 0.7674 (mm)
REVERT: G   13 ARG cc_start: 0.8318 (ttm110) cc_final: 0.8047 (ttm110)
REVERT: G   15 LEU cc_start: 0.8789 (mt) cc_final: 0.8491 (mt)
REVERT: G   18 GLN cc_start: 0.8181 (tp40) cc_final: 0.7489 (tp40)
REVERT: G   19 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8783 (mp)
REVERT: G   20 LYS cc_start: 0.8788 (ptmt) cc_final: 0.8364 (ptpp)
REVERT: G   22 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7832 (mt-10)
REVERT: G   38 MET cc_start: 0.7989 (ttp) cc_final: 0.7437 (tmm)
  outliers start: 33
  outliers final: 20
  residues processed: 308
  average time/residue: 0.2941
  time to fit residues: 118.6240
Evaluate side-chains
  288 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 262
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain A residue  802 GLN
Chi-restraints excluded: chain A residue  970 THR
Chi-restraints excluded: chain A residue  975 ASN
Chi-restraints excluded: chain A residue 1018 THR
Chi-restraints excluded: chain A residue 1021 CYS
Chi-restraints excluded: chain A residue 1025 MET
Chi-restraints excluded: chain A residue 1329 GLN
Chi-restraints excluded: chain A residue 1369 GLU
Chi-restraints excluded: chain A residue 1384 LEU
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1451 LEU
Chi-restraints excluded: chain A residue 1469 THR
Chi-restraints excluded: chain A residue 1514 GLU
Chi-restraints excluded: chain A residue 1582 MET
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   37 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0980
   chunk 29 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0050
   chunk 31 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
A 802 GLN
** A1352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1381 GLN
B 220 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.156438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.134632 restraints weight = 11783.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3782 rms_B_bonded: 2.64
r_work: 0.3634 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9202  Z= 0.207
  Angle     :  0.637   9.689  12445  Z= 0.323
  Chirality :  0.043   0.156   1392
  Planarity :  0.005   0.045   1621
  Dihedral  :  4.831  38.184   1257
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 21.41 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.25), residues: 1137
  helix:  1.25 (0.27), residues: 388
  sheet: -1.28 (0.30), residues: 265
  loop : -1.15 (0.29), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 297 
 HIS   0.005   0.001   HIS A 790 
 PHE   0.017   0.002   PHE A1427 
 TYR   0.019   0.002   TYR A1350 
 ARG   0.009   0.001   ARG B  96 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 280
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  510 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7508 (tt)
REVERT: A  516 ARG cc_start: 0.7735 (ttm110) cc_final: 0.7197 (ttm110)
REVERT: A  530 LYS cc_start: 0.8541 (pttt) cc_final: 0.8180 (ptpp)
REVERT: A  540 LYS cc_start: 0.8014 (tptp) cc_final: 0.7685 (tptp)
REVERT: A  547 LYS cc_start: 0.7853 (tptm) cc_final: 0.7145 (tppt)
REVERT: A  550 ASP cc_start: 0.7416 (t0) cc_final: 0.6954 (t0)
REVERT: A  553 LEU cc_start: 0.8577 (mp) cc_final: 0.8225 (mm)
REVERT: A  561 ARG cc_start: 0.8402 (mtp85) cc_final: 0.7897 (mtp180)
REVERT: A  563 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7400 (mt-10)
REVERT: A  565 VAL cc_start: 0.8541 (m) cc_final: 0.8324 (p)
REVERT: A  574 ASN cc_start: 0.7713 (m110) cc_final: 0.7476 (m110)
REVERT: A  577 MET cc_start: 0.7783 (ptp) cc_final: 0.7380 (mtm)
REVERT: A  587 ARG cc_start: 0.8080 (ttp-110) cc_final: 0.7304 (mtm110)
REVERT: A  618 VAL cc_start: 0.8110 (p) cc_final: 0.7883 (m)
REVERT: A  673 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6678 (mm-30)
REVERT: A  687 ILE cc_start: 0.8081 (mt) cc_final: 0.7682 (mm)
REVERT: A  696 ARG cc_start: 0.7730 (mtt-85) cc_final: 0.7506 (mtt-85)
REVERT: A  699 ARG cc_start: 0.7605 (mtt90) cc_final: 0.6836 (mtm-85)
REVERT: A  701 LEU cc_start: 0.7931 (mp) cc_final: 0.7652 (mt)
REVERT: A  705 LYS cc_start: 0.8164 (mtmm) cc_final: 0.7727 (mmmm)
REVERT: A  715 GLN cc_start: 0.8385 (mt0) cc_final: 0.8158 (mp10)
REVERT: A  723 ILE cc_start: 0.8635 (mt) cc_final: 0.8351 (mm)
REVERT: A  749 GLN cc_start: 0.7255 (mt0) cc_final: 0.6937 (mt0)
REVERT: A  780 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6224 (pp20)
REVERT: A  796 GLN cc_start: 0.7915 (pt0) cc_final: 0.7325 (pt0)
REVERT: A  799 ARG cc_start: 0.7525 (mpt180) cc_final: 0.7194 (mmt180)
REVERT: A  802 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.7099 (pp30)
REVERT: A  852 GLU cc_start: 0.7543 (pt0) cc_final: 0.7024 (pt0)
REVERT: A  872 LYS cc_start: 0.8302 (mtmm) cc_final: 0.7888 (mtpp)
REVERT: A  882 LEU cc_start: 0.8531 (tp) cc_final: 0.8167 (tp)
REVERT: A  939 GLU cc_start: 0.8246 (tp30) cc_final: 0.7835 (tp30)
REVERT: A  974 ILE cc_start: 0.8335 (mt) cc_final: 0.8023 (mm)
REVERT: A 1019 GLN cc_start: 0.8028 (tt0) cc_final: 0.7794 (tt0)
REVERT: A 1322 ARG cc_start: 0.8388 (ttp80) cc_final: 0.8136 (ptm-80)
REVERT: A 1326 ILE cc_start: 0.8352 (pt) cc_final: 0.8053 (tt)
REVERT: A 1327 PHE cc_start: 0.7999 (t80) cc_final: 0.7700 (t80)
REVERT: A 1338 PHE cc_start: 0.7816 (t80) cc_final: 0.7503 (t80)
REVERT: A 1340 GLU cc_start: 0.6877 (tp30) cc_final: 0.6500 (tp30)
REVERT: A 1343 LEU cc_start: 0.8381 (mm) cc_final: 0.8050 (mp)
REVERT: A 1353 ASN cc_start: 0.7691 (m-40) cc_final: 0.7418 (m110)
REVERT: A 1366 LYS cc_start: 0.8582 (pttp) cc_final: 0.8218 (ttpp)
REVERT: A 1405 GLU cc_start: 0.6985 (tp30) cc_final: 0.6341 (tp30)
REVERT: A 1410 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.8032 (m)
REVERT: A 1412 SER cc_start: 0.8154 (m) cc_final: 0.7900 (p)
