Starting phenix.real_space_refine
on Fri Jul 25 15:04:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xot_22279/07_2025/6xot_22279.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xot_22279/07_2025/6xot_22279.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xot_22279/07_2025/6xot_22279.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xot_22279/07_2025/6xot_22279.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xot_22279/07_2025/6xot_22279.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xot_22279/07_2025/6xot_22279.cif"
  }
  resolution = 3.9
  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=   0.001
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      39      5.16       5
     C    4901      2.51       5
     N    1305      2.21       5
     O    1459      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7704
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7704
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 966, 7698
          Classifications: {'peptide': 966}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 903}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 966, 7698
          Classifications: {'peptide': 966}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 903}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 7882
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ASER A 723 " occ=0.42
      ... (10 atoms not shown)
      pdb=" OG BSER A 723 " occ=0.58
  Time building chain proxies: 8.11, per 1000 atoms: 1.05
  Number of scatterers: 7704
  At special positions: 0
  Unit cell: (83.032, 86.456, 101.864, 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      39     16.00
     O    1459      8.00
     N    1305      7.00
     C    4901      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: 1.82
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1826

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 7 sheets defined
      54.1% alpha, 23.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 39
      removed outlier: 3.796A  pdb=" N   ARG A  36 " --> pdb=" O   ALA A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 111
      removed outlier: 3.774A  pdb=" N   LEU A 111 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 128
      removed outlier: 3.827A  pdb=" N   ASN A 128 " --> pdb=" O   PHE A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 169
    Processing helix  chain 'A' and resid 173 through 181
    Processing helix  chain 'A' and resid 200 through 212
    Processing helix  chain 'A' and resid 212 through 226
    Processing helix  chain 'A' and resid 229 through 233
      removed outlier: 3.610A  pdb=" N   VAL A 233 " --> pdb=" O   THR A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 245
      removed outlier: 3.515A  pdb=" N   GLU A 244 " --> pdb=" O   CYS A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 258
    Processing helix  chain 'A' and resid 259 through 261
      No H-bonds generated for 'chain 'A' and resid 259 through 261'
    Processing helix  chain 'A' and resid 272 through 284
      removed outlier: 4.022A  pdb=" N   HIS A 276 " --> pdb=" O   PRO A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 288
      removed outlier: 3.559A  pdb=" N   PHE A 288 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 285 through 288'
    Processing helix  chain 'A' and resid 339 through 355
    Processing helix  chain 'A' and resid 359 through 366
    Processing helix  chain 'A' and resid 367 through 369
      No H-bonds generated for 'chain 'A' and resid 367 through 369'
    Processing helix  chain 'A' and resid 397 through 399
      No H-bonds generated for 'chain 'A' and resid 397 through 399'
    Processing helix  chain 'A' and resid 400 through 419
    Processing helix  chain 'A' and resid 421 through 438
      removed outlier: 3.652A  pdb=" N   ILE A 425 " --> pdb=" O   GLU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 457
      removed outlier: 4.620A  pdb=" N   SER A 453 " --> pdb=" O   SER A 449 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   CYS A 454 " --> pdb=" O   TYR A 450 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   HIS A 457 " --> pdb=" O   SER A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 465
    Processing helix  chain 'A' and resid 466 through 481
      removed outlier: 3.630A  pdb=" N   ASN A 481 " --> pdb=" O   CYS A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 494
    Processing helix  chain 'A' and resid 510 through 528
      removed outlier: 4.156A  pdb=" N   ALA A 528 " --> pdb=" O   GLN A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 550
    Processing helix  chain 'A' and resid 561 through 565
    Processing helix  chain 'A' and resid 608 through 613
      removed outlier: 3.567A  pdb=" N   ARG A 612 " --> pdb=" O   GLU A 609 " (cutoff:3.500A)
      Proline residue:  A 613  - end of helix
    Processing helix  chain 'A' and resid 614 through 622
    Processing helix  chain 'A' and resid 631 through 643
    Processing helix  chain 'A' and resid 676 through 690
    Processing helix  chain 'A' and resid 695 through 713
      removed outlier: 4.031A  pdb=" N   PHE A 699 " --> pdb=" O   GLU A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 717 through 727
    Processing helix  chain 'A' and resid 731 through 742
    Processing helix  chain 'A' and resid 742 through 755
      removed outlier: 3.724A  pdb=" N   VAL A 746 " --> pdb=" O   GLY A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 763
    Processing helix  chain 'A' and resid 764 through 773
    Processing helix  chain 'A' and resid 788 through 802
    Processing helix  chain 'A' and resid 877 through 894
      removed outlier: 4.355A  pdb=" N   ALA A 881 " --> pdb=" O   ASP A 877 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   SER A 882 " --> pdb=" O   PRO A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 901
    Processing helix  chain 'A' and resid 928 through 945
    Processing helix  chain 'A' and resid 948 through 964
      removed outlier: 3.551A  pdb=" N   ASP A 964 " --> pdb=" O   PHE A 960 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 968 through 972
