Starting phenix.real_space_refine
on Tue Mar  3 17:27:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ln9_0928/03_2026/6ln9_0928.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ln9_0928/03_2026/6ln9_0928.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ln9_0928/03_2026/6ln9_0928.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ln9_0928/03_2026/6ln9_0928.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ln9_0928/03_2026/6ln9_0928.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ln9_0928/03_2026/6ln9_0928.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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: 7
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      54      5.16       5
     Be      1      3.05       5
     C    4860      2.51       5
     N    1273      2.21       5
     O    1420      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7612
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 987, 7607
          Classifications: {'peptide': 987}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 46, 'TRANS': 940}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 5
          Unusual residues: {' MG': 1, 'BEF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" F1  BEF A2001 " occ=0.00
      ... (2 atoms not shown)
      pdb="BE   BEF A2001 " occ=0.00
  Time building chain proxies: 1.93, per 1000 atoms: 0.25
  Number of scatterers: 7612
  At special positions: 0
  Unit cell: (87.15, 95.865, 144.42, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      54     16.00
     Mg      1     11.99
     F       3      9.00
     O    1420      8.00
     N    1273      7.00
     C    4860      6.00
     Be      1      4.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 875 " - pdb=" SG  CYS A 887 " distance=2.03

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 210.0 milliseconds
  

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1852

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 8 sheets defined
      50.2% alpha, 12.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 17
    Processing helix  chain 'A' and resid 25 through 37
    Processing helix  chain 'A' and resid 48 through 50
      No H-bonds generated for 'chain 'A' and resid 48 through 50'
    Processing helix  chain 'A' and resid 51 through 57
    Processing helix  chain 'A' and resid 60 through 76
    Processing helix  chain 'A' and resid 89 through 115
      removed outlier: 3.639A  pdb=" N   VAL A  93 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   ILE A  94 " --> pdb=" O   GLU A  90 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   LEU A  95 " --> pdb=" O   PRO A  91 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ALA A 102 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   VAL A 104 " --> pdb=" O   ALA A 100 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   GLY A 105 " --> pdb=" O   ASN A 101 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   GLU A 113 " --> pdb=" O   GLU A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 120
      removed outlier: 3.506A  pdb=" N   LYS A 120 " --> pdb=" O   GLU A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 242
    Processing helix  chain 'A' and resid 247 through 277
      removed outlier: 3.999A  pdb=" N   GLY A 277 " --> pdb=" O   ILE A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 306
      removed outlier: 4.158A  pdb=" N   TYR A 295 " --> pdb=" O   GLY A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 327
      removed outlier: 4.466A  pdb=" N   ALA A 313 " --> pdb=" O   GLU A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 419
    Processing helix  chain 'A' and resid 439 through 452
    Processing helix  chain 'A' and resid 463 through 468
    Processing helix  chain 'A' and resid 469 through 476
    Processing helix  chain 'A' and resid 520 through 522
      No H-bonds generated for 'chain 'A' and resid 520 through 522'
    Processing helix  chain 'A' and resid 537 through 552
      removed outlier: 3.547A  pdb=" N   LYS A 541 " --> pdb=" O   THR A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 586
    Processing helix  chain 'A' and resid 606 through 616
      removed outlier: 3.995A  pdb=" N   LYS A 611 " --> pdb=" O   ALA A 607 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ALA A 616 " --> pdb=" O   LEU A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 638
    Processing helix  chain 'A' and resid 654 through 659
    Processing helix  chain 'A' and resid 661 through 672
    Processing helix  chain 'A' and resid 679 through 693
    Processing helix  chain 'A' and resid 706 through 711
      removed outlier: 3.533A  pdb=" N   LYS A 711 " --> pdb=" O   ALA A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 729
    Processing helix  chain 'A' and resid 739 through 780
      removed outlier: 4.192A  pdb=" N   VAL A 743 " --> pdb=" O   PHE A 739 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ARG A 761 " --> pdb=" O   LYS A 757 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 807
      removed outlier: 4.290A  pdb=" N   ASP A 799 " --> pdb=" O   ASN A 795 " (cutoff:3.500A)
      Proline residue:  A 802  - end of helix
    Processing helix  chain 'A' and resid 829 through 857
      removed outlier: 3.559A  pdb=" N   PHE A 834 " --> pdb=" O   GLY A 830 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLY A 840 " --> pdb=" O   TYR A 836 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 888 through 891
      removed outlier: 3.785A  pdb=" N   GLU A 891 " --> pdb=" O   ALA A 888 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 888 through 891'
    Processing helix  chain 'A' and resid 892 through 914
      removed outlier: 4.339A  pdb=" N   MET A 896 " --> pdb=" O   SER A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 920 through 924
    Processing helix  chain 'A' and resid 925 through 928
    Processing helix  chain 'A' and resid 929 through 949
      removed outlier: 3.639A  pdb=" N   LEU A 947 " --> pdb=" O   HIS A 943 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   VAL A 949 " --> pdb=" O   LEU A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 951 through 955
    Processing helix  chain 'A' and resid 962 through 974
    Processing helix  chain 'A' and resid 974 through 990
      removed outlier: 3.959A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   TYR A 990 " --> pdb=" O   VAL A 986 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1014 through 1028
      removed outlier: 4.213A  pdb=" N   PHE A1018 " --> pdb=" O   ILE A1014 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   MET A1023 " --> pdb=" O   VAL A1019 " (cutoff:3.500A)
      Proline residue:  A1024  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 141
      removed outlier: 4.492A  pdb=" N   LYS A 128 " --> pdb=" O   GLU A 152 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   ILE A 150 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   MET A 220 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188
      removed outlier: 3.740A  pdb=" N   ASN A 213 " --> pdb=" O   ASP A 176 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 333
      removed outlier: 6.916A  pdb=" N   ALA A 718 " --> pdb=" O   LEU A 734 " (cutoff:3.500A)
      removed outlier: 7.748A  pdb=" N   GLY A 701 " --> pdb=" O   MET A 719 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 348
    Processing sheet with id=AA5, first strand: chain 'A' and resid 394 through 396
      removed outlier: 3.669A  pdb=" N   GLU A 394 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
      removed outlier: 4.672A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   GLY A 597 " --> pdb=" O   CYS A 364 " (cutoff:3.500A)
      removed outlier: 4.838A  pdb=" N   MET A 366 " --> pdb=" O   CYS A 595 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   CYS A 595 " --> pdb=" O   MET A 366 " (cutoff:3.500A)
      removed outlier: 5.647A  pdb=" N   ILE A 368 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 9.234A  pdb=" N   VAL A 593 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   LEU A 563 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   CYS A 595 " --> pdb=" O   LEU A 561 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   LEU A 561 " --> pdb=" O   CYS A 595 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   GLY A 597 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   ARG A 559 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   MET A 511 " --> pdb=" O   HIS A 566 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   THR A 499 " --> pdb=" O   LYS A 481 " (cutoff:3.500A)
      removed outlier: 5.428A  pdb=" N   LYS A 481 " --> pdb=" O   THR A 499 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 394 through 396
      removed outlier: 3.669A  pdb=" N   GLU A 394 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
      removed outlier: 4.672A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   GLY A 597 " --> pdb=" O   CYS A 364 " (cutoff:3.500A)
      removed outlier: 4.838A  pdb=" N   MET A 366 " --> pdb=" O   CYS A 595 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   CYS A 595 " --> pdb=" O   MET A 366 " (cutoff:3.500A)
      removed outlier: 5.647A  pdb=" N   ILE A 368 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 9.234A  pdb=" N   VAL A 593 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   LEU A 590 " --> pdb=" O   CYS A 524 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   GLY A 594 " --> pdb=" O   ARG A 528 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 424 through 427
    Processing sheet with id=AA8, first strand: chain 'A' and resid 622 through 623
      removed outlier: 6.375A  pdb=" N   MET A 622 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   PHE A 652 " --> pdb=" O   ALA A 676 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    392 hydrogen bonds defined for protein.
    1131 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.25

