Starting phenix.real_space_refine
on Wed Feb 12 10:39:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xot_22279/02_2025/6xot_22279.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xot_22279/02_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_22279/02_2025/6xot_22279.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xot_22279/02_2025/6xot_22279.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xot_22279/02_2025/6xot_22279.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xot_22279/02_2025/6xot_22279.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      39      5.16       5
     C    4901      2.51       5
     N    1305      2.21       5
     O    1459      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7704
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7704
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 966, 7698
          Classifications: {'peptide': 966}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 903}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 966, 7698
          Classifications: {'peptide': 966}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 903}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 7882
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ASER A 723 " occ=0.42
      ... (10 atoms not shown)
      pdb=" OG BSER A 723 " occ=0.58
  Time building chain proxies: 7.69, per 1000 atoms: 1.00
  Number of scatterers: 7704
  At special positions: 0
  Unit cell: (83.032, 86.456, 101.864, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      39     16.00
     O    1459      8.00
     N    1305      7.00
     C    4901      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.79
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 7 sheets defined
      54.1% alpha, 23.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 39
      removed outlier: 3.796A  pdb=" N   ARG A  36 " --> pdb=" O   ALA A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 111
      removed outlier: 3.774A  pdb=" N   LEU A 111 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 128
      removed outlier: 3.827A  pdb=" N   ASN A 128 " --> pdb=" O   PHE A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 169
    Processing helix  chain 'A' and resid 173 through 181
    Processing helix  chain 'A' and resid 200 through 212
    Processing helix  chain 'A' and resid 212 through 226
    Processing helix  chain 'A' and resid 229 through 233
      removed outlier: 3.610A  pdb=" N   VAL A 233 " --> pdb=" O   THR A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 245
      removed outlier: 3.515A  pdb=" N   GLU A 244 " --> pdb=" O   CYS A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 258
    Processing helix  chain 'A' and resid 259 through 261
      No H-bonds generated for 'chain 'A' and resid 259 through 261'
    Processing helix  chain 'A' and resid 272 through 284
      removed outlier: 4.022A  pdb=" N   HIS A 276 " --> pdb=" O   PRO A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 288
      removed outlier: 3.559A  pdb=" N   PHE A 288 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 285 through 288'
    Processing helix  chain 'A' and resid 339 through 355
    Processing helix  chain 'A' and resid 359 through 366
    Processing helix  chain 'A' and resid 367 through 369
      No H-bonds generated for 'chain 'A' and resid 367 through 369'
    Processing helix  chain 'A' and resid 397 through 399
      No H-bonds generated for 'chain 'A' and resid 397 through 399'
    Processing helix  chain 'A' and resid 400 through 419
    Processing helix  chain 'A' and resid 421 through 438
      removed outlier: 3.652A  pdb=" N   ILE A 425 " --> pdb=" O   GLU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 457
      removed outlier: 4.620A  pdb=" N   SER A 453 " --> pdb=" O   SER A 449 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   CYS A 454 " --> pdb=" O   TYR A 450 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   HIS A 457 " --> pdb=" O   SER A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 465
    Processing helix  chain 'A' and resid 466 through 481
      removed outlier: 3.630A  pdb=" N   ASN A 481 " --> pdb=" O   CYS A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 494
    Processing helix  chain 'A' and resid 510 through 528
      removed outlier: 4.156A  pdb=" N   ALA A 528 " --> pdb=" O   GLN A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 550
    Processing helix  chain 'A' and resid 561 through 565
    Processing helix  chain 'A' and resid 608 through 613
      removed outlier: 3.567A  pdb=" N   ARG A 612 " --> pdb=" O   GLU A 609 " (cutoff:3.500A)
      Proline residue:  A 613  - end of helix
    Processing helix  chain 'A' and resid 614 through 622
    Processing helix  chain 'A' and resid 631 through 643
    Processing helix  chain 'A' and resid 676 through 690
    Processing helix  chain 'A' and resid 695 through 713
      removed outlier: 4.031A  pdb=" N   PHE A 699 " --> pdb=" O   GLU A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 717 through 727
