Starting phenix.real_space_refine
on Wed Mar 12 08:16:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ln9_0928/03_2025/6ln9_0928.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ln9_0928/03_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_0928/03_2025/6ln9_0928.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ln9_0928/03_2025/6ln9_0928.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ln9_0928/03_2025/6ln9_0928.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ln9_0928/03_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.08, per 1000 atoms: 0.67
  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: 2.13
  Conformation dependent library (CDL) restraints added in 894.1 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: 0.98
  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: 2.55

  Time building geometry restraints manager: 2.49 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:             0.310
  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:          0.290
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     22.030
  Find NCS groups from input model:        0.080
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.670
-------------------------------------------------------------------------------
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  : 0.889 
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: 0.2312
  time to fit residues: 44.8023
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  : 0.877 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 46 optimal weight:    9.9990
   chunk 57 optimal weight:    5.9990
   chunk 88 optimal weight:    0.6980
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.4238 r_free = 0.4238 target = 0.203845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.163383 restraints weight = 7864.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 1.79
r_work: 0.3707 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3561 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.1449

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= 0.201
  Angle     :  0.573   7.863  10514  Z= 0.289
  Chirality :  0.043   0.174   1242
  Planarity :  0.004   0.040   1335
  Dihedral  :  3.854  19.226   1040
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 12.53 %
    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 (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: -1.61 (0.26), residues: 973
  helix:  0.13 (0.24), residues: 446
  sheet: -2.38 (0.44), residues: 97
  loop : -2.03 (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   0.010   0.001   TYR A 990 
 ARG   0.004   0.000   ARG A 528 

*********************** 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
  128 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.5938 (tp) cc_final: 0.5710 (tp)
REVERT: A  198 ARG cc_start: 0.8384 (ttm170) cc_final: 0.7225 (tmm160)
REVERT: A  246 ARG cc_start: 0.7484 (mtp85) cc_final: 0.7051 (mtm-85)
REVERT: A  326 MET cc_start: 0.7394 (mmm) cc_final: 0.7106 (tpt)
REVERT: A  452 MET cc_start: 0.7275 (tmm) cc_final: 0.6820 (tmm)
REVERT: A  479 MET cc_start: 0.8500 (mpp) cc_final: 0.7988 (mpp)
REVERT: A  719 MET cc_start: 0.8548 (mmm) cc_final: 0.8236 (mmm)
REVERT: A  756 MET cc_start: 0.8326 (ttp) cc_final: 0.7728 (ttm)
REVERT: A  816 MET cc_start: 0.7201 (mmm) cc_final: 0.6878 (mmm)
  outliers start: 13
  outliers final: 8
  residues processed: 122
  average time/residue: 0.1800
  time to fit residues: 30.7466
Evaluate side-chains
  103 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 63 optimal weight:    6.9990
   chunk 59 optimal weight:    5.9990
   chunk 51 optimal weight:    0.3980
   chunk 11 optimal weight:    5.9990
   chunk 81 optimal weight:    0.6980
   chunk 44 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 86 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4222 r_free = 0.4222 target = 0.202552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.161046 restraints weight = 8059.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3816 rms_B_bonded: 1.82
r_work: 0.3669 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3524 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.1718

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= 0.177
  Angle     :  0.546   7.166  10514  Z= 0.275
  Chirality :  0.042   0.163   1242
  Planarity :  0.004   0.040   1335
  Dihedral  :  3.850  17.869   1040
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 16.35 %
    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 (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: -1.11 (0.26), residues: 973
  helix:  0.57 (0.24), residues: 452
  sheet: -2.07 (0.47), residues: 97
  loop : -1.85 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 854 
 HIS   0.001   0.000   HIS A  15 
 PHE   0.026   0.001   PHE A 759 
 TYR   0.011   0.001   TYR A 990 
 ARG   0.003   0.000   ARG A 528 