      removed outlier: 3.762A  pdb=" N   LYS A 972 " --> pdb=" O   PRO A 969 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 979
    Processing helix  chain 'A' and resid 982 through 995
    Processing helix  chain 'A' and resid 997 through 1008
    Processing helix  chain 'A' and resid 1025 through 1030
    Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46
      removed outlier: 6.450A  pdb=" N   LYS A  66 " --> pdb=" O   ASN A  52 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   VAL A  54 " --> pdb=" O   ALA A  64 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   ALA A  64 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   SER A  56 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   LEU A  62 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   ARG A  75 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   THR A 267 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   LEU A  77 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   PHE A 134 " --> pdb=" O   SER A 149 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46
      removed outlier: 6.450A  pdb=" N   LYS A  66 " --> pdb=" O   ASN A  52 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   VAL A  54 " --> pdb=" O   ALA A  64 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   ALA A  64 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   SER A  56 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   LEU A  62 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   ARG A  75 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   THR A 267 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   LEU A  77 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 186
      removed outlier: 3.640A  pdb=" N   ARG A 183 " --> pdb=" O   LYS A 199 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LYS A 199 " --> pdb=" O   ARG A 183 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 311
      removed outlier: 6.298A  pdb=" N   ARG A 307 " --> pdb=" O   THR A 501 " (cutoff:3.500A)
      removed outlier: 7.783A  pdb=" N   SER A 503 " --> pdb=" O   ARG A 307 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   PHE A 309 " --> pdb=" O   SER A 503 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   THR A 326 " --> pdb=" O   GLY A 395 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   ALA A 387 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ASP A 373 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 311
      removed outlier: 6.298A  pdb=" N   ARG A 307 " --> pdb=" O   THR A 501 " (cutoff:3.500A)
      removed outlier: 7.783A  pdb=" N   SER A 503 " --> pdb=" O   ARG A 307 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   PHE A 309 " --> pdb=" O   SER A 503 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   THR A 326 " --> pdb=" O   GLY A 395 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   ALA A 387 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 575 through 579
      removed outlier: 3.742A  pdb=" N   ASP A 575 " --> pdb=" O   TYR A 587 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   VAL A 782 " --> pdb=" O   PRO A 584 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   GLN A 586 " --> pdb=" O   VAL A 782 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   ALA A 784 " --> pdb=" O   GLN A 586 " (cutoff:3.500A)
      removed outlier: 5.819A  pdb=" N   CYS A 588 " --> pdb=" O   ALA A 784 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LEU A 671 " --> pdb=" O   GLY A 645 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   GLY A 645 " --> pdb=" O   LEU A 671 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 912
      removed outlier: 3.551A  pdb=" N   GLY A 909 " --> pdb=" O   TYR A 921 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   VAL A 866 " --> pdb=" O   SER A 922 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   LYS A 854 " --> pdb=" O   ILE A1035 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   ARG A1037 " --> pdb=" O   LYS A 854 " (cutoff:3.500A)
      removed outlier: 5.894A  pdb=" N   HIS A 856 " --> pdb=" O   ARG A1037 " (cutoff:3.500A)

    465 hydrogen bonds defined for protein.
    1342 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: 3.02

  Time building geometry restraints manager: 2.15 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2042
        1.33 -     1.46: 1640
        1.46 -     1.58: 4152
        1.58 -     1.70: 0
        1.70 -     1.82: 62
  Bond restraints: 7896
  Sorted by residual:
  bond pdb=" C   VAL A 615 "
       pdb=" N   PRO A 616 "
    ideal  model  delta    sigma   weight residual
    1.335  1.369 -0.034 1.36e-02 5.41e+03 6.23e+00
  bond pdb=" C   ASP A 238 "
       pdb=" N   PRO A 239 "
    ideal  model  delta    sigma   weight residual
    1.333  1.367 -0.033 1.44e-02 4.82e+03 5.39e+00
  bond pdb=" C   ILE A 714 "
       pdb=" N   PRO A 715 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.025 1.36e-02 5.41e+03 3.45e+00
  bond pdb=" C   ASP A 321 "
       pdb=" N   PRO A 322 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.025 1.36e-02 5.41e+03 3.43e+00
  bond pdb=" C   VAL A 102 "
       pdb=" N   PRO A 103 "
    ideal  model  delta    sigma   weight residual
    1.336  1.359 -0.023 1.25e-02 6.40e+03 3.37e+00
  ... (remaining 7891 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 10150
        2.12 -     4.23: 457
        4.23 -     6.35: 66
        6.35 -     8.46: 27
        8.46 -    10.58: 8
  Bond angle restraints: 10708
  Sorted by residual:
  angle pdb=" N   LEU A 529 "
        pdb=" CA  LEU A 529 "
        pdb=" C   LEU A 529 "
      ideal   model   delta    sigma   weight residual
     109.76  116.03   -6.27 1.59e+00 3.96e-01 1.55e+01
  angle pdb=" N   LEU A 772 "
        pdb=" CA  LEU A 772 "
        pdb=" C   LEU A 772 "
      ideal   model   delta    sigma   weight residual
     113.88  118.47   -4.59 1.23e+00 6.61e-01 1.39e+01
  angle pdb=" CA  ILE A 242 "
        pdb=" C   ILE A 242 "
        pdb=" N   PRO A 243 "
      ideal   model   delta    sigma   weight residual
     118.88  124.38   -5.50 1.54e+00 4.22e-01 1.27e+01
  angle pdb=" C   ALA A 580 "
        pdb=" N   GLY A 581 "