REVERT: A 1428 TYR cc_start: 0.8271 (m-10) cc_final: 0.8014 (m-10)
REVERT: A 1431 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6843 (tm-30)
REVERT: A 1469 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8812 (p)
REVERT: A 1496 GLN cc_start: 0.7869 (mt0) cc_final: 0.7596 (tt0)
REVERT: A 1507 LYS cc_start: 0.8465 (mttt) cc_final: 0.8084 (mttp)
REVERT: A 1546 MET cc_start: 0.8000 (tpp) cc_final: 0.7703 (tpp)
REVERT: A 1565 ILE cc_start: 0.8492 (mt) cc_final: 0.8251 (mm)
REVERT: A 1596 LEU cc_start: 0.7447 (tp) cc_final: 0.7147 (tp)
REVERT: A 1614 MET cc_start: 0.8231 (tpt) cc_final: 0.7650 (tpt)
REVERT: A 1632 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7776 (mtmt)
REVERT: B    8 ARG cc_start: 0.8295 (mtt90) cc_final: 0.7943 (mtt90)
REVERT: B   15 LYS cc_start: 0.8971 (mttp) cc_final: 0.8684 (mttp)
REVERT: B  118 ASP cc_start: 0.7362 (t0) cc_final: 0.7051 (t0)
REVERT: B  145 TYR cc_start: 0.8334 (p90) cc_final: 0.7945 (p90)
REVERT: B  158 VAL cc_start: 0.7980 (OUTLIER) cc_final: 0.7766 (m)
REVERT: B  168 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.8008 (tt)
REVERT: B  188 MET cc_start: 0.7289 (mmm) cc_final: 0.6529 (mmm)
REVERT: B  230 ASN cc_start: 0.8591 (m-40) cc_final: 0.8189 (m-40)
REVERT: B  279 SER cc_start: 0.8609 (m) cc_final: 0.8308 (t)
REVERT: B  289 TYR cc_start: 0.8615 (m-80) cc_final: 0.8263 (m-80)
REVERT: B  336 LEU cc_start: 0.7901 (mt) cc_final: 0.7682 (mm)
REVERT: G   13 ARG cc_start: 0.8317 (ttm110) cc_final: 0.8096 (ttm110)
REVERT: G   15 LEU cc_start: 0.8772 (mt) cc_final: 0.8442 (mt)
REVERT: G   18 GLN cc_start: 0.8117 (tp40) cc_final: 0.7490 (tp40)
REVERT: G   19 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8729 (mp)
REVERT: G   20 LYS cc_start: 0.8805 (ptmt) cc_final: 0.8525 (ptmm)
REVERT: G   22 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7728 (mt-10)
REVERT: G   38 MET cc_start: 0.7979 (ttp) cc_final: 0.7434 (tmm)
  outliers start: 39
  outliers final: 23
  residues processed: 301
  average time/residue: 0.2674
  time to fit residues: 105.5691
Evaluate side-chains
  300 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 269
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  671 ILE
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  780 GLU
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain A residue  802 GLN
Chi-restraints excluded: chain A residue  875 GLU
Chi-restraints excluded: chain A residue  970 THR
Chi-restraints excluded: chain A residue  975 ASN
Chi-restraints excluded: chain A residue 1018 THR
Chi-restraints excluded: chain A residue 1021 CYS
Chi-restraints excluded: chain A residue 1025 MET
Chi-restraints excluded: chain A residue 1329 GLN
Chi-restraints excluded: chain A residue 1384 LEU
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1451 LEU
Chi-restraints excluded: chain A residue 1469 THR
Chi-restraints excluded: chain A residue 1488 ASP
Chi-restraints excluded: chain A residue 1514 GLU
Chi-restraints excluded: chain A residue 1582 MET
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   37 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 101 optimal weight:    0.0980
   chunk 81 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 78 optimal weight:    0.3980
   chunk 75 optimal weight:    0.6980
   chunk 79 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 105 optimal weight:    0.2980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A 802 GLN
** A1352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1370 GLN
** A1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** 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 = 0.4034 r_free = 0.4034 target = 0.156555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.134811 restraints weight = 11825.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3772 rms_B_bonded: 2.64
r_work: 0.3618 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9202  Z= 0.191
  Angle     :  0.636  12.170  12445  Z= 0.322
  Chirality :  0.043   0.161   1392
  Planarity :  0.004   0.047   1621
  Dihedral  :  4.767  35.908   1257
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 21.61 %
    Favored  : 74.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.25), residues: 1137
  helix:  1.33 (0.27), residues: 387
  sheet: -1.15 (0.30), residues: 256
  loop : -1.10 (0.29), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 297 
 HIS   0.004   0.001   HIS A 790 
 PHE   0.032   0.002   PHE A 637 
 TYR   0.014   0.001   TYR A1350 
 ARG   0.008   0.001   ARG A1515 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 273
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  510 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7389 (tt)
REVERT: A  516 ARG cc_start: 0.7734 (ttm110) cc_final: 0.7238 (ttm110)
REVERT: A  530 LYS cc_start: 0.8553 (pttt) cc_final: 0.8209 (ptpp)
REVERT: A  540 LYS cc_start: 0.7955 (tptp) cc_final: 0.7628 (tptp)
REVERT: A  547 LYS cc_start: 0.7845 (tptm) cc_final: 0.7151 (tppt)
REVERT: A  553 LEU cc_start: 0.8585 (mp) cc_final: 0.8239 (mm)
REVERT: A  561 ARG cc_start: 0.8386 (mtp85) cc_final: 0.7996 (mtp85)
REVERT: A  563 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7383 (mt-10)
REVERT: A  565 VAL cc_start: 0.8547 (m) cc_final: 0.8338 (p)
REVERT: A  574 ASN cc_start: 0.7689 (m110) cc_final: 0.7466 (m110)
REVERT: A  577 MET cc_start: 0.7781 (ptp) cc_final: 0.7394 (mtm)
REVERT: A  587 ARG cc_start: 0.8080 (ttp-110) cc_final: 0.7325 (mtm110)
REVERT: A  673 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6578 (mm-30)
REVERT: A  683 GLU cc_start: 0.7397 (tt0) cc_final: 0.6923 (tt0)
REVERT: A  696 ARG cc_start: 0.7779 (mtt-85) cc_final: 0.7487 (mtt-85)
REVERT: A  701 LEU cc_start: 0.7984 (mp) cc_final: 0.7688 (mt)
