Starting phenix.real_space_refine
on Wed Feb 12 08:10:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ln9_0928/02_2025/6ln9_0928.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ln9_0928/02_2025/6ln9_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ln9_0928/02_2025/6ln9_0928.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ln9_0928/02_2025/6ln9_0928.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ln9_0928/02_2025/6ln9_0928.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ln9_0928/02_2025/6ln9_0928.cif"
  }
  resolution = 3.4
  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=   0.007
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.56, per 1000 atoms: 0.60
  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: 2.12
  Conformation dependent library (CDL) restraints added in 966.8 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: 0.95
  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: 2.79

  Time building geometry restraints manager: 2.37 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:             0.200
  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:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     20.830
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.390
-------------------------------------------------------------------------------
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      :  0.003   0.085   7749  Z= 0.174
  Angle     :  0.544  12.974  10514  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.36 (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
 TRP   0.005   0.001   TRP A 272 
 HIS   0.002   0.000   HIS A   5 
 PHE   0.026   0.001   PHE A 759 
 TYR   0.005   0.001   TYR A 753 
 ARG   0.003   0.000   ARG A 821 

*********************** 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  : 0.836 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.5918 (mt) cc_final: 0.5624 (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: 0.2386
  time to fit residues: 46.2296
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  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 46 optimal weight:    9.9990
   chunk 57 optimal weight:    0.9980
   chunk 88 optimal weight:    0.5980
   overall best weight:    0.8582

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

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

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.203559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.163068 restraints weight = 7872.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3865 rms_B_bonded: 1.78
r_work: 0.3712 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3567 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7749  Z= 0.197
  Angle     :  0.569   7.699  10514  Z= 0.287
  Chirality :  0.043   0.180   1242
  Planarity :  0.004   0.039   1335
  Dihedral  :  3.826  19.065   1040
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 12.77 %
    Favored  : 85.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.26), residues: 973
  helix:  0.12 (0.24), residues: 446
  sheet: -2.35 (0.44), residues: 97
  loop : -2.02 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 854 
 HIS   0.004   0.001   HIS A 526 
 PHE   0.026   0.002   PHE A 759 
 TYR   0.009   0.001   TYR A 990 
 ARG   0.004   0.000   ARG A 677 

*********************** 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: 13
    poor density    : 118
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.6130 (tp) cc_final: 0.5895 (tp)
REVERT: A  198 ARG cc_start: 0.8382 (ttm170) cc_final: 0.7227 (tmm160)
REVERT: A  246 ARG cc_start: 0.7448 (mtp85) cc_final: 0.7018 (mtm-85)
REVERT: A  326 MET cc_start: 0.7378 (mmm) cc_final: 0.7100 (tpt)
REVERT: A  452 MET cc_start: 0.7313 (tmm) cc_final: 0.6881 (tmm)
REVERT: A  479 MET cc_start: 0.8354 (mpp) cc_final: 0.8065 (mpp)
REVERT: A  756 MET cc_start: 0.8321 (ttp) cc_final: 0.7722 (ttm)
  outliers start: 13
  outliers final: 8
  residues processed: 125
  average time/residue: 0.1794
  time to fit residues: 31.3475
Evaluate side-chains
  104 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  478 LEU
Chi-restraints excluded: chain A residue  557 THR
Chi-restraints excluded: chain A residue  653 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 41 optimal weight:    0.0980
   chunk 63 optimal weight:    6.9990
   chunk 59 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 11 optimal weight:   20.0000
   chunk 81 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 46 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9990
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A   5 HIS
** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 421 ASN
A 568 ASN
A 767 ASN
A 795 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 = 0.4243 r_free = 0.4243 target = 0.204669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.163965 restraints weight = 8015.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 1.96
r_work: 0.3720 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3572 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7289
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7749  Z= 0.172
  Angle     :  0.546   7.034  10514  Z= 0.274
  Chirality :  0.042   0.163   1242
  Planarity :  0.004   0.039   1335
  Dihedral  :  3.823  17.804   1040
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 16.47 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.26), residues: 973
  helix:  0.58 (0.24), residues: 452
  sheet: -2.06 (0.47), residues: 97
  loop : -1.84 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 854 
 HIS   0.001   0.000   HIS A 526 
 PHE   0.026   0.001   PHE A 759 
 TYR   0.012   0.001   TYR A 990 
 ARG   0.003   0.000   ARG A 677 