    Processing helix  chain 'A' and resid 731 through 742
    Processing helix  chain 'A' and resid 742 through 755
      removed outlier: 3.724A  pdb=" N   VAL A 746 " --> pdb=" O   GLY A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 763
    Processing helix  chain 'A' and resid 764 through 773
    Processing helix  chain 'A' and resid 788 through 802
    Processing helix  chain 'A' and resid 877 through 894
      removed outlier: 4.355A  pdb=" N   ALA A 881 " --> pdb=" O   ASP A 877 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   SER A 882 " --> pdb=" O   PRO A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 901
    Processing helix  chain 'A' and resid 928 through 945
    Processing helix  chain 'A' and resid 948 through 964
      removed outlier: 3.551A  pdb=" N   ASP A 964 " --> pdb=" O   PHE A 960 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 968 through 972
      removed outlier: 3.762A  pdb=" N   LYS A 972 " --> pdb=" O   PRO A 969 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 979
    Processing helix  chain 'A' and resid 982 through 995
    Processing helix  chain 'A' and resid 997 through 1008
    Processing helix  chain 'A' and resid 1025 through 1030
    Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46
      removed outlier: 6.450A  pdb=" N   LYS A  66 " --> pdb=" O   ASN A  52 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   VAL A  54 " --> pdb=" O   ALA A  64 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   ALA A  64 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   SER A  56 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   LEU A  62 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   ARG A  75 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   THR A 267 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   LEU A  77 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   PHE A 134 " --> pdb=" O   SER A 149 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46
      removed outlier: 6.450A  pdb=" N   LYS A  66 " --> pdb=" O   ASN A  52 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   VAL A  54 " --> pdb=" O   ALA A  64 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   ALA A  64 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   SER A  56 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   LEU A  62 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   ARG A  75 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   THR A 267 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   LEU A  77 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 186
      removed outlier: 3.640A  pdb=" N   ARG A 183 " --> pdb=" O   LYS A 199 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LYS A 199 " --> pdb=" O   ARG A 183 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 311
      removed outlier: 6.298A  pdb=" N   ARG A 307 " --> pdb=" O   THR A 501 " (cutoff:3.500A)
      removed outlier: 7.783A  pdb=" N   SER A 503 " --> pdb=" O   ARG A 307 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   PHE A 309 " --> pdb=" O   SER A 503 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   THR A 326 " --> pdb=" O   GLY A 395 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   ALA A 387 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ASP A 373 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 311
      removed outlier: 6.298A  pdb=" N   ARG A 307 " --> pdb=" O   THR A 501 " (cutoff:3.500A)
      removed outlier: 7.783A  pdb=" N   SER A 503 " --> pdb=" O   ARG A 307 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   PHE A 309 " --> pdb=" O   SER A 503 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   THR A 326 " --> pdb=" O   GLY A 395 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   ALA A 387 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 575 through 579
      removed outlier: 3.742A  pdb=" N   ASP A 575 " --> pdb=" O   TYR A 587 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   VAL A 782 " --> pdb=" O   PRO A 584 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   GLN A 586 " --> pdb=" O   VAL A 782 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   ALA A 784 " --> pdb=" O   GLN A 586 " (cutoff:3.500A)
      removed outlier: 5.819A  pdb=" N   CYS A 588 " --> pdb=" O   ALA A 784 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LEU A 671 " --> pdb=" O   GLY A 645 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   GLY A 645 " --> pdb=" O   LEU A 671 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 912
      removed outlier: 3.551A  pdb=" N   GLY A 909 " --> pdb=" O   TYR A 921 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   VAL A 866 " --> pdb=" O   SER A 922 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   LYS A 854 " --> pdb=" O   ILE A1035 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   ARG A1037 " --> pdb=" O   LYS A 854 " (cutoff:3.500A)
      removed outlier: 5.894A  pdb=" N   HIS A 856 " --> pdb=" O   ARG A1037 " (cutoff:3.500A)