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2477
        1.34 -     1.46: 1256
        1.46 -     1.58: 3933
        1.58 -     1.69: 0
        1.69 -     1.81: 83
  Bond restraints: 7749
  Sorted by residual:
  bond pdb=" F2  BEF A2001 "
       pdb="BE   BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.561 -0.085 2.00e-02 2.50e+03 1.82e+01
  bond pdb=" F3  BEF A2001 "
       pdb="BE   BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.545 -0.069 2.00e-02 2.50e+03 1.19e+01
  bond pdb=" F1  BEF A2001 "
       pdb="BE   BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.533 -0.057 2.00e-02 2.50e+03 8.07e+00
  bond pdb=" N   ASP A 878 "
       pdb=" CA  ASP A 878 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.90e-02 2.77e+03 2.39e+00
  bond pdb=" N   GLY A  46 "
       pdb=" CA  GLY A  46 "
    ideal  model  delta    sigma   weight residual
    1.443  1.451 -0.008 8.60e-03 1.35e+04 8.98e-01
  ... (remaining 7744 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.59: 10447
        2.59 -     5.19: 63
        5.19 -     7.78: 1
        7.78 -    10.38: 1
       10.38 -    12.97: 2
  Bond angle restraints: 10514
  Sorted by residual:
  angle pdb=" F2  BEF A2001 "
        pdb="BE   BEF A2001 "
        pdb=" F3  BEF A2001 "
      ideal   model   delta    sigma   weight residual
     119.96  106.99   12.97 3.00e+00 1.11e-01 1.87e+01
  angle pdb=" F1  BEF A2001 "
        pdb="BE   BEF A2001 "
        pdb=" F3  BEF A2001 "
      ideal   model   delta    sigma   weight residual
     120.12  109.44   10.68 3.00e+00 1.11e-01 1.27e+01
  angle pdb=" F1  BEF A2001 "
        pdb="BE   BEF A2001 "
        pdb=" F2  BEF A2001 "
      ideal   model   delta    sigma   weight residual
     119.91  111.90    8.01 3.00e+00 1.11e-01 7.12e+00
  angle pdb=" CA  LYS A 400 "
        pdb=" CB  LYS A 400 "
        pdb=" CG  LYS A 400 "
      ideal   model   delta    sigma   weight residual
     114.10  118.74   -4.64 2.00e+00 2.50e-01 5.38e+00
  angle pdb=" N   THR A 798 "
        pdb=" CA  THR A 798 "
        pdb=" C   THR A 798 "
      ideal   model   delta    sigma   weight residual
     113.01  110.32    2.69 1.20e+00 6.94e-01 5.01e+00
  ... (remaining 10509 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4351
       17.94 -    35.87: 298
       35.87 -    53.81: 43
       53.81 -    71.74: 5
       71.74 -    89.68: 4
  Dihedral angle restraints: 4701
    sinusoidal: 1850
      harmonic: 2851
  Sorted by residual:
  dihedral pdb=" CB  CYS A 875 "
           pdb=" SG  CYS A 875 "
           pdb=" SG  CYS A 887 "
           pdb=" CB  CYS A 887 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -53.11  -32.89     1      1.00e+01 1.00e-02 1.54e+01
  dihedral pdb=" CA  LYS A 397 "
           pdb=" C   LYS A 397 "
           pdb=" N   ASP A 398 "
           pdb=" CA  ASP A 398 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.05   16.95     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CB  GLU A 950 "
           pdb=" CG  GLU A 950 "
           pdb=" CD  GLU A 950 "
           pdb=" OE1 GLU A 950 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.68   89.68     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 4698 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 901
       0.039 -    0.078: 250
       0.078 -    0.116: 81
       0.116 -    0.155: 8
       0.155 -    0.194: 2
  Chirality restraints: 1242
  Sorted by residual:
  chirality pdb=" CA  ASP A 878 "
            pdb=" N   ASP A 878 "
            pdb=" C   ASP A 878 "
            pdb=" CB  ASP A 878 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.40e-01
  chirality pdb=" CA  PHE A 759 "
            pdb=" N   PHE A 759 "
            pdb=" C   PHE A 759 "
            pdb=" CB  PHE A 759 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.05e-01
  chirality pdb=" CB  ILE A 715 "
            pdb=" CA  ILE A 715 "
            pdb=" CG1 ILE A 715 "
            pdb=" CG2 ILE A 715 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.82e-01
  ... (remaining 1239 not shown)