*********************** 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
  122 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 ARG cc_start: 0.8332 (ttm170) cc_final: 0.7208 (tmm160)
REVERT: A  246 ARG cc_start: 0.7396 (mtp85) cc_final: 0.6969 (mtm-85)
REVERT: A  326 MET cc_start: 0.7334 (mmm) cc_final: 0.7098 (tpt)
REVERT: A  452 MET cc_start: 0.7208 (tmm) cc_final: 0.6733 (tmm)
REVERT: A  523 ARG cc_start: 0.8369 (ptp-110) cc_final: 0.8130 (ptp90)
REVERT: A  699 MET cc_start: 0.8177 (ttt) cc_final: 0.7911 (ttt)
REVERT: A  756 MET cc_start: 0.8328 (ttp) cc_final: 0.7740 (ttm)
REVERT: A  767 ASN cc_start: 0.8039 (OUTLIER) cc_final: 0.7289 (m110)
REVERT: A  816 MET cc_start: 0.7521 (mmm) cc_final: 0.6922 (mmm)
REVERT: A  908 MET cc_start: 0.7875 (mmp) cc_final: 0.7639 (mmm)
  outliers start: 15
  outliers final: 10
  residues processed: 113
  average time/residue: 0.1737
  time to fit residues: 28.1834
Evaluate side-chains
  110 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
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  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  767 ASN
Chi-restraints excluded: chain A residue  798 THR
Chi-restraints excluded: chain A residue  949 VAL
Chi-restraints excluded: chain A residue  959 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 86 optimal weight:    7.9990
   chunk 96 optimal weight:    0.5980
   chunk 12 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 95 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   overall best weight:    1.8784

-------------------------------------------------------------------------------
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 767 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.199444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.157871 restraints weight = 7976.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 1.76
r_work: 0.3624 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3482 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7749  Z= 0.310
  Angle     :  0.617   6.948  10514  Z= 0.312
  Chirality :  0.044   0.179   1242
  Planarity :  0.004   0.042   1335
  Dihedral  :  4.086  17.731   1040
  Min Nonbonded Distance : 1.854

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 17.90 %
    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 (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: -1.13 (0.27), residues: 973
  helix:  0.59 (0.24), residues: 450
  sheet: -2.15 (0.44), residues: 109
  loop : -1.84 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 854 
 HIS   0.002   0.001   HIS A  15 
 PHE   0.027   0.002   PHE A 759 
 TYR   0.015   0.002   TYR A 990 
 ARG   0.002   0.000   ARG A 821 

*********************** 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: 24
    poor density    : 98
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 ARG cc_start: 0.8422 (ttm170) cc_final: 0.7338 (tmm160)
REVERT: A  246 ARG cc_start: 0.7487 (mtp85) cc_final: 0.6973 (mtm-85)
REVERT: A  326 MET cc_start: 0.7432 (mmm) cc_final: 0.7182 (tpt)
REVERT: A  452 MET cc_start: 0.7299 (tmm) cc_final: 0.6769 (tmm)
REVERT: A  719 MET cc_start: 0.8551 (mmm) cc_final: 0.8004 (mmm)
REVERT: A  756 MET cc_start: 0.8354 (ttp) cc_final: 0.7758 (ttm)
  outliers start: 24
  outliers final: 16
  residues processed: 114
  average time/residue: 0.1723
  time to fit residues: 27.7598
Evaluate side-chains
  109 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
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   89 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  402 VAL
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  872 PHE
Chi-restraints excluded: chain A residue  949 VAL
Chi-restraints excluded: chain A residue  959 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9990
   chunk 7 optimal weight:    8.9990
   chunk 48 optimal weight:    4.9990
   chunk 86 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 49 optimal weight:    9.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 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 = 0.4229 r_free = 0.4229 target = 0.203161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.162149 restraints weight = 7935.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3807 rms_B_bonded: 1.80
r_work: 0.3659 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3515 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7749  Z= 0.192
  Angle     :  0.558   7.195  10514  Z= 0.280
  Chirality :  0.042   0.165   1242
  Planarity :  0.004   0.042   1335
  Dihedral  :  3.954  17.687   1040
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 18.50 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.27), residues: 973
  helix:  0.83 (0.24), residues: 450
  sheet: -1.73 (0.49), residues: 97
  loop : -1.67 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 854 
 HIS   0.001   0.000   HIS A  15 
 PHE   0.025   0.001   PHE A 759 
 TYR   0.012   0.001   TYR A 990 
 ARG   0.003   0.000   ARG A 523 