    465 hydrogen bonds defined for protein.
    1342 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.19

  Time building geometry restraints manager: 2.05 seconds

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

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

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

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

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

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

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

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.42 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     25.310
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.580
-------------------------------------------------------------------------------
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= 0.375
  Angle     :  1.071  10.580  10708  Z= 0.577
  Chirality :  0.061   0.345   1174
  Planarity :  0.007   0.058   1398
  Dihedral  : 14.015  88.752   2949
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.75 %
    Favored  : 98.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.24), residues: 965
  helix: -1.00 (0.20), residues: 449
  sheet:  0.31 (0.37), residues: 170
  loop : -1.48 (0.32), residues: 346

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

*********************** 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  : 0.883 
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: 0.2350
  time to fit residues: 61.9809
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  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    7.9990
   chunk 72 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 75 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 56 optimal weight:    4.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    2.5988

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

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

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.069878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.054771 restraints weight = 35230.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.056682 restraints weight = 21630.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.058059 restraints weight = 15233.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3135
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3135
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   7896  Z= 0.295
  Angle     :  0.813   9.711  10708  Z= 0.411
  Chirality :  0.048   0.231   1174
  Planarity :  0.006   0.048   1398
  Dihedral  :  4.687  21.670   1037
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 15.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 15.50 %
    Favored  : 82.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.26), residues: 965
  helix:  0.74 (0.24), residues: 461
  sheet:  0.52 (0.36), residues: 170
  loop : -0.90 (0.35), residues: 334

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

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

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8214 (t80)
REVERT: A   66 LYS cc_start: 0.9233 (ttmt) cc_final: 0.8880 (ptmm)
REVERT: A   85 ASN cc_start: 0.8843 (t0) cc_final: 0.8459 (m-40)
REVERT: A  219 GLN cc_start: 0.8968 (tp40) cc_final: 0.8340 (tp-100)
REVERT: A  229 HIS cc_start: 0.8450 (t-170) cc_final: 0.8192 (t-170)
REVERT: A  400 ASP cc_start: 0.9127 (m-30) cc_final: 0.8663 (t0)
REVERT: A  586 GLN cc_start: 0.9114 (tt0) cc_final: 0.8809 (tp-100)
REVERT: A  587 TYR cc_start: 0.8316 (m-80) cc_final: 0.7748 (m-80)
REVERT: A  595 MET cc_start: 0.8131 (mtt) cc_final: 0.7826 (mtt)
REVERT: A  640 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8606 (tt0)
REVERT: A  721 TYR cc_start: 0.9211 (m-80) cc_final: 0.8900 (m-80)
REVERT: A  782 VAL cc_start: 0.9346 (t) cc_final: 0.9133 (m)
REVERT: A  888 ARG cc_start: 0.8419 (tpp-160) cc_final: 0.8185 (tpp-160)
REVERT: A 1024 GLU cc_start: 0.7740 (tp30) cc_final: 0.7486 (tp30)
  outliers start: 14
  outliers final: 7
  residues processed: 127
  average time/residue: 0.1728
  time to fit residues: 31.5737
Evaluate side-chains
  101 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  679 ASP
Chi-restraints excluded: chain A residue  931 THR
Chi-restraints excluded: chain A residue  932 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9980
   chunk 32 optimal weight:    6.9990
   chunk 60 optimal weight:    0.8980
   chunk 84 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0870
   chunk 0 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   overall best weight:    1.7962

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

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

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.070482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.055204 restraints weight = 35516.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.057190 restraints weight = 21648.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.058566 restraints weight = 15150.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3156
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3156
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.3150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7896  Z= 0.231
  Angle     :  0.750  11.665  10708  Z= 0.366
  Chirality :  0.046   0.237   1174
  Planarity :  0.005   0.050   1398
  Dihedral  :  4.545  19.559   1037
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 15.97 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.27), residues: 965
  helix:  1.03 (0.24), residues: 462
  sheet:  0.58 (0.37), residues: 168
  loop : -0.70 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP A 455 
 HIS   0.012   0.002   HIS A 229 
 PHE   0.019   0.002   PHE A 977 
 TYR   0.017   0.001   TYR A 721 
 ARG   0.007   0.001   ARG A 505 

*********************** 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
  122 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8238 (t80)
REVERT: A   85 ASN cc_start: 0.8873 (t0) cc_final: 0.8638 (m-40)
REVERT: A  219 GLN cc_start: 0.9181 (tp40) cc_final: 0.8525 (tp-100)
REVERT: A  229 HIS cc_start: 0.8482 (t-170) cc_final: 0.8246 (t-170)
REVERT: A  400 ASP cc_start: 0.9129 (m-30) cc_final: 0.8655 (t0)
REVERT: A  587 TYR cc_start: 0.8072 (m-80) cc_final: 0.7826 (m-80)
REVERT: A  595 MET cc_start: 0.8071 (mtt) cc_final: 0.7702 (mtt)
REVERT: A  640 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8630 (tt0)
REVERT: A  659 MET cc_start: 0.7787 (mmt) cc_final: 0.7467 (mmt)
REVERT: A  721 TYR cc_start: 0.9269 (m-80) cc_final: 0.8950 (m-80)
REVERT: A  888 ARG cc_start: 0.8439 (tpp-160) cc_final: 0.7636 (tpm170)
REVERT: A  890 MET cc_start: 0.9182 (tpp) cc_final: 0.8958 (tpp)
REVERT: A 1024 GLU cc_start: 0.7832 (tp30) cc_final: 0.7607 (tp30)
  outliers start: 14
  outliers final: 8
  residues processed: 116
  average time/residue: 0.1854
  time to fit residues: 30.8547
Evaluate side-chains
  103 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  679 ASP
Chi-restraints excluded: chain A residue  931 THR
Chi-restraints excluded: chain A residue  932 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 69 optimal weight:    2.9990
   chunk 4 optimal weight:    8.9990
   chunk 30 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 61 optimal weight:    9.9990
   chunk 94 optimal weight:    6.9990
   chunk 6 optimal weight:    8.9990
   chunk 53 optimal weight:    0.0000
   overall best weight:    2.5790