        pdb=" CA  GLY A 581 "
      ideal   model   delta    sigma   weight residual
     121.70  127.85   -6.15 1.80e+00 3.09e-01 1.17e+01
  angle pdb=" N   THR A 340 "
        pdb=" CA  THR A 340 "
        pdb=" C   THR A 340 "
      ideal   model   delta    sigma   weight residual
     111.11  115.07   -3.96 1.20e+00 6.94e-01 1.09e+01
  ... (remaining 10703 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 4372
       17.75 -    35.50: 304
       35.50 -    53.25: 68
       53.25 -    71.00: 20
       71.00 -    88.75: 11
  Dihedral angle restraints: 4775
    sinusoidal: 1953
      harmonic: 2822
  Sorted by residual:
  dihedral pdb=" CA  PRO A 170 "
           pdb=" C   PRO A 170 "
           pdb=" N   CYS A 171 "
           pdb=" CA  CYS A 171 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.86   22.14     0      5.00e+00 4.00e-02 1.96e+01
  dihedral pdb=" C   VAL A 102 "
           pdb=" N   VAL A 102 "
           pdb=" CA  VAL A 102 "
           pdb=" CB  VAL A 102 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.41    9.41     0      2.50e+00 1.60e-01 1.42e+01
  dihedral pdb=" CA  GLU A 187 "
           pdb=" C   GLU A 187 "
           pdb=" N   ASN A 188 "
           pdb=" CA  ASN A 188 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.45   17.55     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 4772 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 905
       0.069 -    0.138: 234
       0.138 -    0.207: 28
       0.207 -    0.276: 6
       0.276 -    0.345: 1
  Chirality restraints: 1174
  Sorted by residual:
  chirality pdb=" CB  ILE A 242 "
            pdb=" CA  ILE A 242 "
            pdb=" CG1 ILE A 242 "
            pdb=" CG2 ILE A 242 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.35 2.00e-01 2.50e+01 2.98e+00
  chirality pdb=" CA  VAL A 102 "
            pdb=" N   VAL A 102 "
            pdb=" C   VAL A 102 "
            pdb=" CB  VAL A 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.19    0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CB  VAL A1004 "
            pdb=" CA  VAL A1004 "
            pdb=" CG1 VAL A1004 "
            pdb=" CG2 VAL A1004 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.36e+00
  ... (remaining 1171 not shown)

  Planarity restraints: 1398
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A  86 "   -0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" CG  ASN A  86 "    0.055 2.00e-02 2.50e+03
        pdb=" OD1 ASN A  86 "   -0.021 2.00e-02 2.50e+03
        pdb=" ND2 ASN A  86 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 897 "   -0.014 2.00e-02 2.50e+03   2.83e-02 8.03e+00
        pdb=" C   THR A 897 "    0.049 2.00e-02 2.50e+03
        pdb=" O   THR A 897 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   GLU A 898 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 178 "   -0.017 2.00e-02 2.50e+03   1.51e-02 5.66e+00
        pdb=" CG  TRP A 178 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 178 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 178 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 178 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 178 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 178 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 178 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 178 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 178 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1395 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1951
        2.80 -     3.32: 7043
        3.32 -     3.85: 13060
        3.85 -     4.37: 14686
        4.37 -     4.90: 25359
  Nonbonded interactions: 62099
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 729 "
            pdb=" O   TRP A 851 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OG1 THR A 326 "
            pdb=" O   ILE A 396 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OG1 THR A 384 "
            pdb=" O   GLU A 386 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   LEU A 957 "
            pdb=" OG  SER A 961 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   SER A 351 "
            pdb=" OG  SER A 355 "
     model   vdw
     2.308 3.040
  ... (remaining 62094 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.42 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.080
  Set scattering table:                    0.070
  Process input model:                     26.020
  Find NCS groups from input model:        0.090
  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:             0.010
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
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   0.071   7896  Z= 0.268
  Angle     :  1.071  10.580  10708  Z= 0.577
  Chirality :  0.061   0.345   1174
  Planarity :  0.007   0.058   1398
  Dihedral  : 14.015  88.752   2949
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.75 %
    Favored  : 98.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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: -1.51 (0.24), residues: 965
  helix: -1.00 (0.20), residues: 449
  sheet:  0.31 (0.37), residues: 170
  loop : -1.48 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP A 178 
 HIS   0.016   0.002   HIS A 186 
 PHE   0.026   0.003   PHE A 123 
 TYR   0.023   0.003   TYR A 388 
 ARG   0.009   0.001   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16833 (  426)
  hydrogen bonds       : angle       7.56055 ( 1342)
  covalent geometry    : bond        0.00575 ( 7896)
  covalent geometry    : angle       1.07079 (10708)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 LEU cc_start: 0.8864 (tt) cc_final: 0.8626 (mt)
REVERT: A  145 LEU cc_start: 0.9033 (tp) cc_final: 0.8802 (tp)
REVERT: A  219 GLN cc_start: 0.8554 (tp-100) cc_final: 0.8006 (tp-100)
REVERT: A  332 PHE cc_start: 0.7613 (m-80) cc_final: 0.7078 (m-80)
REVERT: A  333 LEU cc_start: 0.8832 (tp) cc_final: 0.8626 (tt)
REVERT: A  400 ASP cc_start: 0.8427 (m-30) cc_final: 0.8166 (t0)
REVERT: A  567 PRO cc_start: 0.7225 (Cg_endo) cc_final: 0.6783 (Cg_exo)
REVERT: A  587 TYR cc_start: 0.7579 (m-80) cc_final: 0.6789 (m-10)
REVERT: A  680 MET cc_start: 0.7767 (ttp) cc_final: 0.7452 (ttm)