*********************** 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
  124 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 0.812 
Fit side-chains
REVERT: A  198 ARG cc_start: 0.8304 (ttm170) cc_final: 0.7390 (tmt170)
REVERT: A  246 ARG cc_start: 0.7546 (mtp85) cc_final: 0.6926 (mtm-85)
REVERT: A  326 MET cc_start: 0.7344 (mmm) cc_final: 0.6987 (tpt)
REVERT: A  452 MET cc_start: 0.7153 (tmm) cc_final: 0.6619 (tmm)
REVERT: A  479 MET cc_start: 0.8488 (mpp) cc_final: 0.8163 (mpp)
REVERT: A  719 MET cc_start: 0.8695 (mmm) cc_final: 0.8146 (mmm)
REVERT: A  756 MET cc_start: 0.8238 (ttp) cc_final: 0.7629 (ttm)
REVERT: A  900 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7304 (tp)
REVERT: A  956 PHE cc_start: 0.5475 (OUTLIER) cc_final: 0.3355 (p90)
  outliers start: 23
  outliers final: 15
  residues processed: 120
  average time/residue: 0.1978
  time to fit residues: 33.0678
Evaluate side-chains
  109 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
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  138 GLN
Chi-restraints excluded: chain A residue  153 ILE
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  421 ASN
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  956 PHE
Chi-restraints excluded: chain A residue  982 THR
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 29 optimal weight:    2.9990
   chunk 85 optimal weight:    0.3980
   chunk 65 optimal weight:    1.9990
   chunk 79 optimal weight:    0.4980
   chunk 87 optimal weight:    1.9990
   chunk 90 optimal weight:    0.3980
   chunk 14 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 4 optimal weight:   20.0000
   chunk 55 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.6584

-------------------------------------------------------------------------------
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 = 0.4226 r_free = 0.4226 target = 0.203114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.161924 restraints weight = 7956.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3812 rms_B_bonded: 1.82
r_work: 0.3667 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3519 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7749  Z= 0.175
  Angle     :  0.548   7.207  10514  Z= 0.274
  Chirality :  0.042   0.165   1242
  Planarity :  0.004   0.042   1335
  Dihedral  :  3.868  17.242   1040
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 19.09 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.27), residues: 973
  helix:  1.01 (0.25), residues: 451
  sheet: -1.57 (0.51), residues: 97
  loop : -1.56 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 854 
 HIS   0.001   0.000   HIS A  15 
 PHE   0.025   0.001   PHE A 759 
 TYR   0.013   0.001   TYR A 990 
 ARG   0.003   0.000   ARG A 523 

*********************** 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
  125 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 98
  time to evaluate  : 0.845 
Fit side-chains
REVERT: A  198 ARG cc_start: 0.8235 (ttm170) cc_final: 0.7358 (tmt170)
REVERT: A  207 MET cc_start: 0.8500 (mtt) cc_final: 0.7991 (mtt)
REVERT: A  246 ARG cc_start: 0.7572 (mtp85) cc_final: 0.6948 (mtm-85)
REVERT: A  452 MET cc_start: 0.7087 (tmm) cc_final: 0.6490 (tmm)
REVERT: A  466 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8367 (tm-30)
REVERT: A  479 MET cc_start: 0.8455 (mpp) cc_final: 0.8143 (mpp)
REVERT: A  719 MET cc_start: 0.8676 (mmm) cc_final: 0.8075 (mmm)
REVERT: A  756 MET cc_start: 0.8215 (ttp) cc_final: 0.7613 (ttm)
REVERT: A  900 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7338 (tp)
REVERT: A  956 PHE cc_start: 0.5215 (OUTLIER) cc_final: 0.3203 (p90)
  outliers start: 27
  outliers final: 19
  residues processed: 122
  average time/residue: 0.1631
  time to fit residues: 28.4945
Evaluate side-chains
  118 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
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  263 VAL
Chi-restraints excluded: chain A residue  342 LEU
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  466 GLU
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  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 79 optimal weight:    0.0670
   chunk 40 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 65 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   chunk 43 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 48 optimal weight:   10.0000
   chunk 52 optimal weight:    6.9990
   overall best weight:    1.7122

