Starting phenix.real_space_refine
on Fri Aug 22 20:35:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xot_22279/08_2025/6xot_22279.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xot_22279/08_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_22279/08_2025/6xot_22279.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xot_22279/08_2025/6xot_22279.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xot_22279/08_2025/6xot_22279.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xot_22279/08_2025/6xot_22279.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.53, per 1000 atoms: 0.46
  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: 0.86
  Conformation dependent library (CDL) restraints added in 583.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.55
  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: 1.55

  Time building geometry restraints manager: 1.13 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:             1.570
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     12.080
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.270
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.009   0.001   ARG A 264 
 TYR   0.023   0.003   TYR A 388 
 PHE   0.026   0.003   PHE A 123 
 TRP   0.040   0.003   TRP A 178 
 HIS   0.016   0.002   HIS A 186 

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

*********************** 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  : 0.313 
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: 0.1064
  time to fit residues: 27.9433
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  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    5.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
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 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 469 ASN
A 476 GLN
A 479 GLN
A 638 GLN
** A 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 777 ASN
A 856 HIS
A 864 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.070515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.055258 restraints weight = 35359.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.057218 restraints weight = 21658.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.058607 restraints weight = 15167.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.059589 restraints weight = 11633.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.060359 restraints weight = 9518.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    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 = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   7896  Z= 0.196
  Angle     :  0.801   9.701  10708  Z= 0.404
  Chirality :  0.047   0.213   1174
  Planarity :  0.006   0.048   1398
  Dihedral  :  4.630  21.283   1037
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 14.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 15.15 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.26), residues: 965
  helix:  0.72 (0.24), residues: 460
  sheet:  0.52 (0.36), residues: 170
  loop : -0.84 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 505 
 TYR   0.026   0.002   TYR A 721 
 PHE   0.034   0.002   PHE A 389 
 TRP   0.014   0.002   TRP A 941 
 HIS   0.019   0.002   HIS A 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 7896)
  covalent geometry    : angle       0.80063 (10708)
  hydrogen bonds       : bond        0.04411 (  426)
  hydrogen bonds       : angle       5.43934 ( 1342)

*********************** 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
  136 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8170 (t80)
REVERT: A   66 LYS cc_start: 0.9213 (ttmt) cc_final: 0.8870 (ptmm)
REVERT: A   85 ASN cc_start: 0.8790 (t0) cc_final: 0.8392 (m-40)
REVERT: A  145 LEU cc_start: 0.9328 (tp) cc_final: 0.9127 (tp)
REVERT: A  219 GLN cc_start: 0.8934 (tp40) cc_final: 0.8286 (tp-100)
REVERT: A  221 LEU cc_start: 0.9650 (tt) cc_final: 0.9418 (mt)
REVERT: A  229 HIS cc_start: 0.8410 (t-170) cc_final: 0.8130 (t-170)
REVERT: A  400 ASP cc_start: 0.9095 (m-30) cc_final: 0.8621 (t0)
REVERT: A  414 GLU cc_start: 0.8948 (pp20) cc_final: 0.8735 (pp20)
REVERT: A  586 GLN cc_start: 0.9106 (tt0) cc_final: 0.8814 (tp-100)
REVERT: A  587 TYR cc_start: 0.8347 (m-80) cc_final: 0.7861 (m-80)
REVERT: A  595 MET cc_start: 0.8072 (mtt) cc_final: 0.7741 (mtt)
REVERT: A  640 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8572 (tt0)
REVERT: A  721 TYR cc_start: 0.9199 (m-80) cc_final: 0.8889 (m-80)
REVERT: A  782 VAL cc_start: 0.9335 (t) cc_final: 0.9132 (m)
REVERT: A  888 ARG cc_start: 0.8431 (tpp-160) cc_final: 0.7652 (tpm170)
REVERT: A 1024 GLU cc_start: 0.7702 (tp30) cc_final: 0.7426 (tp30)
  outliers start: 14
  outliers final: 7
  residues processed: 130
  average time/residue: 0.0800
  time to fit residues: 15.0242
Evaluate side-chains
  104 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
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  479 GLN
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 7 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 79 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.9580