REVERT: A  915 ASN cc_start: 0.8941 (p0) cc_final: 0.8401 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 200
  average time/residue: 0.2272
  time to fit residues: 59.5172
Evaluate side-chains
  119 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    7.9990
   chunk 72 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 75 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 56 optimal weight:    4.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  53 GLN
A 104 HIS
A 151 GLN
A 204 ASN
A 219 GLN
** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 469 ASN
** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 638 GLN
** A 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 777 ASN
A 856 HIS
A 864 ASN
A1016 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.069878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.054776 restraints weight = 35230.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.056696 restraints weight = 21615.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.058063 restraints weight = 15199.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3135
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3135
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   7896  Z= 0.210
  Angle     :  0.813   9.711  10708  Z= 0.411
  Chirality :  0.048   0.231   1174
  Planarity :  0.006   0.048   1398
  Dihedral  :  4.687  21.670   1037
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 15.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 15.50 %
    Favored  : 82.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.16 (0.26), residues: 965
  helix:  0.74 (0.24), residues: 461
  sheet:  0.52 (0.36), residues: 170
  loop : -0.90 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 941 
 HIS   0.020   0.002   HIS A 229 
 PHE   0.034   0.002   PHE A 389 
 TYR   0.029   0.002   TYR A 721 
 ARG   0.011   0.001   ARG A 505 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04429 (  426)
  hydrogen bonds       : angle       5.46619 ( 1342)
  covalent geometry    : bond        0.00449 ( 7896)
  covalent geometry    : angle       0.81263 (10708)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8214 (t80)
REVERT: A   66 LYS cc_start: 0.9233 (ttmt) cc_final: 0.8879 (ptmm)
REVERT: A   85 ASN cc_start: 0.8843 (t0) cc_final: 0.8459 (m-40)
REVERT: A  219 GLN cc_start: 0.8968 (tp40) cc_final: 0.8339 (tp-100)
REVERT: A  229 HIS cc_start: 0.8451 (t-170) cc_final: 0.8192 (t-170)
REVERT: A  400 ASP cc_start: 0.9127 (m-30) cc_final: 0.8663 (t0)
REVERT: A  586 GLN cc_start: 0.9114 (tt0) cc_final: 0.8809 (tp-100)
REVERT: A  587 TYR cc_start: 0.8316 (m-80) cc_final: 0.7748 (m-80)
REVERT: A  595 MET cc_start: 0.8131 (mtt) cc_final: 0.7825 (mtt)
REVERT: A  640 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8607 (tt0)
REVERT: A  721 TYR cc_start: 0.9210 (m-80) cc_final: 0.8899 (m-80)
REVERT: A  782 VAL cc_start: 0.9346 (t) cc_final: 0.9133 (m)
REVERT: A  888 ARG cc_start: 0.8419 (tpp-160) cc_final: 0.8185 (tpp-160)
REVERT: A 1024 GLU cc_start: 0.7740 (tp30) cc_final: 0.7486 (tp30)
  outliers start: 14
  outliers final: 7
  residues processed: 127
  average time/residue: 0.1682
  time to fit residues: 30.7425
Evaluate side-chains
  101 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  679 ASP
Chi-restraints excluded: chain A residue  931 THR
Chi-restraints excluded: chain A residue  932 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9980
   chunk 32 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9990
   chunk 84 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 74 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0870
   chunk 0 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   overall best weight:    1.8164

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

Flipped N/Q/H residues before XYZ refinement:
A  47 HIS
A 104 HIS
** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 325 GLN
A 430 HIS
** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 698 HIS
A 771 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.070331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.055152 restraints weight = 35500.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.057155 restraints weight = 21593.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.058577 restraints weight = 15030.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3157
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3157
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.3193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7896  Z= 0.160
  Angle     :  0.745  11.495  10708  Z= 0.364
  Chirality :  0.046   0.220   1174
  Planarity :  0.005   0.049   1398
  Dihedral  :  4.531  19.351   1037
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 16.32 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.51 (0.27), residues: 965
  helix:  1.04 (0.24), residues: 462
  sheet:  0.59 (0.38), residues: 167
  loop : -0.68 (0.35), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP A 455 
 HIS   0.012   0.002   HIS A 229 
 PHE   0.017   0.002   PHE A 977 
 TYR   0.017   0.001   TYR A 721 
 ARG   0.007   0.001   ARG A 505 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03811 (  426)
  hydrogen bonds       : angle       5.17861 ( 1342)
  covalent geometry    : bond        0.00349 ( 7896)
  covalent geometry    : angle       0.74503 (10708)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8246 (t80)
REVERT: A   85 ASN cc_start: 0.8870 (t0) cc_final: 0.8613 (m-40)
REVERT: A  217 PHE cc_start: 0.9522 (t80) cc_final: 0.9250 (t80)
REVERT: A  219 GLN cc_start: 0.9180 (tp40) cc_final: 0.8512 (tp-100)
REVERT: A  229 HIS cc_start: 0.8502 (t-170) cc_final: 0.8268 (t-170)
REVERT: A  400 ASP cc_start: 0.9128 (m-30) cc_final: 0.8652 (t0)
REVERT: A  587 TYR cc_start: 0.8080 (m-80) cc_final: 0.7835 (m-80)
REVERT: A  595 MET cc_start: 0.8068 (mtt) cc_final: 0.7690 (mtt)
REVERT: A  640 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8632 (tt0)
REVERT: A  659 MET cc_start: 0.7779 (mmt) cc_final: 0.7455 (mmt)
REVERT: A  669 SER cc_start: 0.8355 (t) cc_final: 0.8020 (m)