-------------------------------------------------------------------------------
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 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 568 ASN
A 989 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.199340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.157809 restraints weight = 7999.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 1.88
r_work: 0.3609 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3461 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7749  Z= 0.290
  Angle     :  0.609   6.722  10514  Z= 0.306
  Chirality :  0.044   0.178   1242
  Planarity :  0.004   0.044   1335
  Dihedral  :  4.096  17.449   1040
  Min Nonbonded Distance : 1.819

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 19.45 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.27), residues: 973
  helix:  0.89 (0.24), residues: 451
  sheet: -1.81 (0.50), residues: 92
  loop : -1.56 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 854 
 HIS   0.002   0.001   HIS A  15 
 PHE   0.026   0.002   PHE A 759 
 TYR   0.013   0.002   TYR A 990 
 ARG   0.003   0.000   ARG A 139 

*********************** 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
  134 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 97
  time to evaluate  : 0.807 
Fit side-chains
REVERT: A  198 ARG cc_start: 0.8342 (ttm170) cc_final: 0.7298 (tmm160)
REVERT: A  246 ARG cc_start: 0.7592 (mtp85) cc_final: 0.6932 (mtm-85)
REVERT: A  332 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.7898 (mt)
REVERT: A  452 MET cc_start: 0.7302 (tmm) cc_final: 0.6925 (tmm)
REVERT: A  466 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8290 (tm-30)
REVERT: A  479 MET cc_start: 0.8485 (mpp) cc_final: 0.8100 (mpp)
REVERT: A  699 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7925 (ttt)
REVERT: A  719 MET cc_start: 0.8697 (mmm) cc_final: 0.8063 (mmm)
REVERT: A  756 MET cc_start: 0.8280 (ttp) cc_final: 0.7658 (ttm)
REVERT: A  900 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7418 (tp)
REVERT: A  956 PHE cc_start: 0.5512 (OUTLIER) cc_final: 0.3465 (p90)
  outliers start: 37
  outliers final: 28
  residues processed: 125
  average time/residue: 0.1799
  time to fit residues: 31.6661
Evaluate side-chains
  122 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 89
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
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   49 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  153 ILE
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  357 THR
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  466 GLU
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  699 MET
Chi-restraints excluded: chain A residue  715 ILE
Chi-restraints excluded: chain A residue  776 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  949 VAL
Chi-restraints excluded: chain A residue  956 PHE
Chi-restraints excluded: chain A residue  964 THR
Chi-restraints excluded: chain A residue  970 LEU
Chi-restraints excluded: chain A residue  982 THR
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 84 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 14 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 69 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 52 optimal weight:    7.9990
   chunk 27 optimal weight:    0.0020
   chunk 26 optimal weight:    4.9990
   overall best weight:    0.6188

-------------------------------------------------------------------------------
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 568 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.203308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.162678 restraints weight = 7938.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3853 rms_B_bonded: 1.96
r_work: 0.3695 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3543 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7749  Z= 0.174
  Angle     :  0.553   6.999  10514  Z= 0.276
  Chirality :  0.042   0.165   1242
  Planarity :  0.004   0.043   1335
  Dihedral  :  3.940  17.554   1040
  Min Nonbonded Distance : 1.884

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 20.41 %
    Favored  : 75.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.27), residues: 973
  helix:  1.08 (0.25), residues: 451
  sheet: -1.74 (0.51), residues: 92
  loop : -1.47 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 854 
 HIS   0.001   0.000   HIS A 526 
 PHE   0.025   0.001   PHE A 759 
 TYR   0.019   0.001   TYR A 990 
 ARG   0.003   0.000   ARG A 523 