  Planarity restraints: 1335
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 796 "    0.011 2.00e-02 2.50e+03   2.25e-02 5.06e+00
        pdb=" C   LEU A 796 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   LEU A 796 "    0.015 2.00e-02 2.50e+03
        pdb=" N   VAL A 797 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 759 "   -0.012 2.00e-02 2.50e+03   1.11e-02 2.15e+00
        pdb=" CG  PHE A 759 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 759 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 759 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 759 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 759 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 759 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 974 "   -0.024 5.00e-02 4.00e+02   3.62e-02 2.10e+00
        pdb=" N   PRO A 975 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 975 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 975 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1332 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 85
        2.64 -     3.21: 7162
        3.21 -     3.77: 11808
        3.77 -     4.34: 15564
        4.34 -     4.90: 25983
  Nonbonded interactions: 60602
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 351 "
            pdb="MG    MG A2002 "
     model   vdw
     2.075 2.170
  nonbonded pdb=" OD1 ASP A 702 "
            pdb="MG    MG A2002 "
     model   vdw
     2.092 2.170
  nonbonded pdb=" O   THR A 353 "
            pdb="MG    MG A2002 "
     model   vdw
     2.097 2.170
  nonbonded pdb=" OD2 ASP A 351 "
            pdb=" F2  BEF A2001 "
     model   vdw
     2.128 2.990
  nonbonded pdb=" OG  SER A 916 "
            pdb=" O   GLN A 919 "
     model   vdw
     2.195 3.040
  ... (remaining 60597 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.010
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
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      :  0.011   0.902   7751  Z= 1.032
  Angle     :  0.544  12.974  10516  Z= 0.293
  Chirality :  0.040   0.194   1242
  Planarity :  0.004   0.036   1335
  Dihedral  : 12.315  89.677   2846
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.36 (0.23), residues: 973
  helix: -1.54 (0.20), residues: 452
  sheet: -3.05 (0.37), residues: 109
  loop : -2.68 (0.27), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 821 
 TYR   0.005   0.001   TYR A 753 
 PHE   0.026   0.001   PHE A 759 
 TRP   0.005   0.001   TRP A 272 
 HIS   0.002   0.000   HIS A   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 7749)
  covalent geometry    : angle       0.54386 (10514)
  SS BOND              : bond        0.00063 (    1)
  SS BOND              : angle       0.15350 (    2)
  hydrogen bonds       : bond        0.13766 (  381)
  hydrogen bonds       : angle       6.45886 ( 1131)
  Misc. bond           : bond        0.90151 (    1)