REVERT: A  705 LYS cc_start: 0.8158 (mtmm) cc_final: 0.7736 (mmmm)
REVERT: A  723 ILE cc_start: 0.8580 (mt) cc_final: 0.8363 (mm)
REVERT: A  749 GLN cc_start: 0.7277 (mt0) cc_final: 0.6957 (mt0)
REVERT: A  780 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6200 (pp20)
REVERT: A  796 GLN cc_start: 0.7905 (pt0) cc_final: 0.7454 (pt0)
REVERT: A  841 MET cc_start: 0.8200 (mmm) cc_final: 0.7929 (mmm)
REVERT: A  852 GLU cc_start: 0.7652 (pt0) cc_final: 0.7191 (pt0)
REVERT: A  872 LYS cc_start: 0.8298 (mtmm) cc_final: 0.7891 (mtpp)
REVERT: A 1322 ARG cc_start: 0.8386 (ttp80) cc_final: 0.8150 (ptm-80)
REVERT: A 1326 ILE cc_start: 0.8340 (pt) cc_final: 0.8046 (tt)
REVERT: A 1338 PHE cc_start: 0.7772 (t80) cc_final: 0.7462 (t80)
REVERT: A 1340 GLU cc_start: 0.6771 (tp30) cc_final: 0.6472 (tp30)
REVERT: A 1343 LEU cc_start: 0.8416 (mm) cc_final: 0.8022 (mp)
REVERT: A 1353 ASN cc_start: 0.7673 (m-40) cc_final: 0.7437 (m110)
REVERT: A 1361 ARG cc_start: 0.7732 (ttt-90) cc_final: 0.7516 (ttt180)
REVERT: A 1366 LYS cc_start: 0.8526 (pttp) cc_final: 0.8137 (ttpp)
REVERT: A 1405 GLU cc_start: 0.6943 (tp30) cc_final: 0.6694 (tp30)
REVERT: A 1431 GLU cc_start: 0.7414 (tm-30) cc_final: 0.6885 (tm-30)
REVERT: A 1469 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8816 (p)
REVERT: A 1496 GLN cc_start: 0.7857 (mt0) cc_final: 0.7654 (tt0)
REVERT: A 1503 GLN cc_start: 0.8224 (tp40) cc_final: 0.7608 (mm-40)
REVERT: A 1507 LYS cc_start: 0.8470 (mttt) cc_final: 0.8081 (mttp)
REVERT: A 1546 MET cc_start: 0.7994 (tpp) cc_final: 0.7738 (mpp)
REVERT: A 1565 ILE cc_start: 0.8530 (mt) cc_final: 0.8256 (mm)
REVERT: A 1596 LEU cc_start: 0.7463 (tp) cc_final: 0.7155 (tp)
REVERT: A 1598 GLN cc_start: 0.7339 (mt0) cc_final: 0.6955 (mt0)
REVERT: A 1614 MET cc_start: 0.8165 (tpt) cc_final: 0.7617 (tpt)
REVERT: A 1632 LYS cc_start: 0.8228 (mtmt) cc_final: 0.7624 (mtmm)
REVERT: B    8 ARG cc_start: 0.8358 (mtt90) cc_final: 0.8105 (mtt90)
REVERT: B   15 LYS cc_start: 0.8956 (mttp) cc_final: 0.8685 (mttp)
REVERT: B   96 ARG cc_start: 0.7622 (mtp-110) cc_final: 0.7387 (mtp85)
REVERT: B  118 ASP cc_start: 0.7264 (t0) cc_final: 0.7023 (t0)
REVERT: B  145 TYR cc_start: 0.8376 (p90) cc_final: 0.8059 (p90)
REVERT: B  156 GLN cc_start: 0.7913 (mt0) cc_final: 0.7224 (mp10)
REVERT: B  158 VAL cc_start: 0.8008 (OUTLIER) cc_final: 0.7803 (m)
REVERT: B  188 MET cc_start: 0.7274 (mmm) cc_final: 0.6526 (mmm)
REVERT: B  230 ASN cc_start: 0.8569 (m-40) cc_final: 0.8180 (m-40)
REVERT: B  279 SER cc_start: 0.8592 (m) cc_final: 0.8312 (t)
REVERT: B  289 TYR cc_start: 0.8618 (m-80) cc_final: 0.8243 (m-80)
REVERT: B  336 LEU cc_start: 0.7938 (mt) cc_final: 0.7716 (mm)
REVERT: G   13 ARG cc_start: 0.8342 (ttm110) cc_final: 0.8114 (ttm110)
REVERT: G   15 LEU cc_start: 0.8767 (mt) cc_final: 0.8418 (mt)
REVERT: G   18 GLN cc_start: 0.8078 (tp40) cc_final: 0.7447 (tp40)
REVERT: G   19 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8696 (mp)
REVERT: G   20 LYS cc_start: 0.8743 (ptmt) cc_final: 0.8425 (ptmm)
REVERT: G   22 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7639 (mt-10)
REVERT: G   38 MET cc_start: 0.7952 (ttp) cc_final: 0.7430 (tmm)
  outliers start: 36
  outliers final: 21
  residues processed: 293
  average time/residue: 0.2718
  time to fit residues: 103.6940
Evaluate side-chains
  288 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 262
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  671 ILE
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  738 SER
Chi-restraints excluded: chain A residue  780 GLU
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  970 THR
Chi-restraints excluded: chain A residue 1018 THR
Chi-restraints excluded: chain A residue 1021 CYS
Chi-restraints excluded: chain A residue 1025 MET
Chi-restraints excluded: chain A residue 1370 GLN
Chi-restraints excluded: chain A residue 1384 LEU
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1451 LEU
Chi-restraints excluded: chain A residue 1469 THR
Chi-restraints excluded: chain A residue 1488 ASP
Chi-restraints excluded: chain A residue 1514 GLU
Chi-restraints excluded: chain A residue 1582 MET
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   37 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 95 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 112 optimal weight:    0.0040
   chunk 45 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.9394

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

Flipped N/Q/H residues before XYZ refinement:
** A1352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1370 GLN
A1381 GLN
A1598 GLN
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.154410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.132423 restraints weight = 12110.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3759 rms_B_bonded: 2.66
r_work: 0.3604 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.3401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   9202  Z= 0.295
  Angle     :  0.682  11.169  12445  Z= 0.349
  Chirality :  0.045   0.171   1392
  Planarity :  0.005   0.049   1621
  Dihedral  :  4.822  34.359   1257
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 21.71 %
    Favored  : 74.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.25), residues: 1137
  helix:  1.22 (0.27), residues: 390
  sheet: -1.19 (0.31), residues: 263
  loop : -1.07 (0.29), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 297 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.036   0.002   PHE A 637 
 TYR   0.020   0.002   TYR A1573 
 ARG   0.007   0.001   ARG B 137 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 276
  time to evaluate  : 1.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 ASP cc_start: 0.7819 (p0) cc_final: 0.7541 (p0)