-------------------------------------------------------------------------------
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 108 HIS
** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 325 GLN
A 698 HIS
A 771 HIS
A1016 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.071772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.056247 restraints weight = 34641.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.058289 restraints weight = 21181.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.059713 restraints weight = 14803.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.060760 restraints weight = 11319.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.061495 restraints weight = 9240.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3225
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3225 r_free = 0.3225    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 = 0.3225 r_free = 0.3225    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3225
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7896  Z= 0.137
  Angle     :  0.752  11.914  10708  Z= 0.363
  Chirality :  0.046   0.253   1174
  Planarity :  0.005   0.048   1398
  Dihedral  :  4.461  18.898   1037
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 16.20 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.27), residues: 965
  helix:  1.00 (0.24), residues: 462
  sheet:  0.74 (0.38), residues: 165
  loop : -0.71 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 505 
 TYR   0.019   0.001   TYR A 721 
 PHE   0.022   0.002   PHE A 699 
 TRP   0.038   0.003   TRP A 455 
 HIS   0.012   0.001   HIS A 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7896)
  covalent geometry    : angle       0.75227 (10708)
  hydrogen bonds       : bond        0.03829 (  426)
  hydrogen bonds       : angle       5.08927 ( 1342)

*********************** 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
  126 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8173 (t80)
REVERT: A   85 ASN cc_start: 0.8780 (t0) cc_final: 0.8065 (m-40)
REVERT: A  219 GLN cc_start: 0.9102 (tp40) cc_final: 0.8417 (tp-100)
REVERT: A  229 HIS cc_start: 0.8420 (t-170) cc_final: 0.8195 (t-170)
REVERT: A  400 ASP cc_start: 0.9098 (m-30) cc_final: 0.8661 (t0)
REVERT: A  414 GLU cc_start: 0.8990 (pp20) cc_final: 0.8708 (pp20)
REVERT: A  446 MET cc_start: 0.8933 (mmp) cc_final: 0.8693 (mmp)
REVERT: A  586 GLN cc_start: 0.8974 (tt0) cc_final: 0.8767 (tp-100)
REVERT: A  587 TYR cc_start: 0.8127 (m-80) cc_final: 0.7779 (m-80)
REVERT: A  595 MET cc_start: 0.8036 (mtt) cc_final: 0.7705 (mtt)
REVERT: A  640 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8579 (tt0)
REVERT: A  659 MET cc_start: 0.7750 (mmt) cc_final: 0.7441 (mmt)
REVERT: A  721 TYR cc_start: 0.9236 (m-80) cc_final: 0.8933 (m-80)
REVERT: A  750 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8540 (pttm)
REVERT: A  888 ARG cc_start: 0.8393 (tpp-160) cc_final: 0.7451 (tpm170)
REVERT: A  890 MET cc_start: 0.9188 (tpp) cc_final: 0.8957 (tpp)
  outliers start: 13
  outliers final: 7
  residues processed: 119
  average time/residue: 0.0856
  time to fit residues: 14.5453
Evaluate side-chains
  105 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
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  108 HIS
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  750 LYS
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 55 optimal weight:    0.9990
   chunk 92 optimal weight:    0.7980
   chunk 83 optimal weight:   20.0000
   chunk 86 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 12 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0770
   chunk 38 optimal weight:    1.9990
   chunk 84 optimal weight:    8.9990
   chunk 53 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.7142

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

Flipped N/Q/H residues before XYZ refinement:
A 104 HIS
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.073150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.057573 restraints weight = 35364.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.059601 restraints weight = 22079.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.061007 restraints weight = 15668.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.062055 restraints weight = 12133.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.062833 restraints weight = 9942.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3278
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3278
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7896  Z= 0.127
  Angle     :  0.723  13.202  10708  Z= 0.348
  Chirality :  0.046   0.416   1174
  Planarity :  0.005   0.044   1398
  Dihedral  :  4.385  17.697   1037
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 17.95 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.27), residues: 965
  helix:  1.08 (0.24), residues: 460
  sheet:  0.66 (0.39), residues: 164
  loop : -0.61 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 505 
 TYR   0.017   0.001   TYR A 721 
 PHE   0.022   0.002   PHE A 374 
 TRP   0.024   0.002   TRP A 455 
 HIS   0.011   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7896)
  covalent geometry    : angle       0.72256 (10708)
  hydrogen bonds       : bond        0.03497 (  426)
  hydrogen bonds       : angle       5.04841 ( 1342)