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

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

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.5918 (mt) cc_final: 0.5625 (tt)
REVERT: A  246 ARG cc_start: 0.6992 (mtp85) cc_final: 0.6781 (mtm-85)
REVERT: A  326 MET cc_start: 0.7230 (mmm) cc_final: 0.7003 (tpt)
REVERT: A  452 MET cc_start: 0.6614 (tmm) cc_final: 0.6337 (tmm)
REVERT: A  756 MET cc_start: 0.7535 (ttp) cc_final: 0.7083 (ttm)
REVERT: A  918 ASN cc_start: 0.6699 (m-40) cc_final: 0.6372 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.0971
  time to fit residues: 18.9180
Evaluate side-chains
  101 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    0.3980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0070
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 GLN
A 259 GLN
A 396 HIS
A 421 ASN
A 469 ASN
A 691 GLN
A 795 ASN
A 913 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.204345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.163481 restraints weight = 7971.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3865 rms_B_bonded: 1.85
r_work: 0.3717 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3574 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7219
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7751  Z= 0.124
  Angle     :  0.557   7.665  10516  Z= 0.281
  Chirality :  0.042   0.173   1242
  Planarity :  0.004   0.038   1335
  Dihedral  :  3.748  18.849   1040
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 12.65 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.26), residues: 973
  helix:  0.11 (0.24), residues: 446
  sheet: -2.35 (0.44), residues: 97
  loop : -2.03 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 528 
 TYR   0.009   0.001   TYR A 990 
 PHE   0.026   0.002   PHE A 759 
 TRP   0.010   0.001   TRP A 854 
 HIS   0.004   0.001   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7749)
  covalent geometry    : angle       0.55721 (10514)
  SS BOND              : bond        0.00031 (    1)
  SS BOND              : angle       0.14643 (    2)
  hydrogen bonds       : bond        0.04231 (  381)
  hydrogen bonds       : angle       4.72976 ( 1131)
  Misc. bond           : bond        0.00038 (    1)

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

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

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.6361 (mt) cc_final: 0.5753 (tt)
REVERT: A   60 LEU cc_start: 0.6114 (tp) cc_final: 0.5897 (tp)
REVERT: A  198 ARG cc_start: 0.8299 (ttm170) cc_final: 0.7066 (tmm160)
REVERT: A  246 ARG cc_start: 0.7432 (mtp85) cc_final: 0.7014 (mtm-85)
REVERT: A  326 MET cc_start: 0.7345 (mmm) cc_final: 0.7072 (tpt)
REVERT: A  452 MET cc_start: 0.7281 (tmm) cc_final: 0.6872 (tmm)
REVERT: A  479 MET cc_start: 0.8427 (mpp) cc_final: 0.7946 (mpp)
REVERT: A  719 MET cc_start: 0.8472 (mmm) cc_final: 0.8073 (mmm)
REVERT: A  756 MET cc_start: 0.8282 (ttp) cc_final: 0.7690 (ttm)
  outliers start: 12
  outliers final: 6
  residues processed: 125
  average time/residue: 0.0803
  time to fit residues: 13.7591
Evaluate side-chains
  103 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  421 ASN
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  798 THR
Chi-restraints excluded: chain A residue  959 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 96 optimal weight:    7.9990
   chunk 42 optimal weight:    0.6980
   chunk 54 optimal weight:    6.9990
   chunk 44 optimal weight:    6.9990
   chunk 29 optimal weight:    0.4980
   chunk 14 optimal weight:    0.6980
   chunk 52 optimal weight:    5.9990
   chunk 95 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A   5 HIS
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 421 ASN
A 568 ASN
A 989 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.202087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.160452 restraints weight = 7924.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3809 rms_B_bonded: 1.81
r_work: 0.3660 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3515 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7751  Z= 0.131
  Angle     :  0.558   7.037  10516  Z= 0.281
  Chirality :  0.042   0.165   1242
  Planarity :  0.004   0.038   1335
  Dihedral  :  3.854  17.841   1040
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 16.23 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.26), residues: 973
  helix:  0.52 (0.24), residues: 451
  sheet: -2.09 (0.47), residues: 97
  loop : -1.87 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 677 
 TYR   0.011   0.001   TYR A 990 
 PHE   0.025   0.002   PHE A 759 
 TRP   0.011   0.001   TRP A 854 
 HIS   0.004   0.001   HIS A 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 7749)
  covalent geometry    : angle       0.55822 (10514)
  SS BOND              : bond        0.00054 (    1)
  SS BOND              : angle       0.13378 (    2)
  hydrogen bonds       : bond        0.04071 (  381)
  hydrogen bonds       : angle       4.59187 ( 1131)
  Misc. bond           : bond        0.00059 (    1)

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

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

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 ARG cc_start: 0.8344 (ttm170) cc_final: 0.7204 (tmm160)
REVERT: A  246 ARG cc_start: 0.7395 (mtp85) cc_final: 0.6971 (mtm-85)
REVERT: A  326 MET cc_start: 0.7332 (mmm) cc_final: 0.7090 (tpt)
REVERT: A  452 MET cc_start: 0.7238 (tmm) cc_final: 0.6744 (tmm)
REVERT: A  523 ARG cc_start: 0.8357 (ptp-110) cc_final: 0.8105 (ptp90)
REVERT: A  719 MET cc_start: 0.8620 (mmm) cc_final: 0.8137 (mmm)
REVERT: A  756 MET cc_start: 0.8321 (ttp) cc_final: 0.7725 (ttm)
  outliers start: 14
  outliers final: 11
  residues processed: 110
  average time/residue: 0.0754
  time to fit residues: 11.7312
Evaluate side-chains
  108 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  421 ASN
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  568 ASN
Chi-restraints excluded: chain A residue  653 THR
Chi-restraints excluded: chain A residue  798 THR
Chi-restraints excluded: chain A residue  949 VAL
Chi-restraints excluded: chain A residue  959 THR
Chi-restraints excluded: chain A residue 1023 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 90 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0170
   chunk 39 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.6220