*********************** 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
  121 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 ARG cc_start: 0.8326 (ttm170) cc_final: 0.7203 (tmm160)
REVERT: A  246 ARG cc_start: 0.7400 (mtp85) cc_final: 0.6979 (mtm-85)
REVERT: A  326 MET cc_start: 0.7334 (mmm) cc_final: 0.7086 (tpt)
REVERT: A  452 MET cc_start: 0.7182 (tmm) cc_final: 0.6681 (tmm)
REVERT: A  523 ARG cc_start: 0.8352 (ptp-110) cc_final: 0.8114 (ptp90)
REVERT: A  699 MET cc_start: 0.8159 (ttt) cc_final: 0.7896 (ttt)
REVERT: A  719 MET cc_start: 0.8605 (mmm) cc_final: 0.8147 (mmm)
REVERT: A  756 MET cc_start: 0.8319 (ttp) cc_final: 0.7736 (ttm)
  outliers start: 13
  outliers final: 10
  residues processed: 113
  average time/residue: 0.1794
  time to fit residues: 28.6038
Evaluate side-chains
  111 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
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  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 46 optimal weight:   10.0000
   chunk 86 optimal weight:   10.0000
   chunk 96 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   chunk 42 optimal weight:    0.5980
   chunk 8 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 53 optimal weight:    9.9990
   chunk 95 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 84 optimal weight:    0.8980
   overall best weight:    1.2382

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.202386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.161369 restraints weight = 7950.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3825 rms_B_bonded: 1.77
r_work: 0.3672 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3527 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7749  Z= 0.232
  Angle     :  0.564   6.750  10514  Z= 0.285
  Chirality :  0.043   0.170   1242
  Planarity :  0.004   0.041   1335
  Dihedral  :  3.921  17.401   1040
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 17.42 %
    Favored  : 79.47 %
  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: -0.89 (0.27), residues: 973
  helix:  0.73 (0.24), residues: 450
  sheet: -1.88 (0.48), residues: 97
  loop : -1.73 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 854 
 HIS   0.002   0.000   HIS A  15 
 PHE   0.026   0.002   PHE A 759 
 TYR   0.013   0.001   TYR A 990 
 ARG   0.002   0.000   ARG A 677 

*********************** 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
  129 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 ASN cc_start: 0.7056 (OUTLIER) cc_final: 0.6418 (p0)
REVERT: A  198 ARG cc_start: 0.8415 (ttm170) cc_final: 0.7366 (tmm160)
REVERT: A  246 ARG cc_start: 0.7439 (mtp85) cc_final: 0.6961 (mtm-85)
REVERT: A  326 MET cc_start: 0.7407 (mmm) cc_final: 0.7105 (tpt)
REVERT: A  452 MET cc_start: 0.7148 (tmm) cc_final: 0.6615 (tmm)
REVERT: A  719 MET cc_start: 0.8617 (mmm) cc_final: 0.8066 (mmm)
REVERT: A  756 MET cc_start: 0.8367 (ttp) cc_final: 0.7784 (ttm)
  outliers start: 26
  outliers final: 17
  residues processed: 118
  average time/residue: 0.1600
  time to fit residues: 27.3953
Evaluate side-chains
  118 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
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   89 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  101 ASN
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  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  959 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 30 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 95 optimal weight:    0.5980
   chunk 7 optimal weight:    8.9990
   chunk 48 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.203802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.162800 restraints weight = 7886.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3791 rms_B_bonded: 1.80
r_work: 0.3641 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3495 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
moved from start:          0.2047

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= 0.180
  Angle     :  0.542   6.737  10514  Z= 0.273
  Chirality :  0.042   0.167   1242
  Planarity :  0.004   0.042   1335
  Dihedral  :  3.885  17.490   1040
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 18.97 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.27), residues: 973
  helix:  0.90 (0.25), residues: 450
  sheet: -1.72 (0.49), residues: 97
  loop : -1.64 (0.30), residues: 426

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   0.001   PHE A 759 
 TYR   0.011   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
  120 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 ARG cc_start: 0.8318 (ttm170) cc_final: 0.7402 (tmt170)
REVERT: A  246 ARG cc_start: 0.7498 (mtp85) cc_final: 0.6905 (mtm-85)
REVERT: A  326 MET cc_start: 0.7371 (mmm) cc_final: 0.7088 (tpt)
REVERT: A  452 MET cc_start: 0.7106 (tmm) cc_final: 0.6537 (tmm)
REVERT: A  719 MET cc_start: 0.8641 (mmm) cc_final: 0.8103 (mmm)
REVERT: A  756 MET cc_start: 0.8282 (ttp) cc_final: 0.7678 (ttm)
REVERT: A  816 MET cc_start: 0.7387 (mmm) cc_final: 0.6787 (mmm)
  outliers start: 17
  outliers final: 11
  residues processed: 114
  average time/residue: 0.1781
  time to fit residues: 28.6650
Evaluate side-chains
  109 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
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  402 VAL
Chi-restraints excluded: chain A residue  421 ASN
Chi-restraints excluded: chain A residue  454 VAL
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  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 29 optimal weight:    0.6980
   chunk 85 optimal weight:    0.0000
   chunk 65 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 55 optimal weight:   20.0000
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.6984