*********************** 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
  130 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8144 (t80)
REVERT: A  104 HIS cc_start: 0.7962 (OUTLIER) cc_final: 0.7712 (t-90)
REVERT: A  219 GLN cc_start: 0.9156 (tp40) cc_final: 0.8464 (tp-100)
REVERT: A  388 TYR cc_start: 0.8393 (p90) cc_final: 0.8115 (p90)
REVERT: A  400 ASP cc_start: 0.9090 (m-30) cc_final: 0.8866 (m-30)
REVERT: A  414 GLU cc_start: 0.9011 (pp20) cc_final: 0.8680 (pp20)
REVERT: A  510 TYR cc_start: 0.5868 (t80) cc_final: 0.5650 (t80)
REVERT: A  587 TYR cc_start: 0.8060 (m-80) cc_final: 0.7740 (m-80)
REVERT: A  595 MET cc_start: 0.7819 (mtt) cc_final: 0.7546 (mtt)
REVERT: A  659 MET cc_start: 0.7860 (mmt) cc_final: 0.7521 (mmt)
REVERT: A  721 TYR cc_start: 0.9298 (m-80) cc_final: 0.8965 (m-80)
REVERT: A  868 GLU cc_start: 0.7363 (tp30) cc_final: 0.6983 (tp30)
REVERT: A  888 ARG cc_start: 0.8417 (tpp-160) cc_final: 0.7596 (tpm170)
  outliers start: 14
  outliers final: 5
  residues processed: 123
  average time/residue: 0.0774
  time to fit residues: 13.8536
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  : 0.322 
-------------------------------------------------------------------------------
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  104 HIS
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  203 PHE
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  671 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 24 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   chunk 88 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   chunk 43 optimal weight:    0.6980
   chunk 79 optimal weight:    3.9990
   chunk 8 optimal weight:   10.0000
   chunk 25 optimal weight:    0.0870
   chunk 85 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    3.1564

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

Flipped N/Q/H residues before XYZ refinement:
A 104 HIS
** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 310 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.069548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.054798 restraints weight = 36171.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.056731 restraints weight = 22621.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.058037 restraints weight = 16031.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.059032 restraints weight = 12493.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.059732 restraints weight = 10225.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3213
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.3964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7896  Z= 0.222
  Angle     :  0.763  12.252  10708  Z= 0.380
  Chirality :  0.047   0.404   1174
  Planarity :  0.005   0.047   1398
  Dihedral  :  4.615  18.667   1037
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 16.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 18.18 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.27), residues: 965
  helix:  1.11 (0.24), residues: 466
  sheet:  0.36 (0.38), residues: 169
  loop : -0.77 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1037 
 TYR   0.015   0.002   TYR A  76 
 PHE   0.023   0.002   PHE A 693 
 TRP   0.022   0.002   TRP A 455 
 HIS   0.028   0.003   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 7896)
  covalent geometry    : angle       0.76309 (10708)
  hydrogen bonds       : bond        0.03700 (  426)
  hydrogen bonds       : angle       5.16559 ( 1342)