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 421 ASN
A 568 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.203581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.162467 restraints weight = 8037.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3886 rms_B_bonded: 1.92
r_work: 0.3721 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3574 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7751  Z= 0.113
  Angle     :  0.540   8.408  10516  Z= 0.269
  Chirality :  0.042   0.163   1242
  Planarity :  0.004   0.039   1335
  Dihedral  :  3.789  17.404   1040
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 17.42 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.80 (0.27), residues: 973
  helix:  0.81 (0.25), residues: 451
  sheet: -1.83 (0.48), residues: 97
  loop : -1.69 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 677 
 TYR   0.012   0.001   TYR A 990 
 PHE   0.026   0.001   PHE A 759 
 TRP   0.012   0.001   TRP A 854 
 HIS   0.002   0.000   HIS A 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 7749)
  covalent geometry    : angle       0.53972 (10514)
  SS BOND              : bond        0.00010 (    1)
  SS BOND              : angle       0.13124 (    2)
  hydrogen bonds       : bond        0.03796 (  381)
  hydrogen bonds       : angle       4.43965 ( 1131)
  Misc. bond           : bond        0.00024 (    1)

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

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

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 ASN cc_start: 0.7029 (OUTLIER) cc_final: 0.6413 (p0)
REVERT: A  198 ARG cc_start: 0.8282 (ttm170) cc_final: 0.7159 (tmm160)
REVERT: A  246 ARG cc_start: 0.7430 (mtp85) cc_final: 0.6968 (mtm-85)
REVERT: A  326 MET cc_start: 0.7245 (mmm) cc_final: 0.6997 (tpt)
REVERT: A  452 MET cc_start: 0.7146 (tmm) cc_final: 0.6643 (tmm)
REVERT: A  719 MET cc_start: 0.8649 (mmm) cc_final: 0.8144 (mmm)
REVERT: A  756 MET cc_start: 0.8314 (ttp) cc_final: 0.7723 (ttm)
  outliers start: 17
  outliers final: 12
  residues processed: 116
  average time/residue: 0.0815
  time to fit residues: 13.1273
Evaluate side-chains
  112 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  101 ASN
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  421 ASN
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  568 ASN
Chi-restraints excluded: chain A residue  653 THR
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  798 THR
Chi-restraints excluded: chain A residue 1023 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 69 optimal weight:    0.0670
   chunk 32 optimal weight:    0.6980
   chunk 5 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 7 optimal weight:    9.9990
   chunk 64 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.6720

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 138 GLN
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 421 ASN
A 767 ASN
A 989 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.205951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.165544 restraints weight = 7918.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3832 rms_B_bonded: 1.77
r_work: 0.3678 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3532 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7751  Z= 0.114
  Angle     :  0.534   7.763  10516  Z= 0.267
  Chirality :  0.042   0.163   1242
  Planarity :  0.004   0.039   1335
  Dihedral  :  3.779  17.296   1040
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 17.66 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.27), residues: 973
  helix:  0.94 (0.25), residues: 451
  sheet: -1.70 (0.48), residues: 97
  loop : -1.61 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 523 
 TYR   0.011   0.001   TYR A 990 
 PHE   0.026   0.001   PHE A 759 
 TRP   0.012   0.001   TRP A 854 
 HIS   0.001   0.000   HIS A 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 7749)
  covalent geometry    : angle       0.53430 (10514)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       0.14794 (    2)
  hydrogen bonds       : bond        0.03700 (  381)
  hydrogen bonds       : angle       4.37224 ( 1131)
  Misc. bond           : bond        0.00024 (    1)

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

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

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 ARG cc_start: 0.8227 (ttm170) cc_final: 0.7034 (tmt170)
REVERT: A  246 ARG cc_start: 0.7403 (mtp85) cc_final: 0.6967 (mtm-85)
REVERT: A  326 MET cc_start: 0.7242 (mmm) cc_final: 0.6983 (tpt)
REVERT: A  452 MET cc_start: 0.7102 (tmm) cc_final: 0.6536 (tmm)
REVERT: A  719 MET cc_start: 0.8604 (mmm) cc_final: 0.8111 (mmm)
REVERT: A  756 MET cc_start: 0.8271 (ttp) cc_final: 0.7676 (ttm)
REVERT: A  816 MET cc_start: 0.7390 (mmm) cc_final: 0.6774 (mmm)
REVERT: A  940 MET cc_start: 0.6175 (mmp) cc_final: 0.5915 (mmp)
  outliers start: 21
  outliers final: 14
  residues processed: 114
  average time/residue: 0.0760
  time to fit residues: 12.3348
Evaluate side-chains
  111 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  138 GLN
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  421 ASN
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  653 THR
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  798 THR
Chi-restraints excluded: chain A residue  906 ILE
Chi-restraints excluded: chain A residue 1023 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   chunk 76 optimal weight:    0.5980
   chunk 89 optimal weight:    0.3980
   chunk 43 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 97 optimal weight:    0.7980
   chunk 8 optimal weight:    8.9990
   chunk 80 optimal weight:    4.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 421 ASN
A 568 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.204335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.163856 restraints weight = 7978.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3806 rms_B_bonded: 1.75
r_work: 0.3649 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3504 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7751  Z= 0.127
  Angle     :  0.542   7.508  10516  Z= 0.272
  Chirality :  0.042   0.169   1242
  Planarity :  0.004   0.040   1335
  Dihedral  :  3.799  17.059   1040
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.38 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.27), residues: 973
  helix:  1.01 (0.25), residues: 451
  sheet: -1.66 (0.49), residues: 97
  loop : -1.62 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 523 
 TYR   0.013   0.001   TYR A 990 
 PHE   0.026   0.001   PHE A 759 
 TRP   0.012   0.001   TRP A 854 
 HIS   0.001   0.000   HIS A  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 7749)
  covalent geometry    : angle       0.54248 (10514)
  SS BOND              : bond        0.00040 (    1)
  SS BOND              : angle       0.15797 (    2)
  hydrogen bonds       : bond        0.03765 (  381)
  hydrogen bonds       : angle       4.38788 ( 1131)
  Misc. bond           : bond        0.00035 (    1)