*********************** 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
  129 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 98
  time to evaluate  : 0.927 
Fit side-chains
REVERT: A  138 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7634 (pm20)
REVERT: A  198 ARG cc_start: 0.8299 (ttm170) cc_final: 0.7265 (tmt170)
REVERT: A  207 MET cc_start: 0.8503 (mtt) cc_final: 0.8035 (mtt)
REVERT: A  246 ARG cc_start: 0.7612 (mtp85) cc_final: 0.6956 (mtm-85)
REVERT: A  384 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8231 (mm)
REVERT: A  452 MET cc_start: 0.7218 (tmm) cc_final: 0.6808 (tmm)
REVERT: A  466 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8265 (tm-30)
REVERT: A  479 MET cc_start: 0.8550 (mpp) cc_final: 0.8171 (mpp)
REVERT: A  719 MET cc_start: 0.8692 (mmm) cc_final: 0.8056 (mmm)
REVERT: A  756 MET cc_start: 0.8239 (ttp) cc_final: 0.7648 (ttm)
REVERT: A  900 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7338 (tp)
REVERT: A  956 PHE cc_start: 0.5370 (OUTLIER) cc_final: 0.3463 (p90)
  outliers start: 31
  outliers final: 23
  residues processed: 124
  average time/residue: 0.1705
  time to fit residues: 30.2713
Evaluate side-chains
  120 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 92
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   49 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  263 VAL
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  384 ILE
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  466 GLU
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  949 VAL
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  982 THR
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 32 optimal weight:    0.0980
   chunk 27 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0370
   chunk 42 optimal weight:    0.6980
   chunk 48 optimal weight:    6.9990
   chunk 46 optimal weight:    7.9990
   chunk 4 optimal weight:   30.0000
   chunk 50 optimal weight:    9.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.5058

-------------------------------------------------------------------------------
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 = 0.4244 r_free = 0.4244 target = 0.205093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.164482 restraints weight = 8005.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3858 rms_B_bonded: 1.99
r_work: 0.3705 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3551 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7749  Z= 0.164
  Angle     :  0.547   6.791  10514  Z= 0.272
  Chirality :  0.042   0.163   1242
  Planarity :  0.004   0.043   1335
  Dihedral  :  3.858  17.305   1040
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 20.64 %
    Favored  : 75.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.27), residues: 973
  helix:  1.17 (0.25), residues: 452
  sheet: -1.61 (0.52), residues: 92
  loop : -1.40 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 854 
 HIS   0.001   0.000   HIS A  15 
 PHE   0.025   0.001   PHE A 759 
 TYR   0.011   0.001   TYR A 990 
 ARG   0.004   0.000   ARG A 528 

*********************** 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
  124 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 95
  time to evaluate  : 0.784 
Fit side-chains
REVERT: A  138 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7756 (pm20)
REVERT: A  198 ARG cc_start: 0.8314 (ttm170) cc_final: 0.7241 (tmt170)
REVERT: A  207 MET cc_start: 0.8491 (mtt) cc_final: 0.8032 (mtt)
REVERT: A  246 ARG cc_start: 0.7532 (mtp85) cc_final: 0.6920 (mtm-85)
REVERT: A  384 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8096 (mm)
REVERT: A  452 MET cc_start: 0.7079 (tmm) cc_final: 0.6700 (tmm)
REVERT: A  466 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8270 (tm-30)
REVERT: A  479 MET cc_start: 0.8536 (mpp) cc_final: 0.8234 (mpp)
REVERT: A  719 MET cc_start: 0.8692 (mmm) cc_final: 0.8067 (mmm)
REVERT: A  756 MET cc_start: 0.8180 (ttp) cc_final: 0.7619 (ttm)
REVERT: A  900 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7381 (tp)
REVERT: A  956 PHE cc_start: 0.5448 (OUTLIER) cc_final: 0.3582 (p90)
  outliers start: 29
  outliers final: 21
  residues processed: 120
  average time/residue: 0.1673
  time to fit residues: 29.3160
Evaluate side-chains
  119 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
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  263 VAL
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  384 ILE
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  466 GLU
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  792 LEU
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  949 VAL
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  970 LEU
Chi-restraints excluded: chain A residue  982 THR
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 1 optimal weight:    0.5980
   chunk 63 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 85 optimal weight:    6.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.4235 r_free = 0.4235 target = 0.204070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.163140 restraints weight = 7934.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3857 rms_B_bonded: 1.93
r_work: 0.3704 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3546 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7749  Z= 0.189
  Angle     :  0.555   7.281  10514  Z= 0.276
  Chirality :  0.042   0.169   1242
  Planarity :  0.004   0.043   1335
  Dihedral  :  3.864  16.894   1040
  Min Nonbonded Distance : 1.854