*********************** 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
  115 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.317 
Fit side-chains
REVERT: A   61 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8222 (t80)
REVERT: A  219 GLN cc_start: 0.9171 (tp40) cc_final: 0.8476 (tp-100)
REVERT: A  229 HIS cc_start: 0.8515 (t-170) cc_final: 0.8314 (t-170)
REVERT: A  388 TYR cc_start: 0.8400 (p90) cc_final: 0.8061 (p90)
REVERT: A  400 ASP cc_start: 0.9108 (m-30) cc_final: 0.8890 (m-30)
REVERT: A  414 GLU cc_start: 0.9095 (pp20) cc_final: 0.8764 (pp20)
REVERT: A  595 MET cc_start: 0.7914 (mtt) cc_final: 0.7693 (mtp)
REVERT: A  659 MET cc_start: 0.8053 (mmt) cc_final: 0.7711 (mmt)
REVERT: A  721 TYR cc_start: 0.9432 (m-80) cc_final: 0.9053 (m-80)
REVERT: A  888 ARG cc_start: 0.8557 (tpp-160) cc_final: 0.7658 (tpm170)
  outliers start: 15
  outliers final: 9
  residues processed: 108
  average time/residue: 0.0777
  time to fit residues: 12.2703
Evaluate side-chains
  99 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  643 THR
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 30 optimal weight:    0.0000
   chunk 55 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0970
   chunk 27 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 81 optimal weight:    7.9990
   chunk 64 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3495 r_free = 0.3495 target = 0.072019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.057025 restraints weight = 35356.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.059068 restraints weight = 21904.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.060473 restraints weight = 15412.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.061517 restraints weight = 11891.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.062255 restraints weight = 9686.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3277
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3277 r_free = 0.3277    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3277 r_free = 0.3277    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3277
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.4191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7896  Z= 0.130
  Angle     :  0.747  14.728  10708  Z= 0.357
  Chirality :  0.047   0.412   1174
  Planarity :  0.005   0.046   1398
  Dihedral  :  4.436  16.864   1037
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 20.98 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.27), residues: 965
  helix:  1.19 (0.25), residues: 461
  sheet:  0.44 (0.38), residues: 164
  loop : -0.54 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 801 
 TYR   0.013   0.001   TYR A 721 
 PHE   0.022   0.002   PHE A 217 
 TRP   0.020   0.002   TRP A 455 
 HIS   0.020   0.001   HIS A 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 7896)
  covalent geometry    : angle       0.74704 (10708)
  hydrogen bonds       : bond        0.03402 (  426)
  hydrogen bonds       : angle       4.99403 ( 1342)

*********************** 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
  112 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8181 (t80)
REVERT: A   85 ASN cc_start: 0.7904 (m-40) cc_final: 0.6996 (m-40)
REVERT: A  126 MET cc_start: 0.8226 (mmm) cc_final: 0.7921 (tpt)
REVERT: A  219 GLN cc_start: 0.9189 (tp40) cc_final: 0.8516 (tp-100)
REVERT: A  229 HIS cc_start: 0.8293 (t-170) cc_final: 0.7952 (t-170)
REVERT: A  388 TYR cc_start: 0.8355 (p90) cc_final: 0.8089 (p90)
REVERT: A  400 ASP cc_start: 0.9118 (m-30) cc_final: 0.8894 (m-30)
REVERT: A  414 GLU cc_start: 0.9061 (pp20) cc_final: 0.8674 (pp20)
REVERT: A  595 MET cc_start: 0.7868 (mtt) cc_final: 0.7582 (mtt)
REVERT: A  599 ARG cc_start: 0.8350 (mtt90) cc_final: 0.8149 (mtt90)
REVERT: A  646 MET cc_start: 0.8318 (mmm) cc_final: 0.8060 (mmm)
REVERT: A  659 MET cc_start: 0.8016 (mmt) cc_final: 0.7128 (mmt)
REVERT: A  721 TYR cc_start: 0.9399 (m-80) cc_final: 0.8920 (m-80)
REVERT: A  868 GLU cc_start: 0.7428 (tp30) cc_final: 0.7058 (tp30)
REVERT: A  888 ARG cc_start: 0.8548 (tpp-160) cc_final: 0.7795 (tpm170)
  outliers start: 13
  outliers final: 6
  residues processed: 106
  average time/residue: 0.0817
  time to fit residues: 12.5343
Evaluate side-chains
  102 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  647 SER
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 64 optimal weight:    0.6980
   chunk 62 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 71 optimal weight:    6.9990
   chunk 41 optimal weight:    8.9990
   chunk 21 optimal weight:    0.0570
   chunk 27 optimal weight:    4.9990
   chunk 20 optimal weight:    9.9990
   chunk 48 optimal weight:    9.9990
   chunk 55 optimal weight:    0.0870
   chunk 79 optimal weight:    0.0970
   overall best weight:    0.3674

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

Flipped N/Q/H residues before XYZ refinement:
A 104 HIS
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.072671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.057684 restraints weight = 34283.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.059716 restraints weight = 21304.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.061126 restraints weight = 15041.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.062198 restraints weight = 11584.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.062936 restraints weight = 9412.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3300
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3300 r_free = 0.3300    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3300 r_free = 0.3300    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3300
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.4414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7896  Z= 0.119
  Angle     :  0.717  14.763  10708  Z= 0.339
  Chirality :  0.046   0.429   1174
  Planarity :  0.005   0.044   1398
  Dihedral  :  4.262  15.956   1037
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 21.33 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.28), residues: 965
  helix:  1.34 (0.25), residues: 459
  sheet:  0.45 (0.38), residues: 165
  loop : -0.45 (0.36), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 801 
 TYR   0.022   0.001   TYR A 450 
 PHE   0.027   0.002   PHE A 389 
 TRP   0.022   0.001   TRP A 455 
 HIS   0.015   0.001   HIS A 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 7896)
  covalent geometry    : angle       0.71661 (10708)
  hydrogen bonds       : bond        0.03202 (  426)
  hydrogen bonds       : angle       4.79515 ( 1342)

*********************** 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
  121 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8240 (t80)
REVERT: A   85 ASN cc_start: 0.7769 (m-40) cc_final: 0.6947 (m-40)
REVERT: A  126 MET cc_start: 0.8112 (mmm) cc_final: 0.7777 (tpt)
REVERT: A  219 GLN cc_start: 0.9220 (tp40) cc_final: 0.8557 (tp-100)
REVERT: A  229 HIS cc_start: 0.8270 (t-170) cc_final: 0.7713 (t-170)
REVERT: A  388 TYR cc_start: 0.8240 (p90) cc_final: 0.7950 (p90)
REVERT: A  400 ASP cc_start: 0.9138 (m-30) cc_final: 0.8935 (m-30)
REVERT: A  414 GLU cc_start: 0.9156 (pp20) cc_final: 0.8783 (pp20)
REVERT: A  436 MET cc_start: 0.8750 (mtt) cc_final: 0.8475 (mtt)
REVERT: A  595 MET cc_start: 0.7856 (mtt) cc_final: 0.7574 (mtt)
REVERT: A  646 MET cc_start: 0.8145 (mmm) cc_final: 0.7721 (mmm)
REVERT: A  659 MET cc_start: 0.8098 (mmt) cc_final: 0.7255 (mmt)
REVERT: A  721 TYR cc_start: 0.9416 (m-80) cc_final: 0.8907 (m-80)
REVERT: A  888 ARG cc_start: 0.8588 (tpp-160) cc_final: 0.8295 (tpp-160)
  outliers start: 12
  outliers final: 6
  residues processed: 115
  average time/residue: 0.0808
  time to fit residues: 13.4553
Evaluate side-chains
  106 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
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  163 TYR
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  889 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 16 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 87 optimal weight:    6.9990
   chunk 91 optimal weight:    7.9990
   chunk 59 optimal weight:    6.9990
   chunk 85 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 64 optimal weight:    0.3980
   overall best weight:    2.6788

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3448 r_free = 0.3448 target = 0.070054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.055191 restraints weight = 35341.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.057102 restraints weight = 21852.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.058499 restraints weight = 15448.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.059506 restraints weight = 11843.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.060225 restraints weight = 9652.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.4645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7896  Z= 0.192
  Angle     :  0.771  13.750  10708  Z= 0.374
  Chirality :  0.047   0.426   1174
  Planarity :  0.005   0.049   1398
  Dihedral  :  4.445  17.204   1037
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 17.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 22.38 %
    Favored  : 76.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.27), residues: 965
  helix:  1.14 (0.24), residues: 463
  sheet:  0.40 (0.38), residues: 165
  loop : -0.47 (0.36), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 599 
 TYR   0.021   0.002   TYR A 538 
 PHE   0.028   0.002   PHE A 493 
 TRP   0.030   0.003   TRP A 455 
 HIS   0.013   0.002   HIS A 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 7896)
  covalent geometry    : angle       0.77113 (10708)
  hydrogen bonds       : bond        0.03416 (  426)
  hydrogen bonds       : angle       4.88479 ( 1342)