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

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

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A  198 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7011 (tmt170)
REVERT: A  246 ARG cc_start: 0.7405 (mtp85) cc_final: 0.6952 (mtm-85)
REVERT: A  326 MET cc_start: 0.7353 (mmm) cc_final: 0.7090 (tpt)
REVERT: A  452 MET cc_start: 0.7144 (tmm) cc_final: 0.6561 (tmm)
REVERT: A  479 MET cc_start: 0.8411 (mpp) cc_final: 0.8118 (mpp)
REVERT: A  719 MET cc_start: 0.8625 (mmm) cc_final: 0.8112 (mmm)
REVERT: A  756 MET cc_start: 0.8289 (ttp) cc_final: 0.7674 (ttm)
REVERT: A  956 PHE cc_start: 0.5590 (OUTLIER) cc_final: 0.3246 (p90)
  outliers start: 20
  outliers final: 15
  residues processed: 112
  average time/residue: 0.0815
  time to fit residues: 12.7735
Evaluate side-chains
  110 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  138 GLN
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  421 ASN
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  653 THR
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  798 THR
Chi-restraints excluded: chain A residue  906 ILE
Chi-restraints excluded: chain A residue  956 PHE
Chi-restraints excluded: chain A residue 1023 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 4 optimal weight:   30.0000
   chunk 38 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0060
   chunk 51 optimal weight:    0.0980
   chunk 77 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 132 GLN
A 138 GLN
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 421 ASN
A 568 ASN
A 989 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.205493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.164636 restraints weight = 7889.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3875 rms_B_bonded: 1.81
r_work: 0.3731 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3584 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7751  Z= 0.109
  Angle     :  0.529   7.920  10516  Z= 0.264
  Chirality :  0.041   0.164   1242
  Planarity :  0.004   0.041   1335
  Dihedral  :  3.773  17.083   1040
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 18.26 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.27), residues: 973
  helix:  1.08 (0.25), residues: 454
  sheet: -1.52 (0.49), residues: 97
  loop : -1.58 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 523 
 TYR   0.011   0.001   TYR A 990 
 PHE   0.026   0.001   PHE A 759 
 TRP   0.013   0.001   TRP A 854 
 HIS   0.001   0.000   HIS A   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 7749)
  covalent geometry    : angle       0.52888 (10514)
  SS BOND              : bond        0.00024 (    1)
  SS BOND              : angle       0.11450 (    2)
  hydrogen bonds       : bond        0.03593 (  381)
  hydrogen bonds       : angle       4.30996 ( 1131)
  Misc. bond           : bond        0.00001 (    1)

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

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

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A  101 ASN cc_start: 0.7181 (OUTLIER) cc_final: 0.6284 (p0)
REVERT: A  198 ARG cc_start: 0.8172 (ttm170) cc_final: 0.7012 (tmt170)
REVERT: A  246 ARG cc_start: 0.7433 (mtp85) cc_final: 0.6955 (mtm-85)
REVERT: A  326 MET cc_start: 0.7220 (mmm) cc_final: 0.6946 (tpt)
REVERT: A  452 MET cc_start: 0.7065 (tmm) cc_final: 0.6438 (tmm)
REVERT: A  479 MET cc_start: 0.8393 (mpp) cc_final: 0.8107 (mpp)
REVERT: A  719 MET cc_start: 0.8704 (mmm) cc_final: 0.8062 (mmm)
REVERT: A  756 MET cc_start: 0.8241 (ttp) cc_final: 0.7639 (ttm)
REVERT: A  956 PHE cc_start: 0.5574 (OUTLIER) cc_final: 0.3255 (p90)
  outliers start: 23
  outliers final: 16
  residues processed: 114
  average time/residue: 0.0758
  time to fit residues: 12.2398
Evaluate side-chains
  112 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   70 CYS
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  101 ASN
Chi-restraints excluded: chain A residue  138 GLN
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  421 ASN
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  568 ASN
Chi-restraints excluded: chain A residue  653 THR
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  906 ILE
Chi-restraints excluded: chain A residue  956 PHE
Chi-restraints excluded: chain A residue  964 THR
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue  989 ASN
Chi-restraints excluded: chain A residue 1023 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 58 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0980
   chunk 93 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 47 optimal weight:    9.9990
   chunk 56 optimal weight:    9.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 406 GLN
A 568 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.205177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.164157 restraints weight = 7986.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3807 rms_B_bonded: 1.80
r_work: 0.3660 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3516 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
moved from start:          0.2278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7751  Z= 0.113
  Angle     :  0.533   7.685  10516  Z= 0.266
  Chirality :  0.041   0.167   1242
  Planarity :  0.004   0.040   1335
  Dihedral  :  3.763  16.897   1040
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 18.74 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.27), residues: 973
  helix:  1.11 (0.25), residues: 454
  sheet: -1.61 (0.50), residues: 92
  loop : -1.52 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 523 
 TYR   0.021   0.001   TYR A 990 
 PHE   0.026   0.001   PHE A 759 
 TRP   0.013   0.001   TRP A 854 
 HIS   0.001   0.000   HIS A  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 7749)
  covalent geometry    : angle       0.53316 (10514)
  SS BOND              : bond        0.00026 (    1)
  SS BOND              : angle       0.12960 (    2)
  hydrogen bonds       : bond        0.03606 (  381)
  hydrogen bonds       : angle       4.30681 ( 1131)
  Misc. bond           : bond        0.00005 (    1)