REVERT: A  510 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7535 (tt)
REVERT: A  516 ARG cc_start: 0.7665 (ttm110) cc_final: 0.7066 (ttm110)
REVERT: A  530 LYS cc_start: 0.8572 (pttt) cc_final: 0.8239 (ptpp)
REVERT: A  534 TYR cc_start: 0.7371 (t80) cc_final: 0.6651 (t80)
REVERT: A  535 HIS cc_start: 0.8549 (m170) cc_final: 0.8349 (m-70)
REVERT: A  540 LYS cc_start: 0.7967 (tptp) cc_final: 0.7644 (tptp)
REVERT: A  547 LYS cc_start: 0.7905 (tptm) cc_final: 0.7227 (tppt)
REVERT: A  553 LEU cc_start: 0.8586 (mp) cc_final: 0.8232 (mm)
REVERT: A  561 ARG cc_start: 0.8415 (mtp85) cc_final: 0.8014 (mtp85)
REVERT: A  563 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7281 (mt-10)
REVERT: A  565 VAL cc_start: 0.8578 (m) cc_final: 0.8374 (p)
REVERT: A  574 ASN cc_start: 0.7661 (m110) cc_final: 0.7420 (m110)
REVERT: A  577 MET cc_start: 0.7836 (ptp) cc_final: 0.6971 (mtm)
REVERT: A  587 ARG cc_start: 0.8058 (ttp-110) cc_final: 0.7329 (mtm110)
REVERT: A  683 GLU cc_start: 0.7498 (tt0) cc_final: 0.7040 (tt0)
REVERT: A  696 ARG cc_start: 0.7736 (mtt-85) cc_final: 0.7428 (mtt-85)
REVERT: A  705 LYS cc_start: 0.8141 (mtmm) cc_final: 0.7673 (mmmm)
REVERT: A  749 GLN cc_start: 0.7299 (mt0) cc_final: 0.6980 (mt0)
REVERT: A  780 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6212 (pp20)
REVERT: A  796 GLN cc_start: 0.8120 (pt0) cc_final: 0.7426 (pt0)
REVERT: A  841 MET cc_start: 0.8134 (mmm) cc_final: 0.7816 (mmm)
REVERT: A  852 GLU cc_start: 0.7722 (pt0) cc_final: 0.7480 (pt0)
REVERT: A  858 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7103 (tt0)
REVERT: A  872 LYS cc_start: 0.8311 (mtmm) cc_final: 0.7859 (mtpp)
REVERT: A  939 GLU cc_start: 0.8235 (tp30) cc_final: 0.7950 (tp30)
REVERT: A  960 HIS cc_start: 0.8276 (p-80) cc_final: 0.7775 (p-80)
REVERT: A  977 MET cc_start: 0.7644 (ptp) cc_final: 0.7335 (ptp)
REVERT: A 1322 ARG cc_start: 0.8431 (ttp80) cc_final: 0.8200 (ptm-80)
REVERT: A 1326 ILE cc_start: 0.8370 (pt) cc_final: 0.8069 (tt)
REVERT: A 1327 PHE cc_start: 0.8028 (t80) cc_final: 0.7680 (t80)
REVERT: A 1338 PHE cc_start: 0.7885 (t80) cc_final: 0.7457 (t80)
REVERT: A 1340 GLU cc_start: 0.6954 (tp30) cc_final: 0.6630 (tp30)
REVERT: A 1343 LEU cc_start: 0.8458 (mm) cc_final: 0.8095 (mp)
REVERT: A 1353 ASN cc_start: 0.7778 (m-40) cc_final: 0.7443 (m-40)
REVERT: A 1366 LYS cc_start: 0.8572 (pttp) cc_final: 0.8084 (ttpp)
REVERT: A 1370 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7878 (tm130)
REVERT: A 1405 GLU cc_start: 0.6977 (tp30) cc_final: 0.6715 (tp30)
REVERT: A 1431 GLU cc_start: 0.7490 (tm-30) cc_final: 0.6964 (tm-30)
REVERT: A 1469 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8860 (p)
REVERT: A 1472 LEU cc_start: 0.8076 (mt) cc_final: 0.7793 (tp)
REVERT: A 1496 GLN cc_start: 0.7975 (mt0) cc_final: 0.7742 (tt0)
REVERT: A 1503 GLN cc_start: 0.8230 (tp40) cc_final: 0.7656 (mm-40)
REVERT: A 1507 LYS cc_start: 0.8506 (mttt) cc_final: 0.8117 (mtmt)
REVERT: A 1546 MET cc_start: 0.8032 (tpp) cc_final: 0.7716 (tpp)
REVERT: A 1565 ILE cc_start: 0.8500 (mt) cc_final: 0.8259 (mm)
REVERT: A 1593 SER cc_start: 0.8386 (m) cc_final: 0.8078 (p)
REVERT: A 1596 LEU cc_start: 0.7521 (tp) cc_final: 0.7232 (tp)
REVERT: A 1622 LYS cc_start: 0.8258 (mttp) cc_final: 0.7781 (mmtm)
REVERT: A 1632 LYS cc_start: 0.8265 (mtmt) cc_final: 0.7709 (mtmm)
REVERT: B    8 ARG cc_start: 0.8363 (mtt90) cc_final: 0.8131 (mtt90)
REVERT: B   15 LYS cc_start: 0.9020 (mttp) cc_final: 0.8728 (mttp)
REVERT: B   59 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7768 (m-80)
REVERT: B   61 MET cc_start: 0.7901 (ppp) cc_final: 0.7530 (ptm)
REVERT: B  118 ASP cc_start: 0.7429 (t0) cc_final: 0.7203 (t0)
REVERT: B  145 TYR cc_start: 0.8413 (p90) cc_final: 0.8031 (p90)
REVERT: B  156 GLN cc_start: 0.7918 (mt0) cc_final: 0.7243 (mp10)
REVERT: B  188 MET cc_start: 0.7300 (mmm) cc_final: 0.6460 (mmm)
REVERT: B  230 ASN cc_start: 0.8602 (m-40) cc_final: 0.8234 (m-40)
REVERT: B  247 ASP cc_start: 0.7869 (t70) cc_final: 0.7104 (t0)
REVERT: B  279 SER cc_start: 0.8595 (m) cc_final: 0.8340 (t)
REVERT: B  289 TYR cc_start: 0.8662 (m-80) cc_final: 0.8363 (m-80)
REVERT: B  336 LEU cc_start: 0.7961 (mt) cc_final: 0.7663 (mm)
REVERT: G   13 ARG cc_start: 0.8379 (ttm110) cc_final: 0.8165 (ttm110)
REVERT: G   15 LEU cc_start: 0.8791 (mt) cc_final: 0.8453 (mt)
REVERT: G   18 GLN cc_start: 0.8109 (tp40) cc_final: 0.7605 (tp40)
REVERT: G   19 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8747 (mp)
REVERT: G   20 LYS cc_start: 0.8759 (ptmt) cc_final: 0.8453 (ptmm)
REVERT: G   38 MET cc_start: 0.8030 (ttp) cc_final: 0.7492 (tmm)
REVERT: G   58 GLU cc_start: 0.7892 (tp30) cc_final: 0.7689 (tp30)
  outliers start: 39
  outliers final: 26
  residues processed: 298
  average time/residue: 0.3589
  time to fit residues: 140.4261
Evaluate side-chains
  298 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 266
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  671 ILE
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  738 SER
Chi-restraints excluded: chain A residue  780 GLU
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  970 THR
Chi-restraints excluded: chain A residue 1018 THR
Chi-restraints excluded: chain A residue 1021 CYS
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain A residue 1025 MET
Chi-restraints excluded: chain A residue 1329 GLN
Chi-restraints excluded: chain A residue 1370 GLN
Chi-restraints excluded: chain A residue 1384 LEU
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1451 LEU
Chi-restraints excluded: chain A residue 1469 THR
Chi-restraints excluded: chain A residue 1488 ASP
Chi-restraints excluded: chain A residue 1499 GLU
Chi-restraints excluded: chain A residue 1514 GLU