*********************** 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
  106 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8292 (t80)
REVERT: A  126 MET cc_start: 0.8232 (mmm) cc_final: 0.7927 (tpt)
REVERT: A  219 GLN cc_start: 0.9178 (tp40) cc_final: 0.8491 (tp-100)
REVERT: A  229 HIS cc_start: 0.8454 (t-170) cc_final: 0.8000 (t-170)
REVERT: A  388 TYR cc_start: 0.8483 (p90) cc_final: 0.8277 (p90)
REVERT: A  414 GLU cc_start: 0.9183 (pp20) cc_final: 0.8788 (pp20)
REVERT: A  595 MET cc_start: 0.8014 (mtt) cc_final: 0.7763 (mtp)
REVERT: A  646 MET cc_start: 0.7993 (mmm) cc_final: 0.7681 (mmm)
REVERT: A  659 MET cc_start: 0.8202 (mmt) cc_final: 0.7895 (mmt)
REVERT: A  721 TYR cc_start: 0.9438 (m-80) cc_final: 0.9135 (m-80)
REVERT: A  888 ARG cc_start: 0.8701 (tpp-160) cc_final: 0.8413 (tpp-160)
  outliers start: 11
  outliers final: 6
  residues processed: 102
  average time/residue: 0.0864
  time to fit residues: 12.6417
Evaluate side-chains
  99 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
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  175 LEU
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  889 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 74 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 95 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 47 optimal weight:    9.9990
   chunk 41 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9980
   chunk 16 optimal weight:    4.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 745 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.071572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.056566 restraints weight = 35060.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.058464 restraints weight = 22063.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.059826 restraints weight = 15758.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.060881 restraints weight = 12224.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.061449 restraints weight = 9994.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3258
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3258 r_free = 0.3258    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3258 r_free = 0.3258    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3258
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.4808

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= 0.134
  Angle     :  0.771  14.823  10708  Z= 0.366
  Chirality :  0.047   0.412   1174
  Planarity :  0.005   0.045   1398
  Dihedral  :  4.331  15.721   1037
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 22.73 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.28), residues: 965
  helix:  1.18 (0.24), residues: 462
  sheet:  0.42 (0.39), residues: 159
  loop : -0.47 (0.36), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 505 
 TYR   0.020   0.001   TYR A 538 
 PHE   0.020   0.002   PHE A 217 
 TRP   0.025   0.002   TRP A 455 
 HIS   0.013   0.001   HIS A 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 7896)
  covalent geometry    : angle       0.77077 (10708)
  hydrogen bonds       : bond        0.03308 (  426)
  hydrogen bonds       : angle       4.84298 ( 1342)

*********************** 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
  111 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8244 (t80)
REVERT: A  126 MET cc_start: 0.8157 (mmm) cc_final: 0.7827 (tpt)
REVERT: A  219 GLN cc_start: 0.9189 (tp40) cc_final: 0.8480 (tp-100)
REVERT: A  229 HIS cc_start: 0.8408 (t-170) cc_final: 0.7910 (t-170)
REVERT: A  388 TYR cc_start: 0.8398 (p90) cc_final: 0.7827 (p90)
REVERT: A  414 GLU cc_start: 0.9172 (pp20) cc_final: 0.8764 (pp20)
REVERT: A  659 MET cc_start: 0.8223 (mmt) cc_final: 0.7933 (mmt)
REVERT: A  721 TYR cc_start: 0.9442 (m-80) cc_final: 0.9113 (m-80)
REVERT: A  868 GLU cc_start: 0.7413 (tp30) cc_final: 0.6964 (tp30)
REVERT: A  888 ARG cc_start: 0.8709 (tpp-160) cc_final: 0.8404 (tpp-160)
  outliers start: 12
  outliers final: 7
  residues processed: 104
  average time/residue: 0.0904
  time to fit residues: 13.2092
Evaluate side-chains
  103 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
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  233 VAL
Chi-restraints excluded: chain A residue  671 LEU
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 5 optimal weight:    9.9990
   chunk 51 optimal weight:    8.9990
   chunk 65 optimal weight:    0.8980
   chunk 81 optimal weight:    4.9990
   chunk 86 optimal weight:    5.9990
   chunk 4 optimal weight:    8.9990
   chunk 68 optimal weight:    0.9980
   chunk 71 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    1.9990
   chunk 87 optimal weight:   10.0000
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3429 r_free = 0.3429 target = 0.068936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.054355 restraints weight = 35949.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.056172 restraints weight = 22599.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.057483 restraints weight = 16125.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.058392 restraints weight = 12491.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.059140 restraints weight = 10335.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3205
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3205
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.4997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   7896  Z= 0.212
  Angle     :  0.813  13.678  10708  Z= 0.397
  Chirality :  0.048   0.433   1174
  Planarity :  0.005   0.044   1398
  Dihedral  :  4.584  17.625   1037
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 19.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 23.43 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.27), residues: 965
  helix:  1.02 (0.24), residues: 463
  sheet:  0.19 (0.40), residues: 152
  loop : -0.52 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 173 
 TYR   0.032   0.002   TYR A 450 
 PHE   0.024   0.002   PHE A 217 
 TRP   0.023   0.003   TRP A 455 
 HIS   0.011   0.002   HIS A 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 7896)
  covalent geometry    : angle       0.81285 (10708)
  hydrogen bonds       : bond        0.03610 (  426)
  hydrogen bonds       : angle       5.00798 ( 1342)