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

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

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A  138 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7690 (pm20)
REVERT: A  198 ARG cc_start: 0.8144 (ttm170) cc_final: 0.7009 (tmt170)
REVERT: A  246 ARG cc_start: 0.7487 (mtp85) cc_final: 0.6900 (mtm-85)
REVERT: A  326 MET cc_start: 0.7307 (mmm) cc_final: 0.7029 (tpt)
REVERT: A  452 MET cc_start: 0.7085 (tmm) cc_final: 0.6459 (tmm)
REVERT: A  479 MET cc_start: 0.8388 (mpp) cc_final: 0.8103 (mpp)
REVERT: A  699 MET cc_start: 0.7999 (ttt) cc_final: 0.7546 (ttt)
REVERT: A  719 MET cc_start: 0.8715 (mmm) cc_final: 0.8068 (mmm)
REVERT: A  756 MET cc_start: 0.8242 (ttp) cc_final: 0.7643 (ttm)
REVERT: A  900 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7331 (tp)
REVERT: A  956 PHE cc_start: 0.5572 (OUTLIER) cc_final: 0.3299 (p90)
  outliers start: 25
  outliers final: 20
  residues processed: 112
  average time/residue: 0.0739
  time to fit residues: 11.8592
Evaluate side-chains
  115 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   70 CYS
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  101 ASN
Chi-restraints excluded: chain A residue  138 GLN
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  498 CYS
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  568 ASN
Chi-restraints excluded: chain A residue  653 THR
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  798 THR
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue  906 ILE
Chi-restraints excluded: chain A residue  940 MET
Chi-restraints excluded: chain A residue  956 PHE
Chi-restraints excluded: chain A residue  964 THR
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue 1023 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 69 optimal weight:    0.0060
   chunk 24 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 9 optimal weight:    7.9990
   chunk 25 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 406 GLN
A 421 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.205278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.165232 restraints weight = 7983.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3819 rms_B_bonded: 1.88
r_work: 0.3652 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3506 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7751  Z= 0.109
  Angle     :  0.526   7.837  10516  Z= 0.263
  Chirality :  0.041   0.167   1242
  Planarity :  0.004   0.036   1335
  Dihedral  :  3.768  16.882   1040
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 18.85 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.27), residues: 973
  helix:  1.17 (0.25), residues: 454
  sheet: -1.53 (0.51), residues: 92
  loop : -1.49 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 523 
 TYR   0.012   0.001   TYR A 990 
 PHE   0.027   0.001   PHE A 759 
 TRP   0.013   0.001   TRP A 854 
 HIS   0.001   0.000   HIS A  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 7749)
  covalent geometry    : angle       0.52651 (10514)
  SS BOND              : bond        0.00023 (    1)
  SS BOND              : angle       0.12135 (    2)
  hydrogen bonds       : bond        0.03514 (  381)
  hydrogen bonds       : angle       4.28001 ( 1131)
  Misc. bond           : bond        0.00005 (    1)

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

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

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A  138 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7801 (pm20)
REVERT: A  198 ARG cc_start: 0.8136 (ttm170) cc_final: 0.7001 (tmt170)
REVERT: A  246 ARG cc_start: 0.7497 (mtp85) cc_final: 0.6907 (mtm-85)
REVERT: A  326 MET cc_start: 0.7235 (mmm) cc_final: 0.6956 (tpt)
REVERT: A  452 MET cc_start: 0.7077 (tmm) cc_final: 0.6448 (tmm)
REVERT: A  479 MET cc_start: 0.8432 (mpp) cc_final: 0.8135 (mpp)
REVERT: A  719 MET cc_start: 0.8727 (mmm) cc_final: 0.8058 (mmm)
REVERT: A  756 MET cc_start: 0.8239 (ttp) cc_final: 0.7643 (ttm)
REVERT: A  900 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7345 (tp)
REVERT: A  956 PHE cc_start: 0.5572 (OUTLIER) cc_final: 0.3321 (p90)
  outliers start: 23
  outliers final: 19
  residues processed: 111
  average time/residue: 0.0706
  time to fit residues: 11.3948
Evaluate side-chains
  115 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   70 CYS
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  138 GLN
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  421 ASN
Chi-restraints excluded: chain A residue  498 CYS
Chi-restraints excluded: chain A residue  653 THR
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  798 THR
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue  906 ILE
Chi-restraints excluded: chain A residue  940 MET
Chi-restraints excluded: chain A residue  956 PHE
Chi-restraints excluded: chain A residue  964 THR
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue 1023 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 44 optimal weight:    0.0020
   chunk 90 optimal weight:    0.3980
   chunk 28 optimal weight:    0.9980
   chunk 87 optimal weight:    0.6980
   chunk 84 optimal weight:    0.4980
   chunk 79 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 17 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   overall best weight:    0.4988