REVERT: A  721 TYR cc_start: 0.9296 (m-80) cc_final: 0.9027 (m-80)
REVERT: A  888 ARG cc_start: 0.8446 (tpp-160) cc_final: 0.7660 (tpm170)
REVERT: A  890 MET cc_start: 0.9184 (tpp) cc_final: 0.8960 (tpp)
REVERT: A 1024 GLU cc_start: 0.7823 (tp30) cc_final: 0.7590 (tp30)
  outliers start: 12
  outliers final: 6
  residues processed: 117
  average time/residue: 0.1707
  time to fit residues: 28.5460
Evaluate side-chains
  103 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  679 ASP
Chi-restraints excluded: chain A residue  931 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 69 optimal weight:    7.9990
   chunk 4 optimal weight:    8.9990
   chunk 30 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 61 optimal weight:   10.0000
   chunk 94 optimal weight:    1.9990
   chunk 6 optimal weight:    8.9990
   chunk 53 optimal weight:    0.7980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.070535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.055484 restraints weight = 35108.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.057508 restraints weight = 21263.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.058894 restraints weight = 14762.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3177
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3177
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.3615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7896  Z= 0.145
  Angle     :  0.742  12.815  10708  Z= 0.357
  Chirality :  0.046   0.384   1174
  Planarity :  0.005   0.044   1398
  Dihedral  :  4.476  21.645   1037
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 17.02 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.62 (0.27), residues: 965
  helix:  1.14 (0.24), residues: 463
  sheet:  0.51 (0.39), residues: 165
  loop : -0.57 (0.36), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 455 
 HIS   0.007   0.001   HIS A 229 
 PHE   0.021   0.002   PHE A 977 
 TYR   0.015   0.001   TYR A 721 
 ARG   0.005   0.001   ARG A 505 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03514 (  426)
  hydrogen bonds       : angle       5.05414 ( 1342)
  covalent geometry    : bond        0.00324 ( 7896)
  covalent geometry    : angle       0.74176 (10708)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.908 
Fit side-chains
REVERT: A   61 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8288 (t80)
REVERT: A   85 ASN cc_start: 0.8877 (t0) cc_final: 0.8639 (m-40)
REVERT: A  219 GLN cc_start: 0.9217 (tp40) cc_final: 0.8560 (tp-100)
REVERT: A  229 HIS cc_start: 0.8519 (t-170) cc_final: 0.8259 (t-170)
REVERT: A  388 TYR cc_start: 0.8376 (p90) cc_final: 0.8052 (p90)
REVERT: A  400 ASP cc_start: 0.9145 (m-30) cc_final: 0.8679 (t0)
REVERT: A  595 MET cc_start: 0.7994 (mtt) cc_final: 0.7763 (mtt)
REVERT: A  640 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8564 (tt0)
REVERT: A  646 MET cc_start: 0.8030 (mmm) cc_final: 0.7801 (mmm)
REVERT: A  659 MET cc_start: 0.7934 (mmt) cc_final: 0.6982 (mmt)
REVERT: A  671 LEU cc_start: 0.9113 (mp) cc_final: 0.8173 (tp)
REVERT: A  721 TYR cc_start: 0.9389 (m-80) cc_final: 0.9098 (m-80)
REVERT: A  888 ARG cc_start: 0.8476 (tpp-160) cc_final: 0.7669 (tpm170)
REVERT: A  974 MET cc_start: 0.8975 (mtp) cc_final: 0.8143 (mtp)
REVERT: A 1024 GLU cc_start: 0.7852 (tp30) cc_final: 0.7588 (tp30)
  outliers start: 17
  outliers final: 8
  residues processed: 129
  average time/residue: 0.1720
  time to fit residues: 31.5263
Evaluate side-chains
  109 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  203 PHE
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  932 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 20 optimal weight:   20.0000
   chunk 86 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 74 optimal weight:    0.0060
   chunk 73 optimal weight:    0.8980
   chunk 95 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    2.3802

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.069995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.055317 restraints weight = 35823.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.057269 restraints weight = 22057.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.058668 restraints weight = 15537.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3184
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3184
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.3976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7896  Z= 0.177
  Angle     :  0.743  12.529  10708  Z= 0.361
  Chirality :  0.047   0.414   1174
  Planarity :  0.005   0.047   1398
  Dihedral  :  4.541  19.072   1037
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 14.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 18.88 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.53 (0.27), residues: 965
  helix:  1.20 (0.24), residues: 462
  sheet:  0.27 (0.38), residues: 170
  loop : -0.72 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 455 
 HIS   0.006   0.001   HIS A 719 
 PHE   0.021   0.002   PHE A 374 
 TYR   0.014   0.002   TYR A  76 
 ARG   0.004   0.001   ARG A 801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03501 (  426)
  hydrogen bonds       : angle       5.04109 ( 1342)
  covalent geometry    : bond        0.00384 ( 7896)
  covalent geometry    : angle       0.74339 (10708)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8254 (t80)
REVERT: A   85 ASN cc_start: 0.8950 (t0) cc_final: 0.8650 (m-40)
REVERT: A  219 GLN cc_start: 0.9180 (tp40) cc_final: 0.8495 (tp-100)
REVERT: A  229 HIS cc_start: 0.8590 (t-170) cc_final: 0.8195 (t-170)
REVERT: A  388 TYR cc_start: 0.8414 (p90) cc_final: 0.8186 (p90)
REVERT: A  400 ASP cc_start: 0.9148 (m-30) cc_final: 0.8946 (m-30)
REVERT: A  595 MET cc_start: 0.8003 (mtt) cc_final: 0.7772 (mtp)
REVERT: A  646 MET cc_start: 0.8026 (mmm) cc_final: 0.7793 (mmm)
REVERT: A  659 MET cc_start: 0.8116 (mmt) cc_final: 0.7191 (mmt)
REVERT: A  709 GLU cc_start: 0.9058 (tp30) cc_final: 0.8780 (tp30)
REVERT: A  721 TYR cc_start: 0.9445 (m-80) cc_final: 0.9054 (m-80)
REVERT: A  888 ARG cc_start: 0.8557 (tpp-160) cc_final: 0.7824 (tpm170)
REVERT: A 1024 GLU cc_start: 0.7941 (tp30) cc_final: 0.7668 (tp30)