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.069042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.054196 restraints weight = 35481.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.056134 restraints weight = 21472.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.057510 restraints weight = 14971.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3142
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3142
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.3730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7896  Z= 0.272
  Angle     :  0.767  12.375  10708  Z= 0.375
  Chirality :  0.047   0.406   1174
  Planarity :  0.005   0.045   1398
  Dihedral  :  4.606  22.731   1037
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 15.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.13 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.27), residues: 965
  helix:  1.13 (0.24), residues: 462
  sheet:  0.43 (0.38), residues: 169
  loop : -0.73 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 455 
 HIS   0.007   0.002   HIS A 229 
 PHE   0.025   0.002   PHE A 977 
 TYR   0.013   0.002   TYR A 143 
 ARG   0.004   0.001   ARG A 505 

*********************** 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
  125 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8308 (t80)
REVERT: A   85 ASN cc_start: 0.8938 (t0) cc_final: 0.8660 (m-40)
REVERT: A  219 GLN cc_start: 0.9179 (tp40) cc_final: 0.8528 (tp-100)
REVERT: A  229 HIS cc_start: 0.8587 (t-170) cc_final: 0.8181 (t-170)
REVERT: A  400 ASP cc_start: 0.9145 (m-30) cc_final: 0.8723 (t0)
REVERT: A  595 MET cc_start: 0.8046 (mtt) cc_final: 0.7811 (mtt)
REVERT: A  640 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8585 (tt0)
REVERT: A  659 MET cc_start: 0.8021 (mmt) cc_final: 0.7676 (mmt)
REVERT: A  671 LEU cc_start: 0.9081 (mp) cc_final: 0.8160 (tp)
REVERT: A  721 TYR cc_start: 0.9426 (m-80) cc_final: 0.9190 (m-80)
REVERT: A  888 ARG cc_start: 0.8530 (tpp-160) cc_final: 0.7777 (tpm170)
REVERT: A  971 ASP cc_start: 0.9092 (m-30) cc_final: 0.8796 (m-30)
REVERT: A  974 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8171 (mpp)
REVERT: A  985 MET cc_start: 0.9195 (ptp) cc_final: 0.8993 (ptp)
REVERT: A 1024 GLU cc_start: 0.7884 (tp30) cc_final: 0.7623 (tp30)
  outliers start: 20
  outliers final: 9
  residues processed: 115
  average time/residue: 0.1776
  time to fit residues: 29.0763
Evaluate side-chains
  109 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
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  203 PHE
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue  951 ASP
Chi-restraints excluded: chain A residue  974 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 86 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 74 optimal weight:   10.0000
   chunk 73 optimal weight:    0.7980
   chunk 95 optimal weight:    7.9990
   chunk 63 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
A  85 ASN
** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.068871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.054316 restraints weight = 35634.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.056159 restraints weight = 21982.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.057453 restraints weight = 15504.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3165
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3165 r_free = 0.3165    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3165 r_free = 0.3165    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3165
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.4129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7896  Z= 0.286
  Angle     :  0.756  12.185  10708  Z= 0.371
  Chirality :  0.047   0.403   1174
  Planarity :  0.005   0.047   1398
  Dihedral  :  4.695  19.816   1037
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 15.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 17.72 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.27), residues: 965
  helix:  1.03 (0.24), residues: 465
  sheet:  0.27 (0.39), residues: 166
  loop : -0.63 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 455 
 HIS   0.006   0.002   HIS A 498 
 PHE   0.019   0.002   PHE A 693 
 TYR   0.014   0.002   TYR A  76 
 ARG   0.004   0.001   ARG A 801 