Chi-restraints excluded: chain A residue 1582 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   37 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 45 optimal weight:    0.3980
   chunk 23 optimal weight:    0.8980
   chunk 110 optimal weight:    1.9990
   chunk 98 optimal weight:    0.8980
   chunk 105 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 975 ASN
** A1352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1370 GLN
** A1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** 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 = 0.4018 r_free = 0.4018 target = 0.154819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.132758 restraints weight = 12071.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 2.68
r_work: 0.3593 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.3494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9202  Z= 0.272
  Angle     :  0.692  10.610  12445  Z= 0.349
  Chirality :  0.044   0.188   1392
  Planarity :  0.005   0.049   1621
  Dihedral  :  4.831  33.827   1257
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 23.55 %
    Favored  : 72.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.25), residues: 1137
  helix:  1.23 (0.27), residues: 390
  sheet: -1.23 (0.31), residues: 259
  loop : -1.00 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 297 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.036   0.002   PHE A 637 
 TYR   0.038   0.002   TYR A1446 
 ARG   0.008   0.001   ARG B 137 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 270
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  510 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7624 (tt)
REVERT: A  511 MET cc_start: 0.7450 (mmm) cc_final: 0.7176 (mmm)
REVERT: A  516 ARG cc_start: 0.7664 (ttm110) cc_final: 0.7307 (ttm110)
REVERT: A  530 LYS cc_start: 0.8573 (pttt) cc_final: 0.8232 (ptpp)
REVERT: A  534 TYR cc_start: 0.7342 (t80) cc_final: 0.6686 (t80)
REVERT: A  540 LYS cc_start: 0.7938 (tptp) cc_final: 0.7620 (tptp)
REVERT: A  547 LYS cc_start: 0.7922 (tptm) cc_final: 0.7237 (tppt)
REVERT: A  553 LEU cc_start: 0.8565 (mp) cc_final: 0.8195 (mm)
REVERT: A  561 ARG cc_start: 0.8411 (mtp85) cc_final: 0.7988 (mtp85)
REVERT: A  563 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7461 (mt-10)
REVERT: A  565 VAL cc_start: 0.8574 (m) cc_final: 0.8372 (p)
REVERT: A  574 ASN cc_start: 0.7663 (m110) cc_final: 0.7443 (m110)
REVERT: A  577 MET cc_start: 0.7846 (ptp) cc_final: 0.6971 (mtm)
REVERT: A  587 ARG cc_start: 0.8080 (ttp-110) cc_final: 0.7314 (mtm110)
REVERT: A  672 ASN cc_start: 0.8352 (t0) cc_final: 0.7759 (m-40)
REVERT: A  683 GLU cc_start: 0.7503 (tt0) cc_final: 0.7053 (tt0)
REVERT: A  696 ARG cc_start: 0.7789 (mtt-85) cc_final: 0.7455 (mtt-85)
REVERT: A  699 ARG cc_start: 0.7758 (mtt90) cc_final: 0.6900 (mtm-85)
REVERT: A  705 LYS cc_start: 0.8099 (mtmm) cc_final: 0.7652 (mmmm)
REVERT: A  749 GLN cc_start: 0.7316 (mt0) cc_final: 0.6981 (mt0)
REVERT: A  780 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6198 (pp20)
REVERT: A  796 GLN cc_start: 0.8214 (pt0) cc_final: 0.7523 (pt0)
REVERT: A  841 MET cc_start: 0.8184 (mmm) cc_final: 0.7941 (mmm)
REVERT: A  852 GLU cc_start: 0.7823 (pt0) cc_final: 0.7450 (pt0)
REVERT: A  872 LYS cc_start: 0.8273 (mtmm) cc_final: 0.7834 (mtpp)
REVERT: A  882 LEU cc_start: 0.8521 (tp) cc_final: 0.8227 (tp)
REVERT: A  939 GLU cc_start: 0.8237 (tp30) cc_final: 0.7970 (tp30)
REVERT: A  974 ILE cc_start: 0.8318 (mt) cc_final: 0.8021 (mm)
REVERT: A 1019 GLN cc_start: 0.8012 (tt0) cc_final: 0.7619 (tm-30)
REVERT: A 1322 ARG cc_start: 0.8453 (ttp80) cc_final: 0.8214 (ptm-80)
REVERT: A 1326 ILE cc_start: 0.8370 (pt) cc_final: 0.8061 (tt)
REVERT: A 1327 PHE cc_start: 0.8027 (t80) cc_final: 0.7662 (t80)
REVERT: A 1338 PHE cc_start: 0.7867 (t80) cc_final: 0.7652 (t80)
REVERT: A 1340 GLU cc_start: 0.6938 (tp30) cc_final: 0.6589 (tp30)
REVERT: A 1343 LEU cc_start: 0.8455 (mm) cc_final: 0.8105 (mp)
REVERT: A 1353 ASN cc_start: 0.7784 (m-40) cc_final: 0.7455 (m-40)
REVERT: A 1366 LYS cc_start: 0.8519 (pttp) cc_final: 0.8086 (ttpp)
REVERT: A 1370 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7782 (tm130)
REVERT: A 1405 GLU cc_start: 0.6993 (tp30) cc_final: 0.6714 (tp30)
REVERT: A 1431 GLU cc_start: 0.7482 (tm-30) cc_final: 0.6978 (tm-30)
REVERT: A 1472 LEU cc_start: 0.8065 (mt) cc_final: 0.7821 (tp)
REVERT: A 1496 GLN cc_start: 0.7977 (mt0) cc_final: 0.7738 (tt0)
REVERT: A 1503 GLN cc_start: 0.8232 (tp40) cc_final: 0.7644 (mm-40)
REVERT: A 1507 LYS cc_start: 0.8509 (mttt) cc_final: 0.8115 (mtmt)
REVERT: A 1546 MET cc_start: 0.8056 (tpp) cc_final: 0.7712 (tpp)
REVERT: A 1565 ILE cc_start: 0.8486 (mt) cc_final: 0.8232 (mm)
REVERT: A 1596 LEU cc_start: 0.7487 (tp) cc_final: 0.7201 (tp)
REVERT: A 1598 GLN cc_start: 0.7231 (mt0) cc_final: 0.7029 (mt0)
REVERT: A 1614 MET cc_start: 0.8133 (tpt) cc_final: 0.7478 (tpt)
REVERT: A 1622 LYS cc_start: 0.8241 (mttp) cc_final: 0.7810 (mtpt)
REVERT: A 1632 LYS cc_start: 0.8275 (mtmt) cc_final: 0.7716 (mtmm)
REVERT: B    8 ARG cc_start: 0.8379 (mtt90) cc_final: 0.8128 (mtt90)
REVERT: B   15 LYS cc_start: 0.9041 (mttp) cc_final: 0.8744 (mttp)
REVERT: B   59 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.7743 (m-80)
REVERT: B   61 MET cc_start: 0.7896 (ppp) cc_final: 0.7583 (ptm)
REVERT: B  118 ASP cc_start: 0.7396 (t0) cc_final: 0.7159 (t0)
REVERT: B  145 TYR cc_start: 0.8407 (p90) cc_final: 0.8010 (p90)
REVERT: B  156 GLN cc_start: 0.7929 (mt0) cc_final: 0.7262 (mp10)
REVERT: B  188 MET cc_start: 0.7266 (mmm) cc_final: 0.6410 (mmm)
REVERT: B  230 ASN cc_start: 0.8562 (m-40) cc_final: 0.8183 (m-40)
REVERT: B  279 SER cc_start: 0.8596 (m) cc_final: 0.8335 (t)
REVERT: B  289 TYR cc_start: 0.8655 (m-80) cc_final: 0.8372 (m-80)