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.207254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.167463 restraints weight = 7888.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3861 rms_B_bonded: 1.89
r_work: 0.3695 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3549 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.2376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7751  Z= 0.106
  Angle     :  0.524   8.061  10516  Z= 0.261
  Chirality :  0.041   0.166   1242
  Planarity :  0.004   0.035   1335
  Dihedral  :  3.750  16.683   1040
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 19.45 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.27), residues: 973
  helix:  1.22 (0.25), residues: 455
  sheet: -1.47 (0.51), residues: 92
  loop : -1.48 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 523 
 TYR   0.012   0.001   TYR A 990 
 PHE   0.027   0.001   PHE A 759 
 TRP   0.014   0.001   TRP A 854 
 HIS   0.001   0.000   HIS A  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 7749)
  covalent geometry    : angle       0.52362 (10514)
  SS BOND              : bond        0.00017 (    1)
  SS BOND              : angle       0.12074 (    2)
  hydrogen bonds       : bond        0.03461 (  381)
  hydrogen bonds       : angle       4.24028 ( 1131)
  Misc. bond           : bond        0.00015 (    1)

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

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

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1946 Ramachandran restraints generated.
    973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.300 
Fit side-chains
REVERT: A  138 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7947 (pm20)
REVERT: A  198 ARG cc_start: 0.8131 (ttm170) cc_final: 0.7023 (tmt170)
REVERT: A  207 MET cc_start: 0.8475 (mtt) cc_final: 0.7945 (mtt)
REVERT: A  246 ARG cc_start: 0.7497 (mtp85) cc_final: 0.6901 (mtm-85)
REVERT: A  326 MET cc_start: 0.7226 (mmm) cc_final: 0.6947 (tpt)
REVERT: A  452 MET cc_start: 0.7077 (tmm) cc_final: 0.6462 (tmm)
REVERT: A  479 MET cc_start: 0.8454 (mpp) cc_final: 0.8107 (mpp)
REVERT: A  523 ARG cc_start: 0.8351 (ptp-110) cc_final: 0.7740 (ptp90)
REVERT: A  699 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7510 (ttt)
REVERT: A  719 MET cc_start: 0.8730 (mmm) cc_final: 0.8063 (mmm)
REVERT: A  756 MET cc_start: 0.8177 (ttp) cc_final: 0.7591 (ttm)
REVERT: A  900 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7343 (tp)
REVERT: A  956 PHE cc_start: 0.5617 (OUTLIER) cc_final: 0.3369 (p90)
  outliers start: 22
  outliers final: 18
  residues processed: 108
  average time/residue: 0.0694
  time to fit residues: 10.9685
Evaluate side-chains
  114 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   70 CYS
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  138 GLN
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  498 CYS
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  653 THR
Chi-restraints excluded: chain A residue  699 MET
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  798 THR
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue  906 ILE
Chi-restraints excluded: chain A residue  940 MET
Chi-restraints excluded: chain A residue  956 PHE
Chi-restraints excluded: chain A residue  964 THR
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue 1023 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0270
   chunk 97 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 47 optimal weight:    9.9990
   chunk 78 optimal weight:    0.7980
   chunk 77 optimal weight:    0.5980
   chunk 88 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 138 GLN
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 406 GLN
A 989 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.206405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.166343 restraints weight = 7898.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3878 rms_B_bonded: 1.88
r_work: 0.3714 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3565 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7751  Z= 0.108
  Angle     :  0.523   8.014  10516  Z= 0.261
  Chirality :  0.041   0.167   1242
  Planarity :  0.004   0.036   1335
  Dihedral  :  3.746  16.643   1040
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 18.97 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.27), residues: 973
  helix:  1.23 (0.24), residues: 455
  sheet: -1.42 (0.51), residues: 92
  loop : -1.47 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 139 
 TYR   0.013   0.001   TYR A 990 
 PHE   0.027   0.001   PHE A 759 
 TRP   0.014   0.001   TRP A 854 
 HIS   0.001   0.000   HIS A  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 7749)
  covalent geometry    : angle       0.52305 (10514)
  SS BOND              : bond        0.00023 (    1)
  SS BOND              : angle       0.12425 (    2)
  hydrogen bonds       : bond        0.03446 (  381)
  hydrogen bonds       : angle       4.23211 ( 1131)
  Misc. bond           : bond        0.00010 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2018.17 seconds
wall clock time: 35 minutes 11.15 seconds (2111.15 seconds total)