*********************** 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
  121 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8263 (t80)
REVERT: A   85 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8642 (m-40)
REVERT: A  219 GLN cc_start: 0.9203 (tp40) cc_final: 0.8552 (tp-100)
REVERT: A  229 HIS cc_start: 0.8664 (t-170) cc_final: 0.8324 (t-170)
REVERT: A  388 TYR cc_start: 0.8440 (p90) cc_final: 0.7848 (p90)
REVERT: A  400 ASP cc_start: 0.9150 (m-30) cc_final: 0.8752 (t0)
REVERT: A  595 MET cc_start: 0.8025 (mtt) cc_final: 0.7762 (mtp)
REVERT: A  659 MET cc_start: 0.8153 (mmt) cc_final: 0.7817 (mmt)
REVERT: A  709 GLU cc_start: 0.9068 (tp30) cc_final: 0.8773 (tp30)
REVERT: A  721 TYR cc_start: 0.9463 (m-80) cc_final: 0.9151 (m-80)
REVERT: A  755 MET cc_start: 0.8504 (mtp) cc_final: 0.8284 (ttm)
REVERT: A  888 ARG cc_start: 0.8533 (tpp-160) cc_final: 0.7818 (tpm170)
REVERT: A  985 MET cc_start: 0.9212 (ptp) cc_final: 0.8964 (ptp)
REVERT: A 1024 GLU cc_start: 0.7952 (tp30) cc_final: 0.7690 (tp30)
  outliers start: 23
  outliers final: 12
  residues processed: 111
  average time/residue: 0.1681
  time to fit residues: 27.1261
Evaluate side-chains
  107 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  756 THR
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  889 LEU
Chi-restraints excluded: chain A residue  931 THR
Chi-restraints excluded: chain A residue  932 LEU
Chi-restraints excluded: chain A residue 1030 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 63 optimal weight:    9.9990
   chunk 25 optimal weight:    0.7980
   chunk 51 optimal weight:   20.0000
   chunk 74 optimal weight:    0.6980
   chunk 35 optimal weight:    0.3980
   chunk 57 optimal weight:    4.9990
   chunk 87 optimal weight:    4.9990
   chunk 91 optimal weight:    0.6980
   chunk 77 optimal weight:    4.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  85 ASN
A 204 ASN
** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.071552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.056714 restraints weight = 34169.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.058613 restraints weight = 21088.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.060026 restraints weight = 14894.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3231
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    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 = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3231
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.4250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7896  Z= 0.184
  Angle     :  0.737  14.822  10708  Z= 0.351
  Chirality :  0.046   0.394   1174
  Planarity :  0.005   0.045   1398
  Dihedral  :  4.499  20.164   1037
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 20.28 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.28), residues: 965
  helix:  1.13 (0.24), residues: 466
  sheet:  0.30 (0.40), residues: 164
  loop : -0.44 (0.36), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 455 
 HIS   0.005   0.001   HIS A 457 
 PHE   0.024   0.002   PHE A 217 
 TYR   0.020   0.001   TYR A 450 
 ARG   0.004   0.000   ARG A 801 

*********************** 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
  127 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.8225 (t80)
REVERT: A   85 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8432 (m-40)
REVERT: A  219 GLN cc_start: 0.9165 (tp40) cc_final: 0.8474 (tp-100)
REVERT: A  229 HIS cc_start: 0.8549 (t-170) cc_final: 0.8254 (t-170)
REVERT: A  388 TYR cc_start: 0.8393 (p90) cc_final: 0.8054 (p90)
REVERT: A  393 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8591 (tp)
REVERT: A  400 ASP cc_start: 0.9101 (m-30) cc_final: 0.8593 (t0)
REVERT: A  436 MET cc_start: 0.8770 (mtt) cc_final: 0.8512 (mtt)
REVERT: A  659 MET cc_start: 0.8187 (mmt) cc_final: 0.7871 (mmt)
REVERT: A  721 TYR cc_start: 0.9406 (m-80) cc_final: 0.8822 (m-80)
REVERT: A  797 GLU cc_start: 0.8626 (pt0) cc_final: 0.8328 (pt0)
REVERT: A  868 GLU cc_start: 0.7424 (tp30) cc_final: 0.7080 (tp30)
REVERT: A  888 ARG cc_start: 0.8610 (tpp-160) cc_final: 0.7898 (tpm170)
REVERT: A  972 LYS cc_start: 0.8060 (ptpt) cc_final: 0.7713 (ptpp)
REVERT: A  985 MET cc_start: 0.9221 (ptp) cc_final: 0.9006 (ptp)
REVERT: A 1024 GLU cc_start: 0.8036 (tp30) cc_final: 0.7706 (tp30)
  outliers start: 10
  outliers final: 6
  residues processed: 123
  average time/residue: 0.1842
  time to fit residues: 32.1409
Evaluate side-chains
  111 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
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   85 ASN
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  889 LEU
Chi-restraints excluded: chain A residue  974 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 26 optimal weight:    0.1980
   chunk 73 optimal weight:    0.2980
   chunk 78 optimal weight:    0.5980
   chunk 74 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 19 optimal weight:    0.1980
   chunk 57 optimal weight:    0.0040
   chunk 47 optimal weight:   10.0000
   chunk 31 optimal weight:    7.9990
   chunk 60 optimal weight:    6.9990
   overall best weight:    0.2592