  outliers start: 15
  outliers final: 11
  residues processed: 107
  average time/residue: 0.1936
  time to fit residues: 29.4335
Evaluate side-chains
  109 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  756 THR
Chi-restraints excluded: chain A residue  778 MET
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  889 LEU
Chi-restraints excluded: chain A residue  932 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 89 optimal weight:    9.9990
   chunk 58 optimal weight:    0.9990
   chunk 63 optimal weight:    9.9990
   chunk 25 optimal weight:    0.3980
   chunk 51 optimal weight:   20.0000
   chunk 74 optimal weight:    8.9990
   chunk 35 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 87 optimal weight:    0.6980
   chunk 91 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.071214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.056421 restraints weight = 34688.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.058358 restraints weight = 21779.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.059735 restraints weight = 15495.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3214
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3214
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.4208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7896  Z= 0.125
  Angle     :  0.728  14.099  10708  Z= 0.348
  Chirality :  0.046   0.400   1174
  Planarity :  0.005   0.045   1398
  Dihedral  :  4.407  17.968   1037
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 20.28 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.62 (0.28), residues: 965
  helix:  1.23 (0.25), residues: 464
  sheet:  0.32 (0.39), residues: 164
  loop : -0.60 (0.35), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 455 
 HIS   0.004   0.001   HIS A 719 
 PHE   0.023   0.002   PHE A 374 
 TYR   0.019   0.001   TYR A 450 
 ARG   0.004   0.000   ARG A 801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03343 (  426)
  hydrogen bonds       : angle       4.85551 ( 1342)
  covalent geometry    : bond        0.00280 ( 7896)
  covalent geometry    : angle       0.72830 (10708)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8243 (t80)
REVERT: A   77 LEU cc_start: 0.9386 (mm) cc_final: 0.9024 (tp)
REVERT: A   85 ASN cc_start: 0.8887 (t0) cc_final: 0.8582 (m-40)
REVERT: A  126 MET cc_start: 0.8204 (mmm) cc_final: 0.7888 (tpt)
REVERT: A  219 GLN cc_start: 0.9181 (tp40) cc_final: 0.8490 (tp-100)
REVERT: A  229 HIS cc_start: 0.8494 (t-170) cc_final: 0.8206 (t-170)
REVERT: A  388 TYR cc_start: 0.8347 (p90) cc_final: 0.8099 (p90)
REVERT: A  400 ASP cc_start: 0.9135 (m-30) cc_final: 0.8914 (m-30)
REVERT: A  595 MET cc_start: 0.7958 (mtt) cc_final: 0.7661 (mtt)
REVERT: A  646 MET cc_start: 0.7944 (mmm) cc_final: 0.7695 (mmm)
REVERT: A  659 MET cc_start: 0.8124 (mmt) cc_final: 0.7807 (mmt)
REVERT: A  721 TYR cc_start: 0.9376 (m-80) cc_final: 0.8743 (m-80)
REVERT: A  868 GLU cc_start: 0.7438 (tp30) cc_final: 0.7059 (tp30)
REVERT: A  888 ARG cc_start: 0.8613 (tpp-160) cc_final: 0.7909 (tpm170)
REVERT: A 1024 GLU cc_start: 0.7999 (tp30) cc_final: 0.7674 (tp30)
  outliers start: 13
  outliers final: 9
  residues processed: 115
  average time/residue: 0.1655
  time to fit residues: 27.6515
Evaluate side-chains
  107 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   66 LYS
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  756 THR
Chi-restraints excluded: chain A residue  889 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 73 optimal weight:    0.0470
   chunk 78 optimal weight:    9.9990
   chunk 74 optimal weight:    9.9990
   chunk 55 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 47 optimal weight:   10.0000
   chunk 31 optimal weight:    7.9990
   chunk 60 optimal weight:    6.9990
   overall best weight:    2.4084

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

Flipped N/Q/H residues before XYZ refinement:
** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.069676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.054961 restraints weight = 35585.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.056850 restraints weight = 22273.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.058201 restraints weight = 15831.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3178
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.4472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   7896  Z= 0.177
  Angle     :  0.754  13.493  10708  Z= 0.365
  Chirality :  0.047   0.418   1174
  Planarity :  0.005   0.045   1398
  Dihedral  :  4.483  18.827   1037
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 15.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 20.40 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.58 (0.28), residues: 965
  helix:  1.19 (0.24), residues: 465
  sheet:  0.23 (0.39), residues: 163
  loop : -0.56 (0.36), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 455 
 HIS   0.006   0.001   HIS A 498 
 PHE   0.019   0.002   PHE A 618 
 TYR   0.019   0.002   TYR A 450 
 ARG   0.003   0.000   ARG A 801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03430 (  426)
  hydrogen bonds       : angle       4.88399 ( 1342)
  covalent geometry    : bond        0.00386 ( 7896)
  covalent geometry    : angle       0.75448 (10708)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8284 (t80)
REVERT: A   85 ASN cc_start: 0.9011 (t0) cc_final: 0.8679 (m-40)
REVERT: A  126 MET cc_start: 0.8215 (mmm) cc_final: 0.7897 (tpt)
REVERT: A  219 GLN cc_start: 0.9198 (tp40) cc_final: 0.8464 (tp-100)
REVERT: A  229 HIS cc_start: 0.8627 (t-170) cc_final: 0.8300 (t-170)
REVERT: A  388 TYR cc_start: 0.8383 (p90) cc_final: 0.8131 (p90)
REVERT: A  393 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8645 (tp)
REVERT: A  400 ASP cc_start: 0.9179 (m-30) cc_final: 0.8977 (m-30)
REVERT: A  516 GLN cc_start: 0.9276 (mt0) cc_final: 0.9015 (mt0)
REVERT: A  595 MET cc_start: 0.8042 (mtt) cc_final: 0.7826 (mtp)
REVERT: A  646 MET cc_start: 0.7923 (mmm) cc_final: 0.7723 (mmm)
REVERT: A  659 MET cc_start: 0.8227 (mmt) cc_final: 0.7907 (mmt)
REVERT: A  721 TYR cc_start: 0.9407 (m-80) cc_final: 0.8954 (m-80)