-------------------------------------------------------------------------------
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
A 989 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.204396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.163577 restraints weight = 7902.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3812 rms_B_bonded: 1.76
r_work: 0.3659 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3512 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.2143

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= 0.175
  Angle     :  0.538   7.153  10514  Z= 0.269
  Chirality :  0.041   0.165   1242
  Planarity :  0.004   0.042   1335
  Dihedral  :  3.840  17.183   1040
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.62 %
    Favored  : 78.52 %
  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:  1.02 (0.25), residues: 451
  sheet: -1.59 (0.50), residues: 97
  loop : -1.58 (0.30), residues: 425

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   0.001   PHE A 759 
 TYR   0.012   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
  126 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.774 
Fit side-chains
REVERT: A  198 ARG cc_start: 0.8230 (ttm170) cc_final: 0.7211 (tmt170)
REVERT: A  246 ARG cc_start: 0.7535 (mtp85) cc_final: 0.6937 (mtm-85)
REVERT: A  326 MET cc_start: 0.7283 (mmm) cc_final: 0.7000 (tpt)
REVERT: A  452 MET cc_start: 0.7083 (tmm) cc_final: 0.6496 (tmm)
REVERT: A  479 MET cc_start: 0.8391 (mpp) cc_final: 0.8131 (mpp)
REVERT: A  719 MET cc_start: 0.8702 (mmm) cc_final: 0.8111 (mmm)
REVERT: A  756 MET cc_start: 0.8266 (ttp) cc_final: 0.7676 (ttm)
REVERT: A  900 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7343 (tp)
REVERT: A  956 PHE cc_start: 0.5386 (OUTLIER) cc_final: 0.3216 (p90)
  outliers start: 24
  outliers final: 19
  residues processed: 118
  average time/residue: 0.1530
  time to fit residues: 26.6270
Evaluate side-chains
  118 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
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  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  421 ASN
Chi-restraints excluded: chain A residue  454 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  792 LEU
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  989 ASN
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:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 57 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 48 optimal weight:    7.9990
   chunk 52 optimal weight:    5.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 568 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 = 0.4238 r_free = 0.4238 target = 0.204134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.163109 restraints weight = 7966.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3799 rms_B_bonded: 1.77
r_work: 0.3647 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3501 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7749  Z= 0.186
  Angle     :  0.542   7.061  10514  Z= 0.272
  Chirality :  0.042   0.166   1242
  Planarity :  0.004   0.042   1335
  Dihedral  :  3.843  17.254   1040
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 18.85 %
    Favored  : 77.80 %
  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: -0.48 (0.27), residues: 973
  helix:  1.07 (0.25), residues: 451
  sheet: -1.52 (0.48), residues: 108
  loop : -1.54 (0.30), residues: 414

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   0.001   PHE A 759 
 TYR   0.024   0.001   TYR A 990 
 ARG   0.003   0.000   ARG A 523 

*********************** 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
  128 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 100
  time to evaluate  : 0.735 
Fit side-chains
REVERT: A  101 ASN cc_start: 0.7255 (OUTLIER) cc_final: 0.6333 (p0)
REVERT: A  138 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7588 (pm20)
REVERT: A  198 ARG cc_start: 0.8248 (ttm170) cc_final: 0.7066 (tmt170)
REVERT: A  207 MET cc_start: 0.8703 (mtp) cc_final: 0.8436 (mtp)
REVERT: A  246 ARG cc_start: 0.7514 (mtp85) cc_final: 0.6884 (mtm-85)
REVERT: A  326 MET cc_start: 0.7380 (mmm) cc_final: 0.7089 (tpt)
REVERT: A  452 MET cc_start: 0.7041 (tmm) cc_final: 0.6407 (tmm)
REVERT: A  479 MET cc_start: 0.8411 (mpp) cc_final: 0.8172 (mpp)
REVERT: A  719 MET cc_start: 0.8716 (mmm) cc_final: 0.8094 (mmm)
REVERT: A  756 MET cc_start: 0.8269 (ttp) cc_final: 0.7690 (ttm)
REVERT: A  900 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7354 (tp)
REVERT: A  956 PHE cc_start: 0.5268 (OUTLIER) cc_final: 0.3277 (p90)
  outliers start: 28
  outliers final: 21
  residues processed: 119
  average time/residue: 0.1646
  time to fit residues: 28.1148
Evaluate side-chains
  123 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 98
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
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  153 ILE
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  568 ASN
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 45 optimal weight:    0.3980
   chunk 33 optimal weight:    0.4980
   chunk 6 optimal weight:    0.6980
   chunk 69 optimal weight:    0.0050
   chunk 22 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   chunk 27 optimal weight:    0.1980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.3594