REVERT: B  336 LEU cc_start: 0.7929 (mt) cc_final: 0.7649 (mm)
REVERT: G   13 ARG cc_start: 0.8363 (ttm110) cc_final: 0.8161 (ttm110)
REVERT: G   15 LEU cc_start: 0.8798 (mt) cc_final: 0.8457 (mt)
REVERT: G   18 GLN cc_start: 0.8172 (tp40) cc_final: 0.7710 (tp40)
REVERT: G   19 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8753 (mp)
REVERT: G   20 LYS cc_start: 0.8758 (ptmt) cc_final: 0.8326 (ptmm)
REVERT: G   38 MET cc_start: 0.7998 (ttp) cc_final: 0.7481 (tmm)
  outliers start: 36
  outliers final: 27
  residues processed: 288
  average time/residue: 0.2922
  time to fit residues: 109.8336
Evaluate side-chains
  293 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 261
  time to evaluate  : 1.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  738 SER
Chi-restraints excluded: chain A residue  780 GLU
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  875 GLU
Chi-restraints excluded: chain A residue  970 THR
Chi-restraints excluded: chain A residue 1018 THR
Chi-restraints excluded: chain A residue 1021 CYS
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain A residue 1025 MET
Chi-restraints excluded: chain A residue 1370 GLN
Chi-restraints excluded: chain A residue 1384 LEU
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1451 LEU
Chi-restraints excluded: chain A residue 1488 ASP
Chi-restraints excluded: chain A residue 1499 GLU
Chi-restraints excluded: chain A residue 1514 GLU
Chi-restraints excluded: chain A residue 1571 LEU
Chi-restraints excluded: chain A residue 1582 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   37 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 111 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0770
   chunk 57 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 97 optimal weight:    3.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
A 535 HIS
** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 975 ASN
** A1352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1370 GLN
** A1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.155367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.133792 restraints weight = 11903.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 2.62
r_work: 0.3608 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.3544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9202  Z= 0.234
  Angle     :  0.682  10.366  12445  Z= 0.345
  Chirality :  0.044   0.194   1392
  Planarity :  0.004   0.048   1621
  Dihedral  :  4.806  33.862   1257
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 24.36 %
    Favored  : 72.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.26), residues: 1137
  helix:  1.31 (0.27), residues: 390
  sheet: -1.22 (0.30), residues: 258
  loop : -0.97 (0.29), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 297 
 HIS   0.012   0.001   HIS A 535 
 PHE   0.037   0.002   PHE A 637 
 TYR   0.033   0.002   TYR A1446 
 ARG   0.008   0.001   ARG A1361 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 270
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  511 MET cc_start: 0.7325 (mmm) cc_final: 0.7061 (mmm)
REVERT: A  516 ARG cc_start: 0.7746 (ttm110) cc_final: 0.7162 (ttm110)
REVERT: A  530 LYS cc_start: 0.8552 (pttt) cc_final: 0.8208 (ptpp)
REVERT: A  534 TYR cc_start: 0.7285 (t80) cc_final: 0.7018 (t80)
REVERT: A  535 HIS cc_start: 0.7995 (m90) cc_final: 0.7763 (m-70)
REVERT: A  540 LYS cc_start: 0.7892 (tptp) cc_final: 0.7628 (mmmt)
REVERT: A  547 LYS cc_start: 0.7921 (tptm) cc_final: 0.7249 (tppt)
REVERT: A  553 LEU cc_start: 0.8586 (mp) cc_final: 0.8225 (mm)
REVERT: A  561 ARG cc_start: 0.8401 (mtp85) cc_final: 0.8022 (mtp85)
REVERT: A  563 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7437 (mt-10)
REVERT: A  565 VAL cc_start: 0.8566 (m) cc_final: 0.8362 (p)
REVERT: A  574 ASN cc_start: 0.7665 (m110) cc_final: 0.7448 (m110)
REVERT: A  577 MET cc_start: 0.7834 (ptp) cc_final: 0.6968 (mtt)
REVERT: A  587 ARG cc_start: 0.8100 (ttp-110) cc_final: 0.7364 (mtm110)
REVERT: A  672 ASN cc_start: 0.8309 (t0) cc_final: 0.7563 (m-40)
REVERT: A  683 GLU cc_start: 0.7502 (tt0) cc_final: 0.6975 (tt0)
REVERT: A  696 ARG cc_start: 0.7788 (mtt-85) cc_final: 0.7487 (mtt-85)
REVERT: A  699 ARG cc_start: 0.7736 (mtt90) cc_final: 0.6866 (mtm-85)
REVERT: A  705 LYS cc_start: 0.8109 (mtmm) cc_final: 0.7698 (mmmm)
REVERT: A  749 GLN cc_start: 0.7319 (mt0) cc_final: 0.6966 (mt0)
REVERT: A  766 GLU cc_start: 0.8386 (mp0) cc_final: 0.8139 (mp0)
REVERT: A  780 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6166 (pp20)
REVERT: A  796 GLN cc_start: 0.8273 (pt0) cc_final: 0.7541 (pt0)
REVERT: A  841 MET cc_start: 0.8180 (mmm) cc_final: 0.7958 (mmm)
REVERT: A  852 GLU cc_start: 0.7768 (pt0) cc_final: 0.7453 (pt0)
REVERT: A  872 LYS cc_start: 0.8268 (mtmm) cc_final: 0.7855 (mtpp)
REVERT: A  882 LEU cc_start: 0.8522 (tp) cc_final: 0.8208 (tp)
REVERT: A  939 GLU cc_start: 0.8192 (tp30) cc_final: 0.7910 (tp30)
REVERT: A  974 ILE cc_start: 0.8329 (mt) cc_final: 0.8007 (mm)
REVERT: A  977 MET cc_start: 0.7716 (ptp) cc_final: 0.7367 (ptp)
REVERT: A 1019 GLN cc_start: 0.8030 (tt0) cc_final: 0.7628 (tm-30)
REVERT: A 1322 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8219 (ptm-80)
REVERT: A 1326 ILE cc_start: 0.8362 (pt) cc_final: 0.8071 (tt)
REVERT: A 1338 PHE cc_start: 0.7730 (t80) cc_final: 0.7279 (t80)
REVERT: A 1340 GLU cc_start: 0.6857 (tp30) cc_final: 0.6551 (tp30)
REVERT: A 1343 LEU cc_start: 0.8448 (mm) cc_final: 0.8092 (mp)
REVERT: A 1353 ASN cc_start: 0.7771 (m-40) cc_final: 0.7152 (m110)
REVERT: A 1366 LYS cc_start: 0.8571 (pttp) cc_final: 0.8256 (ttpp)
REVERT: A 1370 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7831 (tm130)
REVERT: A 1405 GLU cc_start: 0.6956 (tp30) cc_final: 0.6676 (tp30)
REVERT: A 1431 GLU cc_start: 0.7445 (tm-30) cc_final: 0.6953 (tm-30)
REVERT: A 1472 LEU cc_start: 0.8036 (mt) cc_final: 0.7784 (tp)
REVERT: A 1496 GLN cc_start: 0.7966 (mt0) cc_final: 0.7728 (tt0)
REVERT: A 1503 GLN cc_start: 0.8200 (tp40) cc_final: 0.7612 (mm-40)
REVERT: A 1507 LYS cc_start: 0.8503 (mttt) cc_final: 0.8108 (mttp)
REVERT: A 1546 MET cc_start: 0.8026 (tpp) cc_final: 0.7678 (tpp)
REVERT: A 1565 ILE cc_start: 0.8505 (mt) cc_final: 0.8252 (mm)
REVERT: A 1622 LYS cc_start: 0.8224 (mttp) cc_final: 0.7759 (mmtm)
REVERT: A 1632 LYS cc_start: 0.8251 (mtmt) cc_final: 0.7690 (mtmm)
REVERT: B    8 ARG cc_start: 0.8382 (mtt90) cc_final: 0.8120 (mtt90)
REVERT: B   15 LYS cc_start: 0.8996 (mttp) cc_final: 0.8706 (mttp)
REVERT: B   59 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7798 (m-80)
REVERT: B  118 ASP cc_start: 0.7317 (t0) cc_final: 0.7069 (t0)
REVERT: B  145 TYR cc_start: 0.8397 (p90) cc_final: 0.8068 (p90)
REVERT: B  156 GLN cc_start: 0.7930 (mt0) cc_final: 0.7241 (mp10)
REVERT: B  188 MET cc_start: 0.7242 (mmm) cc_final: 0.6389 (mmm)
REVERT: B  230 ASN cc_start: 0.8559 (m-40) cc_final: 0.8179 (m-40)
REVERT: B  279 SER cc_start: 0.8591 (m) cc_final: 0.8340 (t)
REVERT: B  289 TYR cc_start: 0.8644 (m-80) cc_final: 0.8323 (m-80)
REVERT: B  336 LEU cc_start: 0.7905 (mt) cc_final: 0.7670 (mm)
REVERT: G   15 LEU cc_start: 0.8802 (mt) cc_final: 0.8474 (mt)
REVERT: G   18 GLN cc_start: 0.8141 (tp40) cc_final: 0.7690 (tp40)
REVERT: G   19 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8673 (mp)
REVERT: G   20 LYS cc_start: 0.8761 (ptmt) cc_final: 0.8475 (ptmm)
REVERT: G   38 MET cc_start: 0.7968 (ttp) cc_final: 0.7493 (tmm)
  outliers start: 34
  outliers final: 27
  residues processed: 288
  average time/residue: 0.2665
  time to fit residues: 100.1537
Evaluate side-chains
  290 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 259
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  671 ILE
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  738 SER
Chi-restraints excluded: chain A residue  780 GLU
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  875 GLU
Chi-restraints excluded: chain A residue  970 THR
Chi-restraints excluded: chain A residue 1018 THR
Chi-restraints excluded: chain A residue 1021 CYS
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain A residue 1025 MET
Chi-restraints excluded: chain A residue 1370 GLN
Chi-restraints excluded: chain A residue 1384 LEU
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1451 LEU
Chi-restraints excluded: chain A residue 1488 ASP
Chi-restraints excluded: chain A residue 1499 GLU
Chi-restraints excluded: chain A residue 1514 GLU
Chi-restraints excluded: chain A residue 1571 LEU
Chi-restraints excluded: chain A residue 1582 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   37 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 5 optimal weight:    0.1980
   chunk 94 optimal weight:    0.2980
   chunk 3 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 81 optimal weight:    0.3980
   chunk 74 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 770 HIS
** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 975 ASN
** A1352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1370 GLN
A1381 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.156028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.134565 restraints weight = 11912.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 2.64
r_work: 0.3623 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.3682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9202  Z= 0.224
  Angle     :  0.687  10.258  12445  Z= 0.348
  Chirality :  0.044   0.191   1392
  Planarity :  0.005   0.048   1621
  Dihedral  :  4.814  34.225   1257
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 24.87 %
    Favored  : 71.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.26), residues: 1137
  helix:  1.33 (0.27), residues: 390
  sheet: -1.18 (0.30), residues: 259
  loop : -0.92 (0.30), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 297 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.036   0.002   PHE A 637 
 TYR   0.031   0.002   TYR A1446 
 ARG   0.009   0.001   ARG G  13 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 272
  time to evaluate  : 1.647 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  511 MET cc_start: 0.7275 (mmm) cc_final: 0.7015 (mmm)
REVERT: A  516 ARG cc_start: 0.7726 (ttm110) cc_final: 0.7163 (ttm110)
REVERT: A  530 LYS cc_start: 0.8561 (pttt) cc_final: 0.8225 (ptpp)
REVERT: A  534 TYR cc_start: 0.7294 (t80) cc_final: 0.7048 (t80)
REVERT: A  540 LYS cc_start: 0.7864 (tptp) cc_final: 0.7618 (mmmt)
REVERT: A  547 LYS cc_start: 0.7901 (tptm) cc_final: 0.7306 (tppt)
REVERT: A  553 LEU cc_start: 0.8582 (mp) cc_final: 0.8226 (mm)
REVERT: A  561 ARG cc_start: 0.8384 (mtp85) cc_final: 0.8036 (mtp85)
REVERT: A  563 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7416 (mt-10)
REVERT: A  565 VAL cc_start: 0.8573 (m) cc_final: 0.8366 (p)
REVERT: A  574 ASN cc_start: 0.7683 (m110) cc_final: 0.7174 (m110)
REVERT: A  577 MET cc_start: 0.7837 (ptp) cc_final: 0.6991 (mtt)
REVERT: A  587 ARG cc_start: 0.8109 (ttp-110) cc_final: 0.7391 (mtm110)
REVERT: A  672 ASN cc_start: 0.8296 (t0) cc_final: 0.7482 (m-40)
REVERT: A  683 GLU cc_start: 0.7475 (tt0) cc_final: 0.6958 (tt0)
REVERT: A  696 ARG cc_start: 0.7783 (mtt-85) cc_final: 0.7493 (mtt-85)
REVERT: A  699 ARG cc_start: 0.7729 (mtt90) cc_final: 0.6967 (mtm-85)
REVERT: A  749 GLN cc_start: 0.7314 (mt0) cc_final: 0.7022 (mt0)
REVERT: A  766 GLU cc_start: 0.8330 (mp0) cc_final: 0.8072 (mp0)
REVERT: A  780 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6128 (pp20)
REVERT: A  796 GLN cc_start: 0.8269 (pt0) cc_final: 0.7527 (pt0)
REVERT: A  852 GLU cc_start: 0.7751 (pt0) cc_final: 0.7323 (pt0)
REVERT: A  872 LYS cc_start: 0.8259 (mtmm) cc_final: 0.7851 (mtpp)
REVERT: A  882 LEU cc_start: 0.8499 (tp) cc_final: 0.8171 (tp)
REVERT: A  939 GLU cc_start: 0.8192 (tp30) cc_final: 0.7901 (tp30)
REVERT: A  974 ILE cc_start: 0.8309 (mt) cc_final: 0.8005 (mm)
REVERT: A  977 MET cc_start: 0.7686 (ptp) cc_final: 0.6783 (ptp)
REVERT: A 1019 GLN cc_start: 0.8017 (tt0) cc_final: 0.7667 (tm-30)
REVERT: A 1322 ARG cc_start: 0.8447 (ttp80) cc_final: 0.8218 (ptm-80)
REVERT: A 1326 ILE cc_start: 0.8402 (pt) cc_final: 0.8115 (tt)
REVERT: A 1340 GLU cc_start: 0.6836 (tp30) cc_final: 0.6454 (tp30)
REVERT: A 1343 LEU cc_start: 0.8451 (mm) cc_final: 0.8084 (mp)
REVERT: A 1358 GLU cc_start: 0.7237 (pt0) cc_final: 0.6726 (tt0)
REVERT: A 1366 LYS cc_start: 0.8540 (pttp) cc_final: 0.8157 (ttpp)
REVERT: A 1370 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7770 (tm130)
REVERT: A 1405 GLU cc_start: 0.6938 (tp30) cc_final: 0.6656 (tp30)
REVERT: A 1431 GLU cc_start: 0.7455 (tm-30) cc_final: 0.6967 (tm-30)
REVERT: A 1472 LEU cc_start: 0.8029 (mt) cc_final: 0.7769 (tp)
REVERT: A 1496 GLN cc_start: 0.7939 (mt0) cc_final: 0.7695 (tt0)
REVERT: A 1503 GLN cc_start: 0.8194 (tp40) cc_final: 0.7573 (mm-40)
REVERT: A 1507 LYS cc_start: 0.8512 (mttt) cc_final: 0.8112 (mttp)
REVERT: A 1546 MET cc_start: 0.8003 (tpp) cc_final: 0.7728 (mpp)
REVERT: A 1565 ILE cc_start: 0.8479 (mt) cc_final: 0.8180 (mm)
REVERT: A 1593 SER cc_start: 0.8375 (m) cc_final: 0.8170 (p)
REVERT: A 1598 GLN cc_start: 0.7452 (mt0) cc_final: 0.6818 (mm-40)
REVERT: A 1614 MET cc_start: 0.8088 (tpt) cc_final: 0.7500 (tpt)
REVERT: A 1622 LYS cc_start: 0.8216 (mttp) cc_final: 0.7748 (mmtm)
REVERT: A 1632 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7661 (mtmm)
REVERT: B    8 ARG cc_start: 0.8334 (mtt90) cc_final: 0.8090 (mtt90)
REVERT: B   15 LYS cc_start: 0.8999 (mttp) cc_final: 0.8617 (mttp)
REVERT: B   19 ARG cc_start: 0.8329 (mtm110) cc_final: 0.7934 (mtm-85)
REVERT: B   59 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.7860 (m-80)
REVERT: B  118 ASP cc_start: 0.7284 (t0) cc_final: 0.7015 (t0)
REVERT: B  145 TYR cc_start: 0.8352 (p90) cc_final: 0.8055 (p90)
REVERT: B  156 GLN cc_start: 0.7944 (mt0) cc_final: 0.7228 (mp10)
REVERT: B  188 MET cc_start: 0.7225 (mmm) cc_final: 0.6368 (mmm)
REVERT: B  230 ASN cc_start: 0.8546 (m-40) cc_final: 0.8167 (m-40)
REVERT: B  279 SER cc_start: 0.8578 (m) cc_final: 0.8353 (t)
REVERT: B  289 TYR cc_start: 0.8637 (m-80) cc_final: 0.8279 (m-80)
REVERT: B  336 LEU cc_start: 0.7933 (mt) cc_final: 0.7694 (mm)
REVERT: G   15 LEU cc_start: 0.8782 (mt) cc_final: 0.8434 (mt)
REVERT: G   18 GLN cc_start: 0.8123 (tp40) cc_final: 0.7703 (tp40)
REVERT: G   19 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8678 (mp)
REVERT: G   20 LYS cc_start: 0.8738 (ptmt) cc_final: 0.8458 (ptmm)
REVERT: G   38 MET cc_start: 0.8017 (ttp) cc_final: 0.7532 (tmm)
  outliers start: 33
  outliers final: 25
  residues processed: 287
  average time/residue: 0.2741
  time to fit residues: 103.7202
Evaluate side-chains
  290 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 261
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  671 ILE
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  738 SER
Chi-restraints excluded: chain A residue  780 GLU
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  875 GLU
Chi-restraints excluded: chain A residue  970 THR
Chi-restraints excluded: chain A residue 1018 THR
Chi-restraints excluded: chain A residue 1021 CYS
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain A residue 1025 MET
Chi-restraints excluded: chain A residue 1370 GLN
Chi-restraints excluded: chain A residue 1384 LEU
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1488 ASP
Chi-restraints excluded: chain A residue 1499 GLU
Chi-restraints excluded: chain A residue 1514 GLU
Chi-restraints excluded: chain A residue 1571 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   37 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 52 optimal weight:    0.0770
   chunk 51 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0020
   chunk 18 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 95 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 56 optimal weight:    0.2980
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.3346

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

Flipped N/Q/H residues before XYZ refinement:
A 535 HIS
A 559 GLN
** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 868 HIS
A 975 ASN
** A1352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1381 GLN
B 220 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.157742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.136246 restraints weight = 11860.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3813 rms_B_bonded: 2.63
r_work: 0.3663 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.3806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9202  Z= 0.204
  Angle     :  0.709  14.344  12445  Z= 0.351
  Chirality :  0.044   0.226   1392
  Planarity :  0.005   0.048   1621
  Dihedral  :  4.771  33.989   1257
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 25.89 %
    Favored  : 70.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.26), residues: 1137
  helix:  1.38 (0.27), residues: 390
  sheet: -1.14 (0.30), residues: 260
  loop : -0.91 (0.30), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 297 
 HIS   0.010   0.001   HIS A 535 
 PHE   0.036   0.002   PHE A 637 
 TYR   0.031   0.002   TYR A1446 
 ARG   0.008   0.001   ARG G  13 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5051.37 seconds
wall clock time: 90 minutes 33.76 seconds (5433.76 seconds total)