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.072375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.057339 restraints weight = 34836.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.059308 restraints weight = 21536.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.060720 restraints weight = 15169.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3250
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    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 = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3250
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.4450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7896  Z= 0.185
  Angle     :  0.781  16.406  10708  Z= 0.364
  Chirality :  0.047   0.428   1174
  Planarity :  0.005   0.056   1398
  Dihedral  :  4.395  18.317   1037
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 21.33 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.28), residues: 965
  helix:  1.14 (0.24), residues: 465
  sheet:  0.39 (0.41), residues: 156
  loop : -0.59 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 455 
 HIS   0.004   0.001   HIS A 457 
 PHE   0.022   0.002   PHE A 217 
 TYR   0.018   0.001   TYR A 450 
 ARG   0.012   0.000   ARG A 534 

*********************** 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
  120 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8204 (t80)
REVERT: A  219 GLN cc_start: 0.9185 (tp40) cc_final: 0.8485 (tp-100)
REVERT: A  229 HIS cc_start: 0.8510 (t-170) cc_final: 0.8225 (t-170)
REVERT: A  388 TYR cc_start: 0.8365 (p90) cc_final: 0.8130 (p90)
REVERT: A  393 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8529 (tp)
REVERT: A  400 ASP cc_start: 0.9116 (m-30) cc_final: 0.8563 (t0)
REVERT: A  595 MET cc_start: 0.7996 (mtp) cc_final: 0.7659 (mtt)
REVERT: A  659 MET cc_start: 0.8196 (mmt) cc_final: 0.7910 (mmt)
REVERT: A  721 TYR cc_start: 0.9420 (m-80) cc_final: 0.8830 (m-80)
REVERT: A  797 GLU cc_start: 0.8641 (pt0) cc_final: 0.8313 (pt0)
REVERT: A  888 ARG cc_start: 0.8606 (tpp-160) cc_final: 0.7921 (tpm170)
REVERT: A 1024 GLU cc_start: 0.8051 (tp30) cc_final: 0.7706 (tp30)
  outliers start: 10
  outliers final: 5
  residues processed: 116
  average time/residue: 0.1711
  time to fit residues: 28.5501
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  : 0.951 
-------------------------------------------------------------------------------
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  393 LEU
Chi-restraints excluded: chain A residue  671 LEU
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 26 optimal weight:    2.9990
   chunk 14 optimal weight:   10.0000
   chunk 36 optimal weight:    9.9990
   chunk 83 optimal weight:   20.0000
   chunk 12 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   chunk 30 optimal weight:    6.9990
   chunk 63 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 28 optimal weight:   20.0000
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
A  85 ASN
** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.069694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.054872 restraints weight = 36122.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.056744 restraints weight = 22477.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.058091 restraints weight = 15954.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3194
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3194
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.4674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   7896  Z= 0.279
  Angle     :  0.787  13.623  10708  Z= 0.381
  Chirality :  0.047   0.419   1174
  Planarity :  0.005   0.056   1398
  Dihedral  :  4.522  19.640   1037
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 16.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 22.14 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.28), residues: 965
  helix:  1.13 (0.24), residues: 465
  sheet:  0.23 (0.40), residues: 163
  loop : -0.42 (0.36), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP A 455 
 HIS   0.008   0.001   HIS A 498 
 PHE   0.018   0.002   PHE A 618 
 TYR   0.016   0.002   TYR A 587 
 ARG   0.011   0.001   ARG A 534 