********************** 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
  100 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8311 (t80)
REVERT: A  126 MET cc_start: 0.8251 (mmm) cc_final: 0.7961 (tpt)
REVERT: A  219 GLN cc_start: 0.9237 (tp40) cc_final: 0.8526 (tp-100)
REVERT: A  229 HIS cc_start: 0.8592 (t-170) cc_final: 0.8147 (t-170)
REVERT: A  388 TYR cc_start: 0.8505 (p90) cc_final: 0.8007 (p90)
REVERT: A  595 MET cc_start: 0.8009 (mtp) cc_final: 0.7725 (mtt)
REVERT: A  659 MET cc_start: 0.8321 (mmt) cc_final: 0.8040 (mmt)
REVERT: A  868 GLU cc_start: 0.7480 (tp30) cc_final: 0.7085 (tp30)
REVERT: A  888 ARG cc_start: 0.8743 (tpp-160) cc_final: 0.8452 (tpp-160)
REVERT: A 1037 ARG cc_start: 0.8693 (mtp85) cc_final: 0.7926 (mtm180)
  outliers start: 8
  outliers final: 5
  residues processed: 96
  average time/residue: 0.0795
  time to fit residues: 11.2762
Evaluate side-chains
  99 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
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  191 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  233 VAL
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 94 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 88 optimal weight:    0.8980
   chunk 87 optimal weight:    6.9990
   chunk 49 optimal weight:    0.0070
   chunk 81 optimal weight:    0.9990
   chunk 1 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   chunk 10 optimal weight:    0.5980
   chunk 80 optimal weight:    6.9990
   chunk 95 optimal weight:    4.9990
   overall best weight:    1.1002

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 745 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.070980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.056040 restraints weight = 34573.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.057958 restraints weight = 21625.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.059360 restraints weight = 15344.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.060395 restraints weight = 11808.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.061117 restraints weight = 9625.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3256
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3256 r_free = 0.3256    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3256 r_free = 0.3256    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3256
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.5088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7896  Z= 0.135
  Angle     :  0.785  14.452  10708  Z= 0.374
  Chirality :  0.048   0.412   1174
  Planarity :  0.005   0.044   1398
  Dihedral  :  4.443  18.790   1037
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 24.01 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.27), residues: 965
  helix:  1.19 (0.24), residues: 459
  sheet:  0.19 (0.41), residues: 146
  loop : -0.46 (0.35), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 385 
 TYR   0.020   0.001   TYR A 538 
 PHE   0.019   0.002   PHE A 618 
 TRP   0.022   0.002   TRP A 455 
 HIS   0.012   0.001   HIS A 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7896)
  covalent geometry    : angle       0.78531 (10708)
  hydrogen bonds       : bond        0.03326 (  426)
  hydrogen bonds       : angle       4.89419 ( 1342)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1646.83 seconds
wall clock time: 29 minutes 21.89 seconds (1761.89 seconds total)