-------------------------------------------------------------------------------
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 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 = 0.4260 r_free = 0.4260 target = 0.206601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.165683 restraints weight = 7913.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3860 rms_B_bonded: 1.81
r_work: 0.3720 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3574 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.2301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7749  Z= 0.150
  Angle     :  0.520   7.036  10514  Z= 0.261
  Chirality :  0.041   0.162   1242
  Planarity :  0.004   0.041   1335
  Dihedral  :  3.759  16.879   1040
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 19.33 %
    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 (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: -0.37 (0.27), residues: 973
  helix:  1.14 (0.25), residues: 454
  sheet: -1.54 (0.51), residues: 92
  loop : -1.47 (0.30), residues: 427

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   0.026   0.001   PHE A 759 
 TYR   0.012   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
  124 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 0.831 
Fit side-chains
REVERT: A  138 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7709 (pm20)
REVERT: A  198 ARG cc_start: 0.8198 (ttm170) cc_final: 0.7033 (tmt170)
REVERT: A  207 MET cc_start: 0.8685 (mtp) cc_final: 0.8437 (mtp)
REVERT: A  246 ARG cc_start: 0.7528 (mtp85) cc_final: 0.6920 (mtm-85)
REVERT: A  452 MET cc_start: 0.7031 (tmm) cc_final: 0.6398 (tmm)
REVERT: A  479 MET cc_start: 0.8403 (mpp) cc_final: 0.8158 (mpp)
REVERT: A  523 ARG cc_start: 0.8309 (ptp-110) cc_final: 0.7816 (ptp90)
REVERT: A  719 MET cc_start: 0.8720 (mmm) cc_final: 0.8073 (mmm)
REVERT: A  756 MET cc_start: 0.8139 (ttp) cc_final: 0.7571 (ttm)
REVERT: A  900 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7292 (tp)
REVERT: A  956 PHE cc_start: 0.5546 (OUTLIER) cc_final: 0.3543 (p90)
  outliers start: 23
  outliers final: 18
  residues processed: 119
  average time/residue: 0.1621
  time to fit residues: 28.3244
Evaluate side-chains
  117 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
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  166 THR
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  498 CYS
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  900 LEU
Chi-restraints excluded: chain A residue  906 ILE
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 1023 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 32 optimal weight:    0.1980
   chunk 27 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 48 optimal weight:    7.9990
   chunk 46 optimal weight:    7.9990
   chunk 4 optimal weight:   30.0000
   chunk 50 optimal weight:    4.9990
   chunk 47 optimal weight:    8.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.4225 r_free = 0.4225 target = 0.202470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.160928 restraints weight = 8084.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3783 rms_B_bonded: 1.82
r_work: 0.3636 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3488 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7749  Z= 0.227
  Angle     :  0.560   6.924  10514  Z= 0.282
  Chirality :  0.042   0.173   1242
  Planarity :  0.004   0.041   1335
  Dihedral  :  3.883  16.984   1040
  Min Nonbonded Distance : 1.845

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 19.09 %
    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 (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: -0.40 (0.27), residues: 973
  helix:  1.11 (0.25), residues: 451
  sheet: -1.58 (0.51), residues: 92
  loop : -1.47 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 854 
 HIS   0.002   0.000   HIS A  15 
 PHE   0.026   0.002   PHE A 759 
 TYR   0.015   0.001   TYR A 990 
 ARG   0.003   0.000   ARG A 523 

*********************** 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
  121 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.750 
Fit side-chains
REVERT: A  138 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7759 (pm20)
REVERT: A  198 ARG cc_start: 0.8253 (ttm170) cc_final: 0.7232 (tmt170)
REVERT: A  246 ARG cc_start: 0.7521 (mtp85) cc_final: 0.6877 (mtm-85)
REVERT: A  452 MