Starting phenix.real_space_refine
on Thu Feb 13 15:40:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pcv_20308/02_2025/6pcv_20308.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pcv_20308/02_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_20308/02_2025/6pcv_20308.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pcv_20308/02_2025/6pcv_20308.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pcv_20308/02_2025/6pcv_20308.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pcv_20308/02_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-5592/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: 5.86, per 1000 atoms: 0.65
  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: 2.25
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 3.58

  Time building geometry restraints manager: 2.63 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:             2.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     24.840
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.820
-------------------------------------------------------------------------------
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  : 0.789 
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: 0.2932
  time to fit residues: 126.2138
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  : 1.014 
-------------------------------------------------------------------------------
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 = 36)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.135305 restraints weight = 11746.151|
|-----------------------------------------------------------------------------|
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  40.627   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  : 1.026 
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: 0.8620 (pttt) cc_final: 0.8277 (ptpp)
REVERT: A  547 LYS cc_start: 0.7662 (tptm) cc_final: 0.7063 (tppt)
REVERT: A  550 ASP cc_start: 0.7437 (t0) cc_final: 0.7029 (t0)
REVERT: A  563 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7424 (mt-10)
REVERT: A  565 VAL cc_start: 0.8499 (m) cc_final: 0.8273 (p)
REVERT: A  587 ARG cc_start: 0.8150 (ttp-110) cc_final: 0.7675 (ttp-110)
REVERT: A  593 PHE cc_start: 0.6927 (m-10) cc_final: 0.6567 (m-10)
REVERT: A  625 ARG cc_start: 0.7314 (ptp90) cc_final: 0.7086 (ptp90)
REVERT: A  638 ASP cc_start: 0.6861 (p0) cc_final: 0.6660 (p0)
REVERT: A  644 LYS cc_start: 0.8890 (mptt) cc_final: 0.8598 (mmtm)
REVERT: A  652 GLN cc_start: 0.8223 (mm-40) cc_final: 0.8023 (mm-40)
REVERT: A  663 GLN cc_start: 0.7867 (mt0) cc_final: 0.7639 (mt0)
REVERT: A  683 GLU cc_start: 0.7491 (tt0) cc_final: 0.7112 (tt0)
REVERT: A  696 ARG cc_start: 0.7823 (mtt-85) cc_final: 0.7322 (mtt-85)
REVERT: A  699 ARG cc_start: 0.7611 (mtt90) cc_final: 0.7316 (mpp80)
REVERT: A  701 LEU cc_start: 0.8226 (mt) cc_final: 0.6151 (mt)
REVERT: A  705 LYS cc_start: 0.8201 (mtmm) cc_final: 0.7841 (mttm)
REVERT: A  715 GLN cc_start: 0.8446 (mt0) cc_final: 0.8180 (mp10)
REVERT: A  723 ILE cc_start: 0.8566 (mt) cc_final: 0.8333 (mm)
REVERT: A  754 VAL cc_start: 0.8338 (t) cc_final: 0.8040 (p)
REVERT: A  777 ARG cc_start: 0.8029 (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: 0.7840 (mtpp)
REVERT: A  939 GLU cc_start: 0.8240 (tp30) cc_final: 0.7888 (tp30)
REVERT: A 1019 GLN cc_start: 0.8048 (tt0) cc_final: 0.7599 (tm-30)
REVERT: A 1025 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8190 (ttt)
REVERT: A 1322 ARG cc_start: 0.8375 (ttp80) cc_final: 0.8148 (ptm-80)
REVERT: A 1326 ILE cc_start: 0.8425 (pt) cc_final: 0.8144 (tt)
REVERT: A 1327 PHE cc_start: 0.7958 (t80) cc_final: 0.7678 (t80)
REVERT: A 1340 GLU cc_start: 0.6949 (tp30) cc_final: 0.6522 (tp30)
REVERT: A 1343 LEU cc_start: 0.8355 (mp) cc_final: 0.8135 (mm)
REVERT: A 1353 ASN cc_start: 0.7579 (m-40) cc_final: 0.7184 (m-40)
REVERT: A 1366 LYS cc_start: 0.8593 (pttp) cc_final: 0.8238 (ttpp)
REVERT: A 1405 GLU cc_start: 0.6878 (tp30) cc_final: 0.6309 (tp30)
REVERT: A 1431 GLU cc_start: 0.7506 (tm-30) cc_final: 0.6973 (tm-30)
REVERT: A 1443 LEU cc_start: 0.8788 (mp) cc_final: 0.8505 (mm)
REVERT: A 1491 GLN cc_start: 0.7701 (tp-100) cc_final: 0.7148 (tm-30)
REVERT: A 1507 LYS cc_start: 0.8431 (mttt) cc_final: 0.8060 (mttp)
REVERT: A 1597 GLU cc_start: 0.7343 (tt0) cc_final: 0.7088 (tt0)
REVERT: A 1632 LYS cc_start: 0.8299 (mtmt) cc_final: 0.7709 (mtmm)
REVERT: B    8 ARG cc_start: 0.8335 (mtt90) cc_final: 0.8003 (mtt90)
REVERT: B   15 LYS cc_start: 0.8916 (mttp) cc_final: 0.8609 (mttp)
REVERT: B   61 MET cc_start: 0.7797 (ppp) cc_final: 0.7324 (ptm)
REVERT: B  168 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8105 (tt)
REVERT: B  188 MET cc_start: 0.7146 (mmm) cc_final: 0.6352 (mmm)
REVERT: B  279 SER cc_start: 0.8772 (m) cc_final: 0.8444 (t)
REVERT: B  286 LEU cc_start: 0.8322 (mp) cc_final: 0.8096 (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: 0.8722 (mt) cc_final: 0.8355 (mt)
REVERT: G   17 GLU cc_start: 0.8662 (pt0) cc_final: 0.8420 (mt-10)
REVERT: G   18 GLN cc_start: 0.8179 (tp40) cc_final: 0.7346 (tp40)
REVERT: G   20 LYS cc_start: 0.8692 (ptmt) cc_final: 0.8283 (ptpp)
REVERT: G   21 MET cc_start: 0.7510 (mmm) cc_final: 0.7264 (mmm)
REVERT: G   22 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7353 (mt-10)
REVERT: G   38 MET cc_start: 0.8004 (ttp) cc_final: 0.7478 (tmm)
  outliers start: 34
  outliers final: 7
  residues processed: 304
  average time/residue: 0.2914
  time to fit residues: 113.7497
Evaluate side-chains
  280 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 270
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 67 optimal weight:    0.3980
   chunk 27 optimal weight:    0.1980
   chunk 26 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 104 optimal weight:    0.0070
   chunk 9 optimal weight:    0.2980
   overall best weight:    0.1998

-------------------------------------------------------------------------------
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**
A1019 GLN
A1381 GLN
A1429 HIS
** 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.159483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.137878 restraints weight = 11976.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3813 rms_B_bonded: 2.68
r_work: 0.3662 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9202  Z= 0.173
  Angle     :  0.626   8.512  12445  Z= 0.320
  Chirality :  0.044   0.271   1392
  Planarity :  0.005   0.048   1621
  Dihedral  :  4.969  36.017   1257
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 18.55 %
    Favored  : 78.70 %
  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: -1.01 (0.24), residues: 1137
  helix:  0.90 (0.26), residues: 381
  sheet: -1.49 (0.29), residues: 268
  loop : -1.38 (0.28), residues: 488

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   0.023   0.002   PHE A 637 
 TYR   0.018   0.001   TYR A1446 
 ARG   0.008   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
  317 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 290
  time to evaluate  : 0.935 
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: 0.8572 (pttt) cc_final: 0.8194 (ptpp)
REVERT: A  540 LYS cc_start: 0.8097 (tptp) cc_final: 0.7725 (tptp)
REVERT: A  547 LYS cc_start: 0.7716 (tptm) cc_final: 0.7125 (tppt)
REVERT: A  550 ASP cc_start: 0.7380 (t0) cc_final: 0.7017 (t0)
REVERT: A  563 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7402 (mt-10)
REVERT: A  565 VAL cc_start: 0.8482 (m) cc_final: 0.8250 (p)
REVERT: A  577 MET cc_start: 0.7665 (ptp) cc_final: 0.6942 (mtt)
REVERT: A  587 ARG cc_start: 0.8105 (ttp-110) cc_final: 0.7831 (ttp-110)
REVERT: A  618 VAL cc_start: 0.8184 (p) cc_final: 0.7948 (m)
REVERT: A  644 LYS cc_start: 0.8830 (mptt) cc_final: 0.8531 (mmtm)
REVERT: A  683 GLU cc_start: 0.7419 (tt0) cc_final: 0.7009 (tt0)
REVERT: A  687 ILE cc_start: 0.7910 (mt) cc_final: 0.7569 (mm)
REVERT: A  696 ARG cc_start: 0.7840 (mtt-85) cc_final: 0.7543 (mtt-85)
REVERT: A  705 LYS cc_start: 0.8188 (mtmm) cc_final: 0.7854 (mttm)
REVERT: A  715 GLN cc_start: 0.8394 (mt0) cc_final: 0.8080 (mp10)
REVERT: A  723 ILE cc_start: 0.8579 (mt) cc_final: 0.8336 (mm)
REVERT: A  777 ARG cc_start: 0.8028 (ptp-170) cc_final: 0.7708 (mtm180)
REVERT: A  802 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7228 (pp30)
REVERT: A  852 GLU cc_start: 0.7389 (pt0) cc_final: 0.6939 (pp20)
REVERT: A  872 LYS cc_start: 0.8361 (mtmm) cc_final: 0.7914 (mtpp)
REVERT: A  882 LEU cc_start: 0.8463 (tp) cc_final: 0.8087 (tp)
REVERT: A  939 GLU cc_start: 0.8246 (tp30) cc_final: 0.7876 (tp30)
REVERT: A 1019 GLN cc_start: 0.8005 (tt0) cc_final: 0.7616 (tm-30)
REVERT: A 1025 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8153 (ttt)
REVERT: A 1322 ARG cc_start: 0.8386 (ttp80) cc_final: 0.8068 (ptm-80)
REVERT: A 1327 PHE cc_start: 0.8011 (t80) cc_final: 0.7766 (t80)
REVERT: A 1338 PHE cc_start: 0.7732 (t80) cc_final: 0.7383 (t80)
REVERT: A 1340 GLU cc_start: 0.6829 (tp30) cc_final: 0.6408 (tp30)
REVERT: A 1343 LEU cc_start: 0.8290 (mp) cc_final: 0.8079 (mm)
REVERT: A 1353 ASN cc_start: 0.7552 (m-40) cc_final: 0.7045 (m-40)
REVERT: A 1361 ARG cc_start: 0.7708 (ttt-90) cc_final: 0.7492 (ttt180)
REVERT: A 1366 LYS cc_start: 0.8585 (pttp) cc_final: 0.8233 (ttpp)
REVERT: A 1405 GLU cc_start: 0.6894 (tp30) cc_final: 0.6282 (tp30)
REVERT: A 1428 TYR cc_start: 0.8255 (m-10) cc_final: 0.7941 (m-10)
REVERT: A 1431 GLU cc_start: 0.7418 (tm-30) cc_final: 0.6864 (tm-30)
REVERT: A 1491 GLN cc_start: 0.7669 (tp-100) cc_final: 0.7108 (tm-30)
REVERT: A 1503 GLN cc_start: 0.8228 (tp40) cc_final: 0.7661 (mm-40)
REVERT: A 1507 LYS cc_start: 0.8434 (mttt) cc_final: 0.8066 (mttp)
REVERT: A 1515 ARG cc_start: 0.7516 (mtp-110) cc_final: 0.7280 (mtp-110)
REVERT: A 1565 ILE cc_start: 0.8532 (mt) cc_final: 0.8178 (mm)
REVERT: A 1596 LEU cc_start: 0.7292 (mt) cc_final: 0.6897 (mt)
REVERT: A 1614 MET cc_start: 0.8216 (tpt) cc_final: 0.7693 (tpt)
REVERT: A 1622 LYS cc_start: 0.8331 (mttp) cc_final: 0.7859 (mmtm)
REVERT: A 1632 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7641 (mtmm)
REVERT: B    8 ARG cc_start: 0.8306 (mtt90) cc_final: 0.8015 (mtt90)
REVERT: B   15 LYS cc_start: 0.8934 (mttp) cc_final: 0.8645 (mttp)
REVERT: B   61 MET cc_start: 0.7768 (ppp) cc_final: 0.7376 (ptm)
REVERT: B  118 ASP cc_start: 0.7147 (t0) cc_final: 0.6851 (t0)
REVERT: B  145 TYR cc_start: 0.8397 (p90) cc_final: 0.7933 (p90)
REVERT: B  168 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8007 (tt)
REVERT: B  188 MET cc_start: 0.7332 (mmm) cc_final: 0.6731 (mmm)
REVERT: B  197 ARG cc_start: 0.7133 (tpp80) cc_final: 0.6831 (tpp80)
REVERT: B  279 SER cc_start: 0.8682 (m) cc_final: 0.8382 (t)
REVERT: B  289 TYR cc_start: 0.8614 (m-80) cc_final: 0.8252 (m-80)
REVERT: B  336 LEU cc_start: 0.7978 (mt) cc_final: 0.7704 (mm)
REVERT: G   15 LEU cc_start: 0.8747 (mt) cc_final: 0.8419 (mt)
REVERT: G   18 GLN cc_start: 0.8120 (tp40) cc_final: 0.6685 (tp40)
REVERT: G   19 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8827 (mp)
REVERT: G   20 LYS cc_start: 0.8697 (ptmt) cc_final: 0.8479 (ptpp)
REVERT: G   38 MET cc_start: 0.7924 (ttp) cc_final: 0.7414 (tmm)
  outliers start: 27
  outliers final: 15
  residues processed: 306
  average time/residue: 0.2797
  time to fit residues: 110.5095
Evaluate side-chains
  289 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 270
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
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  802 GLN
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  970 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 1403 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:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 84 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0670
   chunk 64 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0570
   chunk 2 optimal weight:    3.9990
   chunk 49 optimal weight:    0.2980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.4236

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

Flipped N/Q/H residues before XYZ refinement:
A 555 GLN
** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 802 GLN
** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.157770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.136239 restraints weight = 11878.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3810 rms_B_bonded: 2.65
r_work: 0.3662 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7270
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9202  Z= 0.193
  Angle     :  0.626   8.379  12445  Z= 0.319
  Chirality :  0.043   0.169   1392
  Planarity :  0.004   0.048   1621
  Dihedral  :  4.894  41.188   1257
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 19.06 %
    Favored  : 77.27 %
  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: -0.64 (0.25), residues: 1137
  helix:  1.23 (0.27), residues: 382
  sheet: -1.29 (0.29), residues: 264
  loop : -1.20 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 297 
 HIS   0.003   0.001   HIS A 790 
 PHE   0.027   0.002   PHE A 637 
 TYR   0.017   0.001   TYR A 789 
 ARG   0.007   0.001   ARG A 516 

*********************** 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: 36
    poor density    : 287
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  511 MET cc_start: 0.7192 (tpp) cc_final: 0.6930 (mmm)
REVERT: A  530 LYS cc_start: 0.8558 (pttt) cc_final: 0.8190 (ptpp)
REVERT: A  540 LYS cc_start: 0.8014 (tptp) cc_final: 0.7688 (tptp)
REVERT: A  547 LYS cc_start: 0.7734 (tptm) cc_final: 0.7162 (tppt)
REVERT: A  550 ASP cc_start: 0.7377 (t70) cc_final: 0.6978 (t0)
REVERT: A  553 LEU cc_start: 0.8577 (mp) cc_final: 0.8210 (mm)
REVERT: A  561 ARG cc_start: 0.8436 (mtp85) cc_final: 0.8191 (mtp85)
REVERT: A  563 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7352 (mt-10)
REVERT: A  565 VAL cc_start: 0.8483 (m) cc_final: 0.8251 (p)
REVERT: A  577 MET cc_start: 0.7787 (ptp) cc_final: 0.6998 (mtt)
REVERT: A  618 VAL cc_start: 0.8181 (p) cc_final: 0.7943 (m)
REVERT: A  644 LYS cc_start: 0.8849 (mptt) cc_final: 0.8530 (mmtm)
REVERT: A  683 GLU cc_start: 0.7450 (tt0) cc_final: 0.7080 (tt0)
REVERT: A  694 SER cc_start: 0.7738 (p) cc_final: 0.7156 (t)
REVERT: A  696 ARG cc_start: 0.7760 (mtt-85) cc_final: 0.7180 (mtt-85)
REVERT: A  699 ARG cc_start: 0.7556 (mtt90) cc_final: 0.7305 (mtt90)
REVERT: A  705 LYS cc_start: 0.8177 (mtmm) cc_final: 0.7960 (mptt)
REVERT: A  715 GLN cc_start: 0.8360 (mt0) cc_final: 0.8113 (mp10)
REVERT: A  723 ILE cc_start: 0.8611 (mt) cc_final: 0.8342 (mm)
REVERT: A  796 GLN cc_start: 0.7912 (pt0) cc_final: 0.7341 (pt0)
REVERT: A  799 ARG cc_start: 0.7753 (mpt180) cc_final: 0.7371 (tpp80)
REVERT: A  802 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7293 (pp30)
REVERT: A  841 MET cc_start: 0.8207 (mmm) cc_final: 0.7757 (mmm)
REVERT: A  852 GLU cc_start: 0.7504 (pt0) cc_final: 0.7141 (pp20)
REVERT: A  872 LYS cc_start: 0.8317 (mtmm) cc_final: 0.7922 (mtpp)
REVERT: A 1019 GLN cc_start: 0.7958 (tt0) cc_final: 0.7148 (tm-30)
REVERT: A 1020 HIS cc_start: 0.7834 (m-70) cc_final: 0.7489 (m-70)
REVERT: A 1322 ARG cc_start: 0.8357 (ttp80) cc_final: 0.8044 (ptm-80)
REVERT: A 1327 PHE cc_start: 0.8005 (t80) cc_final: 0.7772 (t80)
REVERT: A 1338 PHE cc_start: 0.7749 (t80) cc_final: 0.7399 (t80)
REVERT: A 1340 GLU cc_start: 0.6863 (tp30) cc_final: 0.6478 (tp30)
REVERT: A 1343 LEU cc_start: 0.8253 (mp) cc_final: 0.8052 (mm)
REVERT: A 1366 LYS cc_start: 0.8545 (pttp) cc_final: 0.8082 (ttpp)
REVERT: A 1405 GLU cc_start: 0.6939 (tp30) cc_final: 0.6290 (tp30)
REVERT: A 1410 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.8032 (m)
REVERT: A 1431 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6828 (tm-30)
REVERT: A 1491 GLN cc_start: 0.7675 (tp-100) cc_final: 0.7136 (tm-30)
REVERT: A 1496 GLN cc_start: 0.7868 (mt0) cc_final: 0.7592 (tt0)
REVERT: A 1503 GLN cc_start: 0.8145 (tp40) cc_final: 0.7536 (mm-40)
REVERT: A 1507 LYS cc_start: 0.8427 (mttt) cc_final: 0.8032 (mttp)
REVERT: A 1546 MET cc_start: 0.7986 (tpp) cc_final: 0.7671 (tpp)
REVERT: A 1565 ILE cc_start: 0.8492 (mt) cc_final: 0.8232 (mm)
REVERT: A 1614 MET cc_start: 0.8241 (tpt) cc_final: 0.7676 (tpt)
REVERT: A 1622 LYS cc_start: 0.8245 (mttp) cc_final: 0.7788 (mmtm)
REVERT: A 1632 LYS cc_start: 0.8214 (mtmt) cc_final: 0.7619 (mtmm)
REVERT: B    8 ARG cc_start: 0.8302 (mtt90) cc_final: 0.8029 (mtt90)
REVERT: B   15 LYS cc_start: 0.8953 (mttp) cc_final: 0.8686 (mttp)
REVERT: B   61 MET cc_start: 0.7835 (ppp) cc_final: 0.7405 (ptm)
REVERT: B  118 ASP cc_start: 0.7224 (t0) cc_final: 0.6908 (t0)
REVERT: B  145 TYR cc_start: 0.8366 (p90) cc_final: 0.7803 (p90)
REVERT: B  158 VAL cc_start: 0.7930 (OUTLIER) cc_final: 0.7713 (m)
REVERT: B  168 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7947 (tt)
REVERT: B  188 MET cc_start: 0.7203 (mmm) cc_final: 0.6473 (mmm)
REVERT: B  230 ASN cc_start: 0.8569 (m-40) cc_final: 0.8169 (m-40)
REVERT: B  279 SER cc_start: 0.8613 (m) cc_final: 0.8317 (t)
REVERT: B  289 TYR cc_start: 0.8635 (m-80) cc_final: 0.8296 (m-80)
REVERT: B  336 LEU cc_start: 0.7992 (mt) cc_final: 0.7697 (mm)
REVERT: G   13 ARG cc_start: 0.8250 (ttm110) cc_final: 0.7996 (ttm110)
REVERT: G   15 LEU cc_start: 0.8772 (mt) cc_final: 0.8457 (mt)
REVERT: G   18 GLN cc_start: 0.8198 (tp40) cc_final: 0.7677 (tp40)
REVERT: G   20 LYS cc_start: 0.8758 (ptmt) cc_final: 0.8186 (ptpp)
REVERT: G   38 MET cc_start: 0.7930 (ttp) cc_final: 0.7413 (tmm)
  outliers start: 36
  outliers final: 23
  residues processed: 306
  average time/residue: 0.2739
  time to fit residues: 108.8591
Evaluate side-chains
  290 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 263
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  626 LEU
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  855 VAL
Chi-restraints excluded: chain A residue  970 THR
Chi-restraints excluded: chain A residue  975 ASN
Chi-restraints excluded: chain A residue 1021 CYS
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 1514 GLU
Chi-restraints excluded: chain A residue 1571 LEU
Chi-restraints excluded: chain A residue 1582 MET
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
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:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 99 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0370
   chunk 106 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.9862

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

Flipped N/Q/H residues before XYZ refinement:
A 535 HIS
A 868 HIS
** A1352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1370 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.154084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.132425 restraints weight = 11890.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 2.63
r_work: 0.3600 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.3207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9202  Z= 0.302
  Angle     :  0.664   8.554  12445  Z= 0.343
  Chirality :  0.045   0.167   1392
  Planarity :  0.005   0.049   1621
  Dihedral  :  4.938  37.591   1257
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 19.16 %
    Favored  : 76.35 %
  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: -0.63 (0.25), residues: 1137
  helix:  1.13 (0.27), residues: 387
  sheet: -1.28 (0.30), residues: 260
  loop : -1.11 (0.29), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 551 
 HIS   0.005   0.001   HIS A 790 
 PHE   0.032   0.002   PHE A 637 
 TYR   0.018   0.002   TYR A 534 
 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
  326 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 282
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
REVERT: A  511 MET cc_start: 0.7302 (tpp) cc_final: 0.7050 (mmm)
REVERT: A  513 LYS cc_start: 0.8392 (mtmt) cc_final: 0.8038 (mtmt)
REVERT: A  530 LYS cc_start: 0.8482 (pttt) cc_final: 0.8136 (ptpp)
REVERT: A  540 LYS cc_start: 0.8048 (tptp) cc_final: 0.7695 (tptp)
REVERT: A  547 LYS cc_start: 0.7923 (tptm) cc_final: 0.7154 (tppt)
REVERT: A  550 ASP cc_start: 0.7344 (t70) cc_final: 0.6927 (t0)
REVERT: A  553 LEU cc_start: 0.8651 (mp) cc_final: 0.8320 (mm)
REVERT: A  561 ARG cc_start: 0.8440 (mtp85) cc_final: 0.8109 (mtp85)
REVERT: A  563 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7400 (mt-10)
REVERT: A  565 VAL cc_start: 0.8574 (m) cc_final: 0.8372 (p)
REVERT: A  577 MET cc_start: 0.7844 (ptp) cc_final: 0.6966 (mtt)
REVERT: A  587 ARG cc_start: 0.8113 (ttp-110) cc_final: 0.7345 (ttm110)
REVERT: A  638 ASP cc_start: 0.7091 (p0) cc_final: 0.6825 (p0)
REVERT: A  644 LYS cc_start: 0.8887 (mptt) cc_final: 0.8498 (mmtm)
REVERT: A  653 ARG cc_start: 0.7876 (ttt-90) cc_final: 0.7593 (ttt-90)
REVERT: A  673 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6667 (mm-30)
REVERT: A  683 GLU cc_start: 0.7599 (tt0) cc_final: 0.7212 (tt0)
REVERT: A  694 SER cc_start: 0.7777 (p) cc_final: 0.7108 (t)
REVERT: A  696 ARG cc_start: 0.7720 (mtt-85) cc_final: 0.7112 (mtt-85)
REVERT: A  699 ARG cc_start: 0.7601 (mtt90) cc_final: 0.6961 (mtm-85)
REVERT: A  715 GLN cc_start: 0.8374 (mt0) cc_final: 0.8146 (mp10)
REVERT: A  723 ILE cc_start: 0.8622 (mt) cc_final: 0.8356 (mm)
REVERT: A  749 GLN cc_start: 0.7320 (mt0) cc_final: 0.7012 (mt0)
REVERT: A  780 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6207 (pp20)
REVERT: A  796 GLN cc_start: 0.7922 (pt0) cc_final: 0.7452 (pt0)
REVERT: A  852 GLU cc_start: 0.7341 (pt0) cc_final: 0.7130 (pt0)
REVERT: A  872 LYS cc_start: 0.8308 (mtmm) cc_final: 0.7806 (mtpp)
REVERT: A  939 GLU cc_start: 0.8256 (tp30) cc_final: 0.7933 (tp30)
REVERT: A  940 PHE cc_start: 0.8868 (m-10) cc_final: 0.8643 (m-10)
REVERT: A 1019 GLN cc_start: 0.7991 (tt0) cc_final: 0.7759 (tt0)
REVERT: A 1322 ARG cc_start: 0.8471 (ttp80) cc_final: 0.8213 (ptm-80)
REVERT: A 1326 ILE cc_start: 0.8390 (pt) cc_final: 0.8083 (tt)
REVERT: A 1327 PHE cc_start: 0.8091 (t80) cc_final: 0.7723 (t80)
REVERT: A 1340 GLU cc_start: 0.7030 (tp30) cc_final: 0.6648 (tp30)
REVERT: A 1353 ASN cc_start: 0.7687 (m-40) cc_final: 0.7341 (m-40)
REVERT: A 1366 LYS cc_start: 0.8634 (pttp) cc_final: 0.8172 (ttpp)
REVERT: A 1405 GLU cc_start: 0.6997 (tp30) cc_final: 0.6751 (tp30)
REVERT: A 1431 GLU cc_start: 0.7483 (tm-30) cc_final: 0.6938 (tm-30)
REVERT: A 1469 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8841 (p)
REVERT: A 1496 GLN cc_start: 0.7929 (mt0) cc_final: 0.7669 (tt0)
REVERT: A 1503 GLN cc_start: 0.8228 (tp40) cc_final: 0.7660 (mm-40)
REVERT: A 1507 LYS cc_start: 0.8488 (mttt) cc_final: 0.8119 (mtmt)
REVERT: A 1546 MET cc_start: 0.8089 (tpp) cc_final: 0.7771 (tpp)
REVERT: A 1565 ILE cc_start: 0.8526 (mt) cc_final: 0.8155 (mm)
REVERT: A 1593 SER cc_start: 0.8418 (m) cc_final: 0.8192 (p)
REVERT: A 1596 LEU cc_start: 0.7464 (tp) cc_final: 0.7167 (tp)
REVERT: A 1598 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7138 (mt0)
REVERT: A 1614 MET cc_start: 0.8212 (tpt) cc_final: 0.7608 (tpt)
REVERT: A 1632 LYS cc_start: 0.8350 (mtmt) cc_final: 0.7752 (mtmm)
REVERT: B    8 ARG cc_start: 0.8343 (mtt90) cc_final: 0.8032 (mtt90)
REVERT: B   14 LEU cc_start: 0.8630 (mt) cc_final: 0.8348 (mt)
REVERT: B   15 LYS cc_start: 0.8949 (mttp) cc_final: 0.8713 (mttp)
REVERT: B   59 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7784 (m-80)
REVERT: B  118 ASP cc_start: 0.7485 (t0) cc_final: 0.7148 (t0)
REVERT: B  145 TYR cc_start: 0.8377 (p90) cc_final: 0.7787 (p90)
REVERT: B  156 GLN cc_start: 0.8052 (mt0) cc_final: 0.7842 (mt0)
REVERT: B  188 MET cc_start: 0.7355 (mmm) cc_final: 0.6559 (mmm)
REVERT: B  230 ASN cc_start: 0.8616 (m-40) cc_final: 0.8230 (m-40)
REVERT: B  279 SER cc_start: 0.8607 (m) cc_final: 0.8289 (t)
REVERT: B  289 TYR cc_start: 0.8650 (m-80) cc_final: 0.8288 (m-80)
REVERT: B  336 LEU cc_start: 0.7977 (mt) cc_final: 0.7702 (mm)
REVERT: G   13 ARG cc_start: 0.8377 (ttm110) cc_final: 0.8149 (ttm110)
REVERT: G   15 LEU cc_start: 0.8794 (mt) cc_final: 0.8462 (mt)
REVERT: G   18 GLN cc_start: 0.8253 (tp40) cc_final: 0.7777 (tp40)
REVERT: G   19 LEU cc_start: 0.8946 (mp) cc_final: 0.8734 (mp)
REVERT: G   20 LYS cc_start: 0.8812 (ptmt) cc_final: 0.8467 (ptmm)
REVERT: G   38 MET cc_start: 0.8019 (ttp) cc_final: 0.7478 (tmm)
  outliers start: 44
  outliers final: 24
  residues processed: 306
  average time/residue: 0.2829
  time to fit residues: 111.8224
Evaluate side-chains
  299 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 271
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  626 LEU
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  849 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 1384 LEU
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1424 THR
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 A residue 1598 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   30 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 81 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 23 optimal weight:    0.3980
   chunk 68 optimal weight:    0.9990
   chunk 78 optimal weight:    0.0170
   chunk 75 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   chunk 76 optimal weight:    0.8980
   chunk 95 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9990
   overall best weight:    0.6018

-------------------------------------------------------------------------------
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 975 ASN
A1020 HIS
** A1352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1606 HIS
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.155869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.134424 restraints weight = 11862.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 2.61
r_work: 0.3613 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9202  Z= 0.240
  Angle     :  0.652   8.040  12445  Z= 0.334
  Chirality :  0.044   0.173   1392
  Planarity :  0.004   0.046   1621
  Dihedral  :  4.842  33.146   1257
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 22.83 %
    Favored  : 73.70 %
  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: -0.47 (0.25), residues: 1137
  helix:  1.25 (0.27), residues: 388
  sheet: -1.15 (0.30), residues: 258
  loop : -1.04 (0.29), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 297 
 HIS   0.006   0.001   HIS A 790 
 PHE   0.033   0.002   PHE A 637 
 TYR   0.035   0.002   TYR A1446 
 ARG   0.007   0.001   ARG A1361 

*********************** 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
  307 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 273
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  511 MET cc_start: 0.7330 (tpp) cc_final: 0.7127 (mmm)
REVERT: A  524 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8603 (pp)
REVERT: A  530 LYS cc_start: 0.8534 (pttt) cc_final: 0.8190 (ptpp)
REVERT: A  540 LYS cc_start: 0.7972 (tptp) cc_final: 0.7644 (tptp)
REVERT: A  547 LYS cc_start: 0.7837 (tptm) cc_final: 0.7135 (tppt)
REVERT: A  553 LEU cc_start: 0.8616 (mp) cc_final: 0.8273 (mm)
REVERT: A  559 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8129 (mm110)
REVERT: A  561 ARG cc_start: 0.8435 (mtp85) cc_final: 0.8118 (mtp85)
REVERT: A  563 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7230 (mt-10)
REVERT: A  565 VAL cc_start: 0.8561 (m) cc_final: 0.8351 (p)
REVERT: A  574 ASN cc_start: 0.7720 (m110) cc_final: 0.7140 (m110)
REVERT: A  577 MET cc_start: 0.7763 (ptp) cc_final: 0.7371 (mtm)
REVERT: A  587 ARG cc_start: 0.8146 (ttp-110) cc_final: 0.7420 (ttm110)
REVERT: A  625 ARG cc_start: 0.7162 (ptp90) cc_final: 0.6936 (ptp90)
REVERT: A  653 ARG cc_start: 0.7807 (ttt-90) cc_final: 0.7495 (ttt-90)
REVERT: A  672 ASN cc_start: 0.8135 (t0) cc_final: 0.7866 (m-40)
REVERT: A  673 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6996 (mm-30)
REVERT: A  683 GLU cc_start: 0.7517 (tt0) cc_final: 0.7182 (tt0)
REVERT: A  696 ARG cc_start: 0.7813 (mtt-85) cc_final: 0.7488 (mtt-85)
REVERT: A  699 ARG cc_start: 0.7746 (mtt90) cc_final: 0.7217 (mtm-85)
REVERT: A  715 GLN cc_start: 0.8329 (mt0) cc_final: 0.8125 (mp10)
REVERT: A  723 ILE cc_start: 0.8595 (mt) cc_final: 0.8354 (mm)
REVERT: A  749 GLN cc_start: 0.7277 (mt0) cc_final: 0.6948 (mt0)
REVERT: A  780 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6173 (pp20)
REVERT: A  796 GLN cc_start: 0.7895 (pt0) cc_final: 0.7407 (pt0)
REVERT: A  799 ARG cc_start: 0.7680 (mmt180) cc_final: 0.7182 (mpt180)
REVERT: A  802 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7306 (pp30)
REVERT: A  852 GLU cc_start: 0.7228 (pt0) cc_final: 0.6963 (pt0)
REVERT: A  858 GLU cc_start: 0.7601 (tm-30) cc_final: 0.6796 (tt0)
REVERT: A  872 LYS cc_start: 0.8288 (mtmm) cc_final: 0.7788 (mtpp)
REVERT: A  882 LEU cc_start: 0.8478 (tp) cc_final: 0.8069 (tp)
REVERT: A  939 GLU cc_start: 0.8215 (tp30) cc_final: 0.7887 (tp30)
REVERT: A 1322 ARG cc_start: 0.8384 (ttp80) cc_final: 0.8149 (ptm-80)
REVERT: A 1326 ILE cc_start: 0.8344 (pt) cc_final: 0.8051 (tt)
REVERT: A 1327 PHE cc_start: 0.7960 (t80) cc_final: 0.7670 (t80)
REVERT: A 1338 PHE cc_start: 0.7853 (t80) cc_final: 0.7609 (t80)
REVERT: A 1340 GLU cc_start: 0.6900 (tp30) cc_final: 0.6551 (tp30)
REVERT: A 1343 LEU cc_start: 0.8398 (mm) cc_final: 0.8053 (mp)
REVERT: A 1353 ASN cc_start: 0.7701 (m-40) cc_final: 0.7362 (m-40)
REVERT: A 1366 LYS cc_start: 0.8548 (pttp) cc_final: 0.8109 (ttpp)
REVERT: A 1405 GLU cc_start: 0.6954 (tp30) cc_final: 0.6341 (tp30)
REVERT: A 1431 GLU cc_start: 0.7424 (tm-30) cc_final: 0.6935 (tm-30)
REVERT: A 1469 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8841 (p)
REVERT: A 1472 LEU cc_start: 0.8058 (mt) cc_final: 0.7753 (tp)
REVERT: A 1488 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8257 (t0)
REVERT: A 1496 GLN cc_start: 0.7896 (mt0) cc_final: 0.7628 (tt0)
REVERT: A 1503 GLN cc_start: 0.8150 (tp40) cc_final: 0.7592 (mm-40)
REVERT: A 1507 LYS cc_start: 0.8478 (mttt) cc_final: 0.8092 (mttp)
REVERT: A 1532 LEU cc_start: 0.7905 (tp) cc_final: 0.7694 (tt)
REVERT: A 1546 MET cc_start: 0.8005 (tpp) cc_final: 0.7720 (tpp)
REVERT: A 1565 ILE cc_start: 0.8495 (mt) cc_final: 0.8185 (mm)
REVERT: A 1593 SER cc_start: 0.8310 (m) cc_final: 0.8091 (p)
REVERT: A 1606 HIS cc_start: 0.8056 (m170) cc_final: 0.7779 (m170)
REVERT: A 1614 MET cc_start: 0.8186 (tpt) cc_final: 0.7585 (tpt)
REVERT: A 1632 LYS cc_start: 0.8244 (mtmt) cc_final: 0.7663 (mtmm)
REVERT: B    8 ARG cc_start: 0.8358 (mtt90) cc_final: 0.8008 (mtt90)
REVERT: B   14 LEU cc_start: 0.8570 (mt) cc_final: 0.8345 (mt)
REVERT: B   15 LYS cc_start: 0.8947 (mttp) cc_final: 0.8716 (mttp)
REVERT: B   61 MET cc_start: 0.7849 (ppp) cc_final: 0.7471 (ptm)
REVERT: B  118 ASP cc_start: 0.7392 (t0) cc_final: 0.7169 (t0)
REVERT: B  145 TYR cc_start: 0.8374 (p90) cc_final: 0.7940 (p90)
REVERT: B  156 GLN cc_start: 0.8040 (mt0) cc_final: 0.7818 (mt0)
REVERT: B  188 MET cc_start: 0.7274 (mmm) cc_final: 0.6515 (mmm)
REVERT: B  230 ASN cc_start: 0.8567 (m-40) cc_final: 0.8230 (m-40)
REVERT: B  279 SER cc_start: 0.8602 (m) cc_final: 0.8342 (t)
REVERT: B  289 TYR cc_start: 0.8649 (m-80) cc_final: 0.8372 (m-80)
REVERT: B  336 LEU cc_start: 0.7931 (mt) cc_final: 0.7651 (mm)
REVERT: G   13 ARG cc_start: 0.8329 (ttm110) cc_final: 0.8096 (ttm110)
REVERT: G   15 LEU cc_start: 0.8797 (mt) cc_final: 0.8418 (mt)
REVERT: G   18 GLN cc_start: 0.8188 (tp40) cc_final: 0.7706 (tp40)
REVERT: G   19 LEU cc_start: 0.8903 (mp) cc_final: 0.8627 (mp)
REVERT: G   20 LYS cc_start: 0.8736 (ptmt) cc_final: 0.8468 (ptmm)
REVERT: G   38 MET cc_start: 0.7993 (ttp) cc_final: 0.7464 (tmm)
  outliers start: 34
  outliers final: 20
  residues processed: 290
  average time/residue: 0.2747
  time to fit residues: 103.7001
Evaluate side-chains
  285 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 260
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  626 LEU
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  802 GLN
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 1384 LEU
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1424 THR
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  114 CYS
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
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:    0.0370
   chunk 63 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 112 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.7260

-------------------------------------------------------------------------------
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**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.156385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.134636 restraints weight = 12084.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 2.65
r_work: 0.3607 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.3502

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= 0.258
  Angle     :  0.674  10.906  12445  Z= 0.342
  Chirality :  0.044   0.177   1392
  Planarity :  0.004   0.047   1621
  Dihedral  :  4.833  31.920   1257
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 22.53 %
    Favored  : 74.01 %
  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: -0.44 (0.25), residues: 1137
  helix:  1.33 (0.27), residues: 388
  sheet: -1.27 (0.30), residues: 265
  loop : -0.98 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 297 
 HIS   0.005   0.001   HIS A 790 
 PHE   0.019   0.002   PHE A 890 
 TYR   0.029   0.002   TYR A1446 
 ARG   0.007   0.001   ARG A1361 

*********************** 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
  309 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 275
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  511 MET cc_start: 0.7354 (tpp) cc_final: 0.7108 (mmm)
REVERT: A  524 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8572 (pp)
REVERT: A  530 LYS cc_start: 0.8538 (pttt) cc_final: 0.8187 (ptpp)
REVERT: A  534 TYR cc_start: 0.7374 (t80) cc_final: 0.6709 (t80)
REVERT: A  540 LYS cc_start: 0.7953 (tptp) cc_final: 0.7639 (tptp)
REVERT: A  547 LYS cc_start: 0.7868 (tptm) cc_final: 0.7192 (tppt)
REVERT: A  553 LEU cc_start: 0.8611 (mp) cc_final: 0.8262 (mm)
REVERT: A  559 GLN cc_start: 0.8468 (mm-40) cc_final: 0.8204 (mm110)
REVERT: A  561 ARG cc_start: 0.8447 (mtp85) cc_final: 0.8136 (mtp85)
REVERT: A  563 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7245 (mt-10)
REVERT: A  565 VAL cc_start: 0.8561 (m) cc_final: 0.8360 (p)
REVERT: A  574 ASN cc_start: 0.7722 (m110) cc_final: 0.7156 (m110)
REVERT: A  577 MET cc_start: 0.7804 (ptp) cc_final: 0.7378 (mtm)
REVERT: A  587 ARG cc_start: 0.8108 (ttp-110) cc_final: 0.7399 (ttm110)
REVERT: A  625 ARG cc_start: 0.7165 (ptp90) cc_final: 0.6962 (ptp90)
REVERT: A  653 ARG cc_start: 0.7885 (ttt-90) cc_final: 0.7648 (ttt-90)
REVERT: A  672 ASN cc_start: 0.8141 (t0) cc_final: 0.7497 (m-40)
REVERT: A  683 GLU cc_start: 0.7545 (tt0) cc_final: 0.7117 (tt0)
REVERT: A  696 ARG cc_start: 0.7686 (mtt-85) cc_final: 0.7145 (mtt-85)
REVERT: A  699 ARG cc_start: 0.7727 (mtt90) cc_final: 0.7085 (mtm-85)
REVERT: A  715 GLN cc_start: 0.8328 (mt0) cc_final: 0.8126 (mp10)
REVERT: A  723 ILE cc_start: 0.8568 (mt) cc_final: 0.8356 (mm)
REVERT: A  749 GLN cc_start: 0.7285 (mt0) cc_final: 0.6944 (mt0)
REVERT: A  780 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6141 (pp20)
REVERT: A  796 GLN cc_start: 0.7891 (pt0) cc_final: 0.7498 (pt0)
REVERT: A  852 GLU cc_start: 0.7312 (pt0) cc_final: 0.7033 (pt0)
REVERT: A  858 GLU cc_start: 0.7585 (tm-30) cc_final: 0.6880 (tt0)
REVERT: A  872 LYS cc_start: 0.8294 (mtmm) cc_final: 0.7772 (mtpp)
REVERT: A  882 LEU cc_start: 0.8522 (tp) cc_final: 0.8214 (tp)
REVERT: A  960 HIS cc_start: 0.8287 (p-80) cc_final: 0.7896 (p90)
REVERT: A 1019 GLN cc_start: 0.7843 (tt0) cc_final: 0.7547 (tm-30)
REVERT: A 1322 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8204 (ptm-80)
REVERT: A 1326 ILE cc_start: 0.8359 (pt) cc_final: 0.8061 (tt)
REVERT: A 1327 PHE cc_start: 0.7986 (t80) cc_final: 0.7674 (t80)
REVERT: A 1338 PHE cc_start: 0.7854 (t80) cc_final: 0.7558 (t80)
REVERT: A 1340 GLU cc_start: 0.6955 (tp30) cc_final: 0.6503 (tp30)
REVERT: A 1343 LEU cc_start: 0.8404 (mm) cc_final: 0.8064 (mp)
REVERT: A 1353 ASN cc_start: 0.7735 (m-40) cc_final: 0.7424 (m-40)
REVERT: A 1366 LYS cc_start: 0.8598 (pttp) cc_final: 0.8156 (ttpp)
REVERT: A 1405 GLU cc_start: 0.6971 (tp30) cc_final: 0.6700 (tp30)
REVERT: A 1431 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6944 (tm-30)
REVERT: A 1472 LEU cc_start: 0.8080 (mt) cc_final: 0.7815 (tp)
REVERT: A 1496 GLN cc_start: 0.7917 (mt0) cc_final: 0.7655 (tt0)
REVERT: A 1503 GLN cc_start: 0.8171 (tp40) cc_final: 0.7567 (mm-40)
REVERT: A 1507 LYS cc_start: 0.8507 (mttt) cc_final: 0.8111 (mttp)
REVERT: A 1532 LEU cc_start: 0.7839 (tp) cc_final: 0.7610 (tt)
REVERT: A 1546 MET cc_start: 0.8089 (tpp) cc_final: 0.7765 (tpp)
REVERT: A 1596 LEU cc_start: 0.7433 (tp) cc_final: 0.7199 (tp)
REVERT: A 1632 LYS cc_start: 0.8259 (mtmt) cc_final: 0.7680 (mtmm)
REVERT: A 1648 TYR cc_start: 0.7662 (m-80) cc_final: 0.7423 (m-80)
REVERT: B    8 ARG cc_start: 0.8372 (mtt90) cc_final: 0.8026 (mtt90)
REVERT: B   14 LEU cc_start: 0.8572 (mt) cc_final: 0.8338 (mt)
REVERT: B   15 LYS cc_start: 0.8970 (mttp) cc_final: 0.8745 (mttp)
REVERT: B   59 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.7723 (m-80)
REVERT: B   61 MET cc_start: 0.7871 (ppp) cc_final: 0.7540 (ptm)
REVERT: B  118 ASP cc_start: 0.7342 (t0) cc_final: 0.7104 (t0)
REVERT: B  145 TYR cc_start: 0.8367 (p90) cc_final: 0.7883 (p90)
REVERT: B  156 GLN cc_start: 0.8031 (mt0) cc_final: 0.7792 (mt0)
REVERT: B  188 MET cc_start: 0.7311 (mmm) cc_final: 0.6518 (mmm)
REVERT: B  230 ASN cc_start: 0.8591 (m-40) cc_final: 0.8208 (m-40)
REVERT: B  279 SER cc_start: 0.8606 (m) cc_final: 0.8334 (t)
REVERT: B  289 TYR cc_start: 0.8665 (m-80) cc_final: 0.8375 (m-80)
REVERT: B  336 LEU cc_start: 0.7920 (mt) cc_final: 0.7636 (mm)
REVERT: G   13 ARG cc_start: 0.8311 (ttm110) cc_final: 0.8108 (ttm110)
REVERT: G   15 LEU cc_start: 0.8812 (mt) cc_final: 0.8428 (mt)
REVERT: G   18 GLN cc_start: 0.8206 (tp40) cc_final: 0.7748 (tp40)
REVERT: G   19 LEU cc_start: 0.8917 (mp) cc_final: 0.8624 (mp)
REVERT: G   20 LYS cc_start: 0.8711 (ptmt) cc_final: 0.8387 (ptmm)
REVERT: G   38 MET cc_start: 0.8008 (ttp) cc_final: 0.7441 (tmm)
  outliers start: 34
  outliers final: 26
  residues processed: 294
  average time/residue: 0.2930
  time to fit residues: 114.9900
Evaluate side-chains
  296 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 267
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  626 LEU
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 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 1421 VAL
Chi-restraints excluded: chain A residue 1424 THR
Chi-restraints excluded: chain A residue 1488 ASP
Chi-restraints excluded: chain A residue 1514 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  327 VAL
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:    0.1980
   chunk 87 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 110 optimal weight:    0.2980
   chunk 98 optimal weight:    0.0970
   chunk 105 optimal weight:    2.9990
   overall best weight:    0.3778

-------------------------------------------------------------------------------
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 802 GLN
A 975 ASN
** A1352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4052 r_free = 0.4052 target = 0.158426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.136746 restraints weight = 12056.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 2.66
r_work: 0.3633 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.3672

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= 0.202
  Angle     :  0.666   9.898  12445  Z= 0.337
  Chirality :  0.043   0.181   1392
  Planarity :  0.004   0.048   1621
  Dihedral  :  4.760  32.464   1257
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 24.36 %
    Favored  : 72.48 %
  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: -0.38 (0.25), residues: 1137
  helix:  1.37 (0.27), residues: 387
  sheet: -1.17 (0.30), residues: 258
  loop : -0.98 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 297 
 HIS   0.009   0.001   HIS A 535 
 PHE   0.031   0.002   PHE A 637 
 TYR   0.026   0.002   TYR A 534 
 ARG   0.008   0.001   ARG B  19 

*********************** 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
  292 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 261
  time to evaluate  : 1.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  511 MET cc_start: 0.7343 (tpp) cc_final: 0.7090 (mmm)
REVERT: A  524 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8524 (pp)
REVERT: A  530 LYS cc_start: 0.8548 (pttt) cc_final: 0.8199 (ptpp)
REVERT: A  534 TYR cc_start: 0.7327 (t80) cc_final: 0.7083 (t80)
REVERT: A  540 LYS cc_start: 0.7856 (tptp) cc_final: 0.7613 (mmmt)
REVERT: A  547 LYS cc_start: 0.7797 (tptm) cc_final: 0.7139 (tppt)
REVERT: A  553 LEU cc_start: 0.8596 (mp) cc_final: 0.8244 (mm)
REVERT: A  559 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8165 (mm110)
REVERT: A  561 ARG cc_start: 0.8407 (mtp85) cc_final: 0.8139 (mtp85)
REVERT: A  563 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7342 (mt-10)
REVERT: A  565 VAL cc_start: 0.8541 (m) cc_final: 0.8328 (p)
REVERT: A  574 ASN cc_start: 0.7695 (m110) cc_final: 0.7144 (m110)
REVERT: A  577 MET cc_start: 0.7754 (ptp) cc_final: 0.7358 (mtm)
REVERT: A  587 ARG cc_start: 0.8101 (ttp-110) cc_final: 0.7385 (ttm110)
REVERT: A  640 GLU cc_start: 0.7570 (tp30) cc_final: 0.7205 (tp30)
REVERT: A  653 ARG cc_start: 0.7824 (ttt-90) cc_final: 0.7624 (ttt-90)
REVERT: A  672 ASN cc_start: 0.8137 (t0) cc_final: 0.7551 (m-40)
REVERT: A  683 GLU cc_start: 0.7495 (tt0) cc_final: 0.7004 (tt0)
REVERT: A  696 ARG cc_start: 0.7698 (mtt-85) cc_final: 0.7253 (mtt-85)
REVERT: A  699 ARG cc_start: 0.7809 (mtt90) cc_final: 0.7198 (mtm-85)
REVERT: A  749 GLN cc_start: 0.7295 (mt0) cc_final: 0.6964 (mt0)
REVERT: A  780 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6141 (pp20)
REVERT: A  796 GLN cc_start: 0.8092 (pt0) cc_final: 0.7345 (pt0)
REVERT: A  802 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7218 (pp30)
REVERT: A  858 GLU cc_start: 0.7545 (tm-30) cc_final: 0.6946 (tt0)
REVERT: A  872 LYS cc_start: 0.8269 (mtmm) cc_final: 0.7776 (mtpp)
REVERT: A 1019 GLN cc_start: 0.8010 (tt0) cc_final: 0.7361 (tm-30)
REVERT: A 1322 ARG cc_start: 0.8407 (ttp80) cc_final: 0.8170 (ptm-80)
REVERT: A 1326 ILE cc_start: 0.8384 (pt) cc_final: 0.8102 (tt)
REVERT: A 1338 PHE cc_start: 0.7739 (t80) cc_final: 0.7496 (t80)
REVERT: A 1340 GLU cc_start: 0.6793 (tp30) cc_final: 0.6405 (tp30)
REVERT: A 1343 LEU cc_start: 0.8380 (mm) cc_final: 0.8009 (mp)
REVERT: A 1353 ASN cc_start: 0.7665 (m-40) cc_final: 0.7444 (m110)
REVERT: A 1366 LYS cc_start: 0.8505 (pttp) cc_final: 0.8177 (ttpp)
REVERT: A 1405 GLU cc_start: 0.6975 (tp30) cc_final: 0.6707 (tp30)
REVERT: A 1410 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.7997 (m)
REVERT: A 1431 GLU cc_start: 0.7440 (tm-30) cc_final: 0.6953 (tm-30)
REVERT: A 1462 ARG cc_start: 0.7699 (mtp85) cc_final: 0.7460 (mtp85)
REVERT: A 1472 LEU cc_start: 0.7984 (mt) cc_final: 0.7728 (tp)
REVERT: A 1496 GLN cc_start: 0.7873 (mt0) cc_final: 0.7666 (tt0)
REVERT: A 1503 GLN cc_start: 0.8138 (tp40) cc_final: 0.7526 (mm-40)
REVERT: A 1507 LYS cc_start: 0.8509 (mttt) cc_final: 0.8115 (mttp)
REVERT: A 1532 LEU cc_start: 0.7879 (tp) cc_final: 0.7643 (tt)
REVERT: A 1546 MET cc_start: 0.8034 (tpp) cc_final: 0.7730 (tpp)
REVERT: A 1596 LEU cc_start: 0.7402 (tp) cc_final: 0.7175 (tp)
REVERT: A 1614 MET cc_start: 0.8167 (tpt) cc_final: 0.7537 (tpt)
REVERT: A 1622 LYS cc_start: 0.8137 (mttp) cc_final: 0.7730 (mptt)
REVERT: A 1632 LYS cc_start: 0.8261 (mtmt) cc_final: 0.7657 (mtmm)
REVERT: A 1648 TYR cc_start: 0.7598 (m-80) cc_final: 0.7370 (m-80)
REVERT: B    8 ARG cc_start: 0.8376 (mtt90) cc_final: 0.8136 (mtt90)
REVERT: B   15 LYS cc_start: 0.8987 (mttp) cc_final: 0.8629 (mttp)
REVERT: B   19 ARG cc_start: 0.8297 (mtm110) cc_final: 0.7892 (mtm-85)
REVERT: B   59 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.7832 (m-80)
REVERT: B  118 ASP cc_start: 0.7107 (t0) cc_final: 0.6830 (t0)
REVERT: B  145 TYR cc_start: 0.8326 (p90) cc_final: 0.7923 (p90)
REVERT: B  156 GLN cc_start: 0.8014 (mt0) cc_final: 0.7781 (mt0)
REVERT: B  188 MET cc_start: 0.7194 (mmm) cc_final: 0.6410 (mmm)
REVERT: B  230 ASN cc_start: 0.8547 (m-40) cc_final: 0.8183 (m-40)
REVERT: B  247 ASP cc_start: 0.7896 (t70) cc_final: 0.7166 (t0)
REVERT: B  279 SER cc_start: 0.8559 (m) cc_final: 0.8321 (t)
REVERT: B  289 TYR cc_start: 0.8629 (m-80) cc_final: 0.8291 (m-80)
REVERT: B  336 LEU cc_start: 0.7929 (mt) cc_final: 0.7704 (mm)
REVERT: G   15 LEU cc_start: 0.8790 (mt) cc_final: 0.8465 (mt)
REVERT: G   18 GLN cc_start: 0.8154 (tp40) cc_final: 0.7637 (tp40)
REVERT: G   19 LEU cc_start: 0.8837 (mp) cc_final: 0.8530 (mp)
REVERT: G   20 LYS cc_start: 0.8739 (ptmt) cc_final: 0.8491 (ptmm)
REVERT: G   38 MET cc_start: 0.7962 (ttp) cc_final: 0.7441 (tmm)
REVERT: G   59 ASN cc_start: 0.8066 (p0) cc_final: 0.7703 (p0)
  outliers start: 31
  outliers final: 20
  residues processed: 278
  average time/residue: 0.2690
  time to fit residues: 98.0787
Evaluate side-chains
  281 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 256
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  626 LEU
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  738 SER
Chi-restraints excluded: chain A residue  780 GLU
Chi-restraints excluded: chain A residue  802 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 1025 MET
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 1424 THR
Chi-restraints excluded: chain A residue 1488 ASP
Chi-restraints excluded: chain A residue 1514 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  114 CYS
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   37 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 111 optimal weight:    0.5980
   chunk 49 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 90 optimal weight:    0.6980
   chunk 46 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 97 optimal weight:    0.1980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 975 ASN
** A1352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 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 = 0.4046 r_free = 0.4046 target = 0.157741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.136112 restraints weight = 11842.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 2.63
r_work: 0.3625 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.3765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9202  Z= 0.230
  Angle     :  0.680  10.334  12445  Z= 0.345
  Chirality :  0.044   0.178   1392
  Planarity :  0.004   0.048   1621
  Dihedral  :  4.755  33.521   1257
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 25.08 %
    Favored  : 71.97 %
  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: -0.35 (0.25), residues: 1137
  helix:  1.42 (0.27), residues: 388
  sheet: -1.25 (0.30), residues: 262
  loop : -0.93 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 297 
 HIS   0.013   0.001   HIS A 535 
 PHE   0.014   0.002   PHE A 721 
 TYR   0.035   0.002   TYR A 534 
 ARG   0.008   0.001   ARG G  13 

*********************** 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
  299 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 270
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  511 MET cc_start: 0.7306 (tpp) cc_final: 0.7047 (mmm)
REVERT: A  524 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8513 (pp)
REVERT: A  530 LYS cc_start: 0.8543 (pttt) cc_final: 0.8196 (ptpp)
REVERT: A  534 TYR cc_start: 0.7240 (t80) cc_final: 0.6984 (t80)
REVERT: A  535 HIS cc_start: 0.7676 (m90) cc_final: 0.7418 (m170)
REVERT: A  540 LYS cc_start: 0.7823 (tptp) cc_final: 0.7574 (mmmt)
REVERT: A  547 LYS cc_start: 0.7837 (tptm) cc_final: 0.7273 (tppt)
REVERT: A  553 LEU cc_start: 0.8595 (mp) cc_final: 0.8228 (mm)
REVERT: A  555 GLN cc_start: 0.6940 (mp-120) cc_final: 0.6734 (mp10)
REVERT: A  559 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8156 (mm110)
REVERT: A  561 ARG cc_start: 0.8417 (mtp85) cc_final: 0.8154 (mtp85)
REVERT: A  563 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7403 (mt-10)
REVERT: A  565 VAL cc_start: 0.8551 (m) cc_final: 0.8348 (p)
REVERT: A  574 ASN cc_start: 0.7687 (m110) cc_final: 0.7132 (m110)
REVERT: A  577 MET cc_start: 0.7772 (ptp) cc_final: 0.7381 (mtm)
REVERT: A  587 ARG cc_start: 0.8113 (ttp-110) cc_final: 0.7403 (ttm110)
REVERT: A  635 TYR cc_start: 0.7903 (m-80) cc_final: 0.7677 (m-80)
REVERT: A  658 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7653 (pt0)
REVERT: A  672 ASN cc_start: 0.8170 (t0) cc_final: 0.7585 (m-40)
REVERT: A  683 GLU cc_start: 0.7516 (tt0) cc_final: 0.7018 (tt0)
REVERT: A  696 ARG cc_start: 0.7581 (mtt-85) cc_final: 0.7264 (mtt-85)
REVERT: A  699 ARG cc_start: 0.7844 (mtt90) cc_final: 0.7235 (mtm-85)
REVERT: A  749 GLN cc_start: 0.7329 (mt0) cc_final: 0.6990 (mt0)
REVERT: A  780 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6162 (pp20)
REVERT: A  796 GLN cc_start: 0.7957 (pt0) cc_final: 0.7591 (tp-100)
REVERT: A  858 GLU cc_start: 0.7589 (tm-30) cc_final: 0.6973 (tt0)
REVERT: A  872 LYS cc_start: 0.8242 (mtmm) cc_final: 0.7736 (mtpp)
REVERT: A  974 ILE cc_start: 0.8292 (mt) cc_final: 0.7980 (mm)
REVERT: A 1019 GLN cc_start: 0.8067 (tt0) cc_final: 0.7352 (tm-30)
REVERT: A 1322 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8208 (ptm-80)
REVERT: A 1326 ILE cc_start: 0.8389 (pt) cc_final: 0.8112 (tt)
REVERT: A 1327 PHE cc_start: 0.7972 (t80) cc_final: 0.7652 (t80)
REVERT: A 1338 PHE cc_start: 0.7722 (t80) cc_final: 0.7429 (t80)
REVERT: A 1340 GLU cc_start: 0.6859 (tp30) cc_final: 0.6522 (tp30)
REVERT: A 1343 LEU cc_start: 0.8386 (mm) cc_final: 0.8026 (mp)
REVERT: A 1353 ASN cc_start: 0.7737 (m-40) cc_final: 0.7492 (m110)
REVERT: A 1366 LYS cc_start: 0.8533 (pttp) cc_final: 0.8161 (ttpp)
REVERT: A 1405 GLU cc_start: 0.6959 (tp30) cc_final: 0.6677 (tp30)
REVERT: A 1431 GLU cc_start: 0.7455 (tm-30) cc_final: 0.6984 (tm-30)
REVERT: A 1462 ARG cc_start: 0.7745 (mtp85) cc_final: 0.7505 (mtp85)
REVERT: A 1472 LEU cc_start: 0.7988 (mt) cc_final: 0.7742 (tp)
REVERT: A 1496 GLN cc_start: 0.7943 (mt0) cc_final: 0.7696 (tt0)
REVERT: A 1502 GLN cc_start: 0.8298 (mt0) cc_final: 0.7967 (mm-40)
REVERT: A 1503 GLN cc_start: 0.8104 (tp40) cc_final: 0.7472 (mm-40)
REVERT: A 1507 LYS cc_start: 0.8520 (mttt) cc_final: 0.8125 (mttp)
REVERT: A 1532 LEU cc_start: 0.7917 (tp) cc_final: 0.7684 (tt)
REVERT: A 1546 MET cc_start: 0.8044 (tpp) cc_final: 0.7715 (tpp)
REVERT: A 1596 LEU cc_start: 0.7402 (tp) cc_final: 0.7187 (tp)
REVERT: A 1614 MET cc_start: 0.8167 (tpt) cc_final: 0.7537 (tpt)
REVERT: A 1622 LYS cc_start: 0.8184 (mttp) cc_final: 0.7787 (mtpt)
REVERT: A 1632 LYS cc_start: 0.8247 (mtmt) cc_final: 0.7665 (mtmm)
REVERT: A 1648 TYR cc_start: 0.7630 (m-80) cc_final: 0.7378 (m-80)
REVERT: B    8 ARG cc_start: 0.8363 (mtt90) cc_final: 0.8113 (mtt90)
REVERT: B   15 LYS cc_start: 0.8988 (mttp) cc_final: 0.8623 (mttp)
REVERT: B   19 ARG cc_start: 0.8322 (mtm110) cc_final: 0.7910 (mtm-85)
REVERT: B   59 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7785 (m-80)
REVERT: B   61 MET cc_start: 0.7825 (ppp) cc_final: 0.7548 (ptm)
REVERT: B  118 ASP cc_start: 0.7129 (t0) cc_final: 0.6843 (t0)
REVERT: B  145 TYR cc_start: 0.8322 (p90) cc_final: 0.7929 (p90)
REVERT: B  156 GLN cc_start: 0.8021 (mt0) cc_final: 0.7787 (mt0)
REVERT: B  188 MET cc_start: 0.7178 (mmm) cc_final: 0.6288 (mmm)
REVERT: B  230 ASN cc_start: 0.8583 (m-40) cc_final: 0.8233 (m-40)
REVERT: B  247 ASP cc_start: 0.7927 (t70) cc_final: 0.7171 (t0)
REVERT: B  279 SER cc_start: 0.8565 (m) cc_final: 0.8337 (t)
REVERT: B  289 TYR cc_start: 0.8655 (m-80) cc_final: 0.8303 (m-80)
REVERT: B  336 LEU cc_start: 0.7938 (mt) cc_final: 0.7668 (mm)
REVERT: G   15 LEU cc_start: 0.8793 (mt) cc_final: 0.8397 (mt)
REVERT: G   18 GLN cc_start: 0.8166 (tp40) cc_final: 0.7674 (tp40)
REVERT: G   19 LEU cc_start: 0.8891 (mp) cc_final: 0.8573 (mp)
REVERT: G   20 LYS cc_start: 0.8766 (ptmt) cc_final: 0.8482 (ptmm)
REVERT: G   38 MET cc_start: 0.7972 (ttp) cc_final: 0.7446 (tmm)
REVERT: G   59 ASN cc_start: 0.8065 (p0) cc_final: 0.7702 (p0)
  outliers start: 29
  outliers final: 22
  residues processed: 288
  average time/residue: 0.2693
  time to fit residues: 101.7411
Evaluate side-chains
  284 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 258
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  626 LEU
Chi-restraints excluded: chain A residue  658 GLU
Chi-restraints excluded: chain A residue  678 LEU
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 1384 LEU
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1421 VAL
Chi-restraints excluded: chain A residue 1424 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 B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  327 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:    0.9980
   chunk 94 optimal weight:    0.6980
   chunk 3 optimal weight:    0.4980
   chunk 7 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 75 optimal weight:    0.6980
   chunk 90 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 975 ASN
** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1352 ASN
** 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 = 0.4038 r_free = 0.4038 target = 0.156853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.135598 restraints weight = 11942.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3772 rms_B_bonded: 2.64
r_work: 0.3623 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.3866

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= 0.252
  Angle     :  0.693  10.536  12445  Z= 0.351
  Chirality :  0.044   0.187   1392
  Planarity :  0.004   0.049   1621
  Dihedral  :  4.811  34.295   1257
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 25.69 %
    Favored  : 71.25 %
  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: -0.38 (0.26), residues: 1137
  helix:  1.41 (0.27), residues: 387
  sheet: -1.26 (0.29), residues: 267
  loop : -0.95 (0.30), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 297 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.031   0.002   PHE A 637 
 TYR   0.027   0.002   TYR A 534 
 ARG   0.008   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
  306 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 276
  time to evaluate  : 1.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  511 MET cc_start: 0.7279 (tpp) cc_final: 0.6986 (mmm)
REVERT: A  524 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8550 (pp)
REVERT: A  530 LYS cc_start: 0.8516 (pttt) cc_final: 0.8163 (ptpp)
REVERT: A  540 LYS cc_start: 0.7838 (tptp) cc_final: 0.7574 (mmmt)
REVERT: A  547 LYS cc_start: 0.7880 (tptm) cc_final: 0.7297 (tppt)
REVERT: A  553 LEU cc_start: 0.8601 (mp) cc_final: 0.8237 (mm)
REVERT: A  559 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8209 (mm110)
REVERT: A  561 ARG cc_start: 0.8406 (mtp85) cc_final: 0.8138 (mtp85)
REVERT: A  563 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7391 (mt-10)
REVERT: A  565 VAL cc_start: 0.8552 (m) cc_final: 0.8351 (p)
REVERT: A  574 ASN cc_start: 0.7713 (m110) cc_final: 0.7145 (m110)
REVERT: A  577 MET cc_start: 0.7779 (ptp) cc_final: 0.7353 (mtm)
REVERT: A  587 ARG cc_start: 0.8123 (ttp-110) cc_final: 0.7402 (ttm110)
REVERT: A  658 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7681 (pt0)
REVERT: A  667 LYS cc_start: 0.8316 (ttpp) cc_final: 0.7936 (tttp)
REVERT: A  672 ASN cc_start: 0.8218 (t0) cc_final: 0.7584 (m-40)
REVERT: A  683 GLU cc_start: 0.7536 (tt0) cc_final: 0.7034 (tt0)
REVERT: A  696 ARG cc_start: 0.7607 (mtt-85) cc_final: 0.7233 (mtt-85)
REVERT: A  699 ARG cc_start: 0.7828 (mtt90) cc_final: 0.7186 (mtm-85)
REVERT: A  749 GLN cc_start: 0.7323 (mt0) cc_final: 0.6971 (mt0)
REVERT: A  780 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6146 (pp20)
REVERT: A  796 GLN cc_start: 0.8061 (pt0) cc_final: 0.7310 (pt0)
REVERT: A  852 GLU cc_start: 0.7626 (pt0) cc_final: 0.7231 (pt0)
REVERT: A  858 GLU cc_start: 0.7566 (tm-30) cc_final: 0.6930 (tt0)
REVERT: A  872 LYS cc_start: 0.8276 (mtmm) cc_final: 0.7766 (mtpp)
REVERT: A  882 LEU cc_start: 0.8541 (tp) cc_final: 0.8239 (tp)
REVERT: A  974 ILE cc_start: 0.8335 (mt) cc_final: 0.8035 (mm)
REVERT: A  977 MET cc_start: 0.7663 (ptp) cc_final: 0.7394 (pmm)
REVERT: A 1019 GLN cc_start: 0.8146 (tt0) cc_final: 0.7406 (tm-30)
REVERT: A 1326 ILE cc_start: 0.8402 (pt) cc_final: 0.8114 (tt)
REVERT: A 1338 PHE cc_start: 0.7701 (t80) cc_final: 0.7270 (t80)
REVERT: A 1340 GLU cc_start: 0.6900 (tp30) cc_final: 0.6440 (tp30)
REVERT: A 1343 LEU cc_start: 0.8412 (mm) cc_final: 0.8074 (mp)
REVERT: A 1353 ASN cc_start: 0.7724 (m-40) cc_final: 0.7444 (m110)
REVERT: A 1366 LYS cc_start: 0.8647 (pttp) cc_final: 0.8244 (ttpp)
REVERT: A 1405 GLU cc_start: 0.6966 (tp30) cc_final: 0.6681 (tp30)
REVERT: A 1431 GLU cc_start: 0.7500 (tm-30) cc_final: 0.6995 (tm-30)
REVERT: A 1460 SER cc_start: 0.7297 (m) cc_final: 0.6511 (p)
REVERT: A 1462 ARG cc_start: 0.7725 (mtp85) cc_final: 0.7505 (mtp85)
REVERT: A 1472 LEU cc_start: 0.8103 (mt) cc_final: 0.7821 (tp)
REVERT: A 1496 GLN cc_start: 0.7939 (mt0) cc_final: 0.7689 (tt0)
REVERT: A 1503 GLN cc_start: 0.8125 (tp40) cc_final: 0.7475 (mm-40)
REVERT: A 1507 LYS cc_start: 0.8526 (mttt) cc_final: 0.8136 (mtmt)
REVERT: A 1532 LEU cc_start: 0.7883 (tp) cc_final: 0.7652 (tt)
REVERT: A 1540 ASP cc_start: 0.7361 (p0) cc_final: 0.7127 (p0)
REVERT: A 1546 MET cc_start: 0.8065 (tpp) cc_final: 0.7693 (tpp)
REVERT: A 1565 ILE cc_start: 0.8523 (mt) cc_final: 0.8200 (mm)
REVERT: A 1596 LEU cc_start: 0.7415 (tp) cc_final: 0.7192 (tp)
REVERT: A 1614 MET cc_start: 0.8167 (tpt) cc_final: 0.7518 (tpt)
REVERT: A 1622 LYS cc_start: 0.8213 (mttp) cc_final: 0.7817 (mtpt)
REVERT: A 1632 LYS cc_start: 0.8278 (mtmt) cc_final: 0.7677 (mtmm)
REVERT: B    8 ARG cc_start: 0.8329 (mtt90) cc_final: 0.8084 (mtt90)
REVERT: B   15 LYS cc_start: 0.8991 (mttp) cc_final: 0.8632 (mttp)
REVERT: B   19 ARG cc_start: 0.8332 (mtm110) cc_final: 0.7928 (mtm-85)
REVERT: B   59 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7728 (m-80)
REVERT: B   61 MET cc_start: 0.7880 (ppp) cc_final: 0.7633 (ptm)
REVERT: B  145 TYR cc_start: 0.8318 (p90) cc_final: 0.7908 (p90)
REVERT: B  156 GLN cc_start: 0.8055 (mt0) cc_final: 0.7802 (mt0)
REVERT: B  188 MET cc_start: 0.7208 (mmm) cc_final: 0.6298 (mmm)
REVERT: B  230 ASN cc_start: 0.8592 (m-40) cc_final: 0.8218 (m-40)
REVERT: B  247 ASP cc_start: 0.7972 (t70) cc_final: 0.7241 (t0)
REVERT: B  279 SER cc_start: 0.8576 (m) cc_final: 0.8346 (t)
REVERT: B  289 TYR cc_start: 0.8675 (m-80) cc_final: 0.8330 (m-80)
REVERT: B  332 TRP cc_start: 0.8680 (m-10) cc_final: 0.8474 (m-10)
REVERT: B  336 LEU cc_start: 0.7943 (mt) cc_final: 0.7651 (mm)
REVERT: G   15 LEU cc_start: 0.8803 (mt) cc_final: 0.8411 (mt)
REVERT: G   18 GLN cc_start: 0.8197 (tp40) cc_final: 0.7697 (tp40)
REVERT: G   19 LEU cc_start: 0.8916 (mp) cc_final: 0.8593 (mp)
REVERT: G   20 LYS cc_start: 0.8768 (ptmt) cc_final: 0.8477 (ptmm)
REVERT: G   38 MET cc_start: 0.7994 (ttp) cc_final: 0.7476 (tmm)
REVERT: G   59 ASN cc_start: 0.8096 (p0) cc_final: 0.7744 (p0)
  outliers start: 30
  outliers final: 24
  residues processed: 291
  average time/residue: 0.2709
  time to fit residues: 103.1486
Evaluate side-chains
  297 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 269
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  626 LEU
Chi-restraints excluded: chain A residue  658 GLU
Chi-restraints excluded: chain A residue  678 LEU
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  797 GLU
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 1384 LEU
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1421 VAL
Chi-restraints excluded: chain A residue 1424 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 B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  177 THR
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   37 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 52 optimal weight:    0.0670
   chunk 51 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 92 optimal weight:    1.9990
   chunk 73 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 95 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0870
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.4696

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

Flipped N/Q/H residues before XYZ refinement:
A 535 HIS
A 770 HIS
** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 975 ASN
** A1020 HIS ** 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 = 0.4051 r_free = 0.4051 target = 0.157975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.137079 restraints weight = 11861.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3808 rms_B_bonded: 2.62
r_work: 0.3665 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.3960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9202  Z= 0.218
  Angle     :  0.688  10.514  12445  Z= 0.346
  Chirality :  0.044   0.201   1392
  Planarity :  0.004   0.048   1621
  Dihedral  :  4.758  34.440   1257
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 26.50 %
    Favored  : 70.54 %
  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: -0.33 (0.25), residues: 1137
  helix:  1.41 (0.27), residues: 389
  sheet: -1.21 (0.29), residues: 265
  loop : -0.91 (0.30), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 297 
 HIS   0.007   0.001   HIS A 535 
 PHE   0.032   0.002   PHE A 637 
 TYR   0.017   0.002   TYR A1573 
 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: 4789.04 seconds
wall clock time: 85 minutes 46.13 seconds (5146.13 seconds total)