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 20.53 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.27), residues: 973
  helix:  1.13 (0.24), residues: 455
  sheet: -1.58 (0.51), residues: 92
  loop : -1.35 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 854 
 HIS   0.001   0.000   HIS A 566 
 PHE   0.025   0.001   PHE A 759 
 TYR   0.013   0.001   TYR A 990 
 ARG   0.004   0.000   ARG A 523 

********************** 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
  124 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 95
  time to evaluate  : 0.978 
Fit side-chains
REVERT: A  138 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7844 (pm20)
REVERT: A  198 ARG cc_start: 0.8326 (ttm170) cc_final: 0.7266 (tmt170)
REVERT: A  207 MET cc_start: 0.8499 (mtt) cc_final: 0.8046 (mtt)
REVERT: A  220 MET cc_start: 0.7933 (ptp) cc_final: 0.7690 (ptp)
REVERT: A  246 ARG cc_start: 0.7514 (mtp85) cc_final: 0.6878 (mtm-85)
REVERT: A  332 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.7914 (mp)
REVERT: A  384 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8213 (mm)
REVERT: A  452 MET cc_start: 0.7143 (tmm) cc_final: 0.6759 (tmm)
REVERT: A  466 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8276 (tm-30)
REVERT: A  479 MET cc_start: 0.8492 (mpp) cc_final: 0.8127 (mpp)
REVERT: A  699 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7607 (ttt)
REVERT: A  719 MET cc_start: 0.8715 (mmm) cc_final: 0.8075 (mmm)
REVERT: A  756 MET cc_start: 0.8221 (ttp) cc_final: 0.7658 (ttm)
REVERT: A  900 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7384 (tp)
REVERT: A  956 PHE cc_start: 0.5377 (OUTLIER) cc_final: 0.3462 (p90)
  outliers start: 29
  outliers final: 22
  residues processed: 119
  average time/residue: 0.1522
  time to fit residues: 26.4718
Evaluate side-chains
  123 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 94
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
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  263 VAL
Chi-restraints excluded: chain A residue  318 CYS
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  384 ILE
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  466 GLU
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  900 LEU
Chi-restraints excluded: chain A residue  906 ILE
Chi-restraints excluded: chain A residue  940 MET
Chi-restraints excluded: chain A residue  949 VAL
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  970 LEU
Chi-restraints excluded: chain A residue  982 THR
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 10 optimal weight:    3.9990
   chunk 4 optimal weight:   30.0000
   chunk 83 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 989 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.200938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.156653 restraints weight = 7933.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 1.86
r_work: 0.3622 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3472 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.2558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7749  Z= 0.241
  Angle     :  0.589   8.507  10514  Z= 0.291
  Chirality :  0.043   0.173   1242
  Planarity :  0.004   0.039   1335
  Dihedral  :  3.977  17.002   1040
  Min Nonbonded Distance : 1.794

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 20.88 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.27), residues: 973
  helix:  1.11 (0.24), residues: 452
  sheet: -1.38 (0.55), residues: 82
  loop : -1.45 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 854 
 HIS   0.001   0.000   HIS A  15 
 PHE   0.026   0.002   PHE A 759 
 TYR   0.014   0.001   TYR A 990 
 ARG   0.004   0.000   ARG A 523 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3975.17 seconds
wall clock time: 71 minutes 10.14 seconds (4270.14 seconds total)