*********************** 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
  110 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8310 (t80)
REVERT: A  219 GLN cc_start: 0.9216 (tp40) cc_final: 0.8488 (tp-100)
REVERT: A  229 HIS cc_start: 0.8668 (t-170) cc_final: 0.8342 (t-170)
REVERT: A  388 TYR cc_start: 0.8418 (p90) cc_final: 0.8181 (p90)
REVERT: A  393 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8675 (tp)
REVERT: A  400 ASP cc_start: 0.9161 (m-30) cc_final: 0.8670 (t0)
REVERT: A  436 MET cc_start: 0.8817 (mtt) cc_final: 0.8586 (mtt)
REVERT: A  516 GLN cc_start: 0.9292 (mt0) cc_final: 0.9040 (mt0)
REVERT: A  595 MET cc_start: 0.7954 (mtp) cc_final: 0.7664 (mtt)
REVERT: A  659 MET cc_start: 0.8304 (mmt) cc_final: 0.8000 (mmt)
REVERT: A  680 MET cc_start: 0.8831 (ttt) cc_final: 0.8620 (mtp)
REVERT: A  721 TYR cc_start: 0.9414 (m-80) cc_final: 0.8959 (m-80)
REVERT: A  853 MET cc_start: 0.8807 (mpp) cc_final: 0.8547 (mmp)
REVERT: A  888 ARG cc_start: 0.8689 (tpp-160) cc_final: 0.8406 (tpp-160)
REVERT: A 1024 GLU cc_start: 0.8135 (tp30) cc_final: 0.7817 (tp30)
REVERT: A 1037 ARG cc_start: 0.8680 (mtp85) cc_final: 0.8374 (mtp85)
  outliers start: 11
  outliers final: 7
  residues processed: 106
  average time/residue: 0.1713
  time to fit residues: 26.4032
Evaluate side-chains
  104 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
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  233 VAL
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  889 LEU
Chi-restraints excluded: chain A residue 1030 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 82 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 88 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9990
   chunk 63 optimal weight:    8.9990
   chunk 69 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.9582

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.071349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.056311 restraints weight = 35789.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.058291 restraints weight = 22136.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.059675 restraints weight = 15600.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3232
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3232 r_free = 0.3232    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3232 r_free = 0.3232    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3232
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.4791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7896  Z= 0.207
  Angle     :  0.776  14.569  10708  Z= 0.368
  Chirality :  0.047   0.408   1174
  Planarity :  0.005   0.050   1398
  Dihedral  :  4.428  19.722   1037
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 22.26 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.28), residues: 965
  helix:  1.19 (0.24), residues: 465
  sheet:  0.24 (0.41), residues: 158
  loop : -0.41 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 455 
 HIS   0.004   0.001   HIS A 719 
 PHE   0.018   0.001   PHE A 618 
 TYR   0.038   0.001   TYR A 450 
 ARG   0.010   0.000   ARG A 534 

*********************** 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
  112 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8306 (t80)
REVERT: A  219 GLN cc_start: 0.9206 (tp40) cc_final: 0.8466 (tp-100)
REVERT: A  229 HIS cc_start: 0.8647 (t-170) cc_final: 0.8347 (t-170)
REVERT: A  388 TYR cc_start: 0.8367 (p90) cc_final: 0.8100 (p90)
REVERT: A  393 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8637 (tp)
REVERT: A  400 ASP cc_start: 0.9118 (m-30) cc_final: 0.8595 (t0)
REVERT: A  436 MET cc_start: 0.8829 (mtt) cc_final: 0.8569 (mtt)
REVERT: A  516 GLN cc_start: 0.9317 (mt0) cc_final: 0.9108 (mt0)
REVERT: A  595 MET cc_start: 0.7926 (mtp) cc_final: 0.7668 (mtt)
REVERT: A  659 MET cc_start: 0.8300 (mmt) cc_final: 0.7753 (mmt)
REVERT: A  721 TYR cc_start: 0.9412 (m-80) cc_final: 0.8939 (m-80)
REVERT: A  868 GLU cc_start: 0.7463 (tp30) cc_final: 0.7034 (tp30)
REVERT: A  888 ARG cc_start: 0.8709 (tpp-160) cc_final: 0.8432 (tpp-160)
REVERT: A  912 LEU cc_start: 0.8345 (tp) cc_final: 0.8086 (tp)
REVERT: A 1024 GLU cc_start: 0.8120 (tp30) cc_final: 0.7756 (tp30)
REVERT: A 1037 ARG cc_start: 0.8556 (mtp85) cc_final: 0.8268 (mtp85)
  outliers start: 9
  outliers final: 5
  residues processed: 107
  average time/residue: 0.1775
  time to fit residues: 27.5304
Evaluate side-chains
  109 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
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  393 LEU
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 1 optimal weight:    6.9990
   chunk 5 optimal weight:   10.0000
   chunk 26 optimal weight:    8.9990
   chunk 54 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   overall best weight:    1.5986