REVERT: A  888 ARG cc_start: 0.8679 (tpp-160) cc_final: 0.8373 (tpp-160)
REVERT: A 1024 GLU cc_start: 0.8061 (tp30) cc_final: 0.7752 (tp30)
  outliers start: 16
  outliers final: 12
  residues processed: 109
  average time/residue: 0.1713
  time to fit residues: 26.8930
Evaluate side-chains
  110 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   66 LYS
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  317 SER
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  889 LEU
Chi-restraints excluded: chain A residue 1030 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 14 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 83 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 63 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 28 optimal weight:    7.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.069618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.054981 restraints weight = 35902.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.056874 restraints weight = 22414.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.058215 restraints weight = 15919.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3181
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.4684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7896  Z= 0.164
  Angle     :  0.753  13.840  10708  Z= 0.362
  Chirality :  0.046   0.402   1174
  Planarity :  0.005   0.046   1398
  Dihedral  :  4.506  18.813   1037
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 14.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 20.75 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.28), residues: 965
  helix:  1.23 (0.24), residues: 459
  sheet:  0.12 (0.39), residues: 164
  loop : -0.50 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 455 
 HIS   0.005   0.001   HIS A 719 
 PHE   0.019   0.002   PHE A 618 
 TYR   0.012   0.001   TYR A 587 
 ARG   0.003   0.000   ARG A 505 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03356 (  426)
  hydrogen bonds       : angle       4.85847 ( 1342)
  covalent geometry    : bond        0.00360 ( 7896)
  covalent geometry    : angle       0.75334 (10708)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 1.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8309 (t80)
REVERT: A  126 MET cc_start: 0.8192 (mmm) cc_final: 0.7870 (tpt)
REVERT: A  219 GLN cc_start: 0.9215 (tp40) cc_final: 0.8466 (tp-100)
REVERT: A  229 HIS cc_start: 0.8660 (t-170) cc_final: 0.8348 (t-170)
REVERT: A  388 TYR cc_start: 0.8399 (p90) cc_final: 0.8138 (p90)
REVERT: A  393 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8690 (tp)
REVERT: A  400 ASP cc_start: 0.9184 (m-30) cc_final: 0.8982 (m-30)
REVERT: A  516 GLN cc_start: 0.9296 (mt0) cc_final: 0.9059 (mt0)
REVERT: A  595 MET cc_start: 0.8135 (mtt) cc_final: 0.7906 (mtp)
REVERT: A  646 MET cc_start: 0.7956 (mmm) cc_final: 0.7754 (mmm)
REVERT: A  659 MET cc_start: 0.8291 (mmt) cc_final: 0.7991 (mmt)
REVERT: A  721 TYR cc_start: 0.9424 (m-80) cc_final: 0.9004 (m-80)
REVERT: A  868 GLU cc_start: 0.7424 (tp30) cc_final: 0.7022 (tp30)
REVERT: A  888 ARG cc_start: 0.8657 (tpp-160) cc_final: 0.8388 (tpp-160)
REVERT: A  912 LEU cc_start: 0.8422 (tp) cc_final: 0.8219 (tp)
REVERT: A 1024 GLU cc_start: 0.8133 (tp30) cc_final: 0.7807 (tp30)
  outliers start: 14
  outliers final: 11
  residues processed: 109
  average time/residue: 0.1822
  time to fit residues: 28.4773
Evaluate side-chains
  111 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   66 LYS
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  889 LEU
Chi-restraints excluded: chain A residue 1030 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0070
   chunk 82 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9980
   chunk 63 optimal weight:    9.9990
   chunk 69 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.071503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.056661 restraints weight = 35239.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.058619 restraints weight = 22034.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.060015 restraints weight = 15601.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3224
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3224
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.4783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7896  Z= 0.122
  Angle     :  0.761  14.943  10708  Z= 0.357
  Chirality :  0.046   0.411   1174
  Planarity :  0.004   0.044   1398
  Dihedral  :  4.378  18.234   1037
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 21.33 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.69 (0.28), residues: 965
  helix:  1.36 (0.24), residues: 462
  sheet:  0.17 (0.41), residues: 158
  loop : -0.55 (0.36), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 455 
 HIS   0.005   0.001   HIS A 719 
 PHE   0.019   0.002   PHE A 618 
 TYR   0.039   0.001   TYR A 450 
 ARG   0.003   0.000   ARG A 505 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03228 (  426)
  hydrogen bonds       : angle       4.73831 ( 1342)
  covalent geometry    : bond        0.00276 ( 7896)
  covalent geometry    : angle       0.76079 (10708)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8274 (t80)
REVERT: A   85 ASN cc_start: 0.8974 (t0) cc_final: 0.8625 (m-40)
REVERT: A  126 MET cc_start: 0.8113 (mmm) cc_final: 0.7778 (tpt)
REVERT: A  219 GLN cc_start: 0.9202 (tp40) cc_final: 0.8447 (tp-100)
REVERT: A  229 HIS cc_start: 0.8617 (t-170) cc_final: 0.8330 (t-170)
REVERT: A  388 TYR cc_start: 0.8327 (p90) cc_final: 0.8047 (p90)
REVERT: A  393 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8655 (tp)
REVERT: A  400 ASP cc_start: 0.9173 (m-30) cc_final: 0.8969 (m-30)
REVERT: A  516 GLN cc_start: 0.9314 (mt0) cc_final: 0.9080 (mt0)
REVERT: A  595 MET cc_start: 0.7998 (mtt) cc_final: 0.7795 (mtp)
REVERT: A  646 MET cc_start: 0.8112 (mmm) cc_final: 0.7813 (mmm)
REVERT: A  659 MET cc_start: 0.8334 (mmt) cc_final: 0.7758 (mmt)
REVERT: A  721 TYR cc_start: 0.9409 (m-80) cc_final: 0.8962 (m-80)
REVERT: A  868 GLU cc_start: 0.7459 (tp30) cc_final: 0.7024 (tp30)
REVERT: A  888 ARG cc_start: 0.8717 (tpp-160) cc_final: 0.8439 (tpp-160)
REVERT: A  912 LEU cc_start: 0.8280 (tp) cc_final: 0.8055 (tp)
REVERT: A 1024 GLU cc_start: 0.8145 (tp30) cc_final: 0.7785 (tp30)
REVERT: A 1037 ARG cc_start: 0.8469 (mtp85) cc_final: 0.7767 (mtm180)
  outliers start: 11
  outliers final: 8
  residues processed: 116
  average time/residue: 0.1975
  time to fit residues: 32.3831
Evaluate side-chains
  115 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   66 LYS
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  889 LEU
Chi-restraints excluded: chain A residue 1030 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 26 optimal weight:    9.9990
   chunk 54 optimal weight:    7.9990
   chunk 68 optimal weight:    0.8980
   chunk 43 optimal weight:    0.4980
   chunk 42 optimal weight:    0.0370
   chunk 24 optimal weight:    0.9990
   chunk 55 optimal weight:    8.9990
   chunk 10 optimal weight:    4.9990
   chunk 79 optimal weight:    0.6980
   overall best weight:    0.6260

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

Flipped N/Q/H residues before XYZ refinement:
** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.072226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.057287 restraints weight = 35432.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.059235 restraints weight = 22250.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.060634 restraints weight = 15858.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3239
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3239 r_free = 0.3239    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3239 r_free = 0.3239    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3239
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.4912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   7896  Z= 0.128
  Angle     :  0.792  22.317  10708  Z= 0.370
  Chirality :  0.047   0.423   1174
  Planarity :  0.005   0.060   1398
  Dihedral  :  4.349  18.425   1037
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 21.56 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.78 (0.28), residues: 965
  helix:  1.45 (0.24), residues: 462
  sheet:  0.21 (0.41), residues: 158
  loop : -0.52 (0.36), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 455 
 HIS   0.004   0.001   HIS A 719 
 PHE   0.019   0.001   PHE A 618 
 TYR   0.010   0.001   TYR A 587 
 ARG   0.014   0.001   ARG A 534 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03196 (  426)
  hydrogen bonds       : angle       4.67587 ( 1342)
  covalent geometry    : bond        0.00295 ( 7896)
  covalent geometry    : angle       0.79209 (10708)

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8304 (t80)
REVERT: A   85 ASN cc_start: 0.8945 (t0) cc_final: 0.8551 (m-40)
REVERT: A  126 MET cc_start: 0.8100 (mmm) cc_final: 0.7808 (tpt)
REVERT: A  219 GLN cc_start: 0.9211 (tp40) cc_final: 0.8453 (tp-100)
REVERT: A  229 HIS cc_start: 0.8595 (t-170) cc_final: 0.8307 (t-170)
REVERT: A  388 TYR cc_start: 0.8305 (p90) cc_final: 0.8018 (p90)
REVERT: A  393 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8643 (tp)
REVERT: A  595 MET cc_start: 0.7924 (mtt) cc_final: 0.7715 (mtt)
REVERT: A  646 MET cc_start: 0.8131 (mmm) cc_final: 0.7835 (mmm)
REVERT: A  659 MET cc_start: 0.8293 (mmt) cc_final: 0.7789 (mmt)
REVERT: A  721 TYR cc_start: 0.9415 (m-80) cc_final: 0.9014 (m-80)
REVERT: A  868 GLU cc_start: 0.7434 (tp30) cc_final: 0.7029 (tp30)
REVERT: A  888 ARG cc_start: 0.8753 (tpp-160) cc_final: 0.8463 (tpp-160)
REVERT: A  912 LEU cc_start: 0.8278 (tp) cc_final: 0.8022 (tp)
REVERT: A 1024 GLU cc_start: 0.8135 (tp30) cc_final: 0.7766 (tp30)
REVERT: A 1037 ARG cc_start: 0.8442 (mtp85) cc_final: 0.8097 (mtp85)
  outliers start: 10
  outliers final: 7
  residues processed: 114
  average time/residue: 0.2643
  time to fit residues: 43.6012
Evaluate side-chains
  108 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 1.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   66 LYS
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  756 THR
Chi-restraints excluded: chain A residue  889 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 73 optimal weight:    0.0170
   chunk 39 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 31 optimal weight:    9.9990
   chunk 17 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 77 optimal weight:    7.9990
   chunk 92 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   overall best weight:    0.6822

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

Flipped N/Q/H residues before XYZ refinement:
** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.072579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.057594 restraints weight = 35354.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.059584 restraints weight = 22104.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.061002 restraints weight = 15714.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3252
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3252 r_free = 0.3252    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3252 r_free = 0.3252    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3252
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.5052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7896  Z= 0.123
  Angle     :  0.818  24.639  10708  Z= 0.377
  Chirality :  0.047   0.417   1174
  Planarity :  0.005   0.070   1398
  Dihedral  :  4.284  18.996   1037
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 22.84 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.73 (0.28), residues: 965
  helix:  1.45 (0.24), residues: 461
  sheet:  0.07 (0.42), residues: 152
  loop : -0.53 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 455 
 HIS   0.004   0.001   HIS A 719 
 PHE   0.016   0.001   PHE A 668 
 TYR   0.034   0.002   TYR A 450 
 ARG   0.013   0.001   ARG A 534 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03211 (  426)
  hydrogen bonds       : angle       4.64504 ( 1342)
  covalent geometry    : bond        0.00281 ( 7896)
  covalent geometry    : angle       0.81802 (10708)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3262.82 seconds
wall clock time: 58 minutes 53.37 seconds (3533.37 seconds total)