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.070605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.055816 restraints weight = 35796.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.057730 restraints weight = 22197.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.058972 restraints weight = 15685.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3212
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.4917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7896  Z= 0.227
  Angle     :  0.796  14.213  10708  Z= 0.379
  Chirality :  0.047   0.417   1174
  Planarity :  0.005   0.054   1398
  Dihedral  :  4.447  18.233   1037
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 14.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 22.03 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.28), residues: 965
  helix:  1.20 (0.24), residues: 466
  sheet:  0.31 (0.41), residues: 157
  loop : -0.43 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 455 
 HIS   0.004   0.001   HIS A 719 
 PHE   0.019   0.001   PHE A 618 
 TYR   0.014   0.001   TYR A 587 
 ARG   0.011   0.001   ARG A 534 

********************** 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
  108 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8333 (t80)
REVERT: A  219 GLN cc_start: 0.9214 (tp40) cc_final: 0.8477 (tp-100)
REVERT: A  229 HIS cc_start: 0.8687 (t-170) cc_final: 0.8367 (t-170)
REVERT: A  388 TYR cc_start: 0.8382 (p90) cc_final: 0.8122 (p90)
REVERT: A  393 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8676 (tp)
REVERT: A  400 ASP cc_start: 0.9123 (m-30) cc_final: 0.8606 (t0)
REVERT: A  436 MET cc_start: 0.8824 (mtt) cc_final: 0.8581 (mtt)
REVERT: A  516 GLN cc_start: 0.9303 (mt0) cc_final: 0.9094 (mt0)
REVERT: A  595 MET cc_start: 0.7944 (mtp) cc_final: 0.7647 (mtt)
REVERT: A  659 MET cc_start: 0.8375 (mmt) cc_final: 0.7836 (mmt)
REVERT: A  721 TYR cc_start: 0.9416 (m-80) cc_final: 0.9018 (m-80)
REVERT: A  868 GLU cc_start: 0.7437 (tp30) cc_final: 0.7003 (tp30)
REVERT: A  888 ARG cc_start: 0.8754 (tpp-160) cc_final: 0.8485 (tpp-160)
REVERT: A  912 LEU cc_start: 0.8413 (tp) cc_final: 0.8154 (tp)
REVERT: A 1024 GLU cc_start: 0.8146 (tp30) cc_final: 0.7804 (tp30)
  outliers start: 9
  outliers final: 7
  residues processed: 104
  average time/residue: 0.1870
  time to fit residues: 28.2377
Evaluate side-chains
  107 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
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  393 LEU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  756 THR
Chi-restraints excluded: chain A residue  889 LEU
Chi-restraints excluded: chain A residue 1030 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 73 optimal weight:    0.0070
   chunk 39 optimal weight:    0.8980
   chunk 34 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 17 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 25 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   chunk 92 optimal weight:    8.9990
   chunk 69 optimal weight:    8.9990
   overall best weight:    1.9602

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.069950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.055185 restraints weight = 35343.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.057149 restraints weight = 21693.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.058562 restraints weight = 15201.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3204
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3204
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.5037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   7896  Z= 0.243
  Angle     :  0.792  14.400  10708  Z= 0.379
  Chirality :  0.047   0.403   1174
  Planarity :  0.005   0.047   1398
  Dihedral  :  4.468  20.604   1037
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 14.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 22.61 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.28), residues: 965
  helix:  1.22 (0.24), residues: 466
  sheet:  0.14 (0.42), residues: 151
  loop : -0.43 (0.36), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 455 
 HIS   0.005   0.001   HIS A 719 
 PHE   0.020   0.002   PHE A 618 
 TYR   0.037   0.002   TYR A 450 
 ARG   0.010   0.001   ARG A 534 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2974.83 seconds
wall clock time: 54 minutes 17.71 seconds (3257.71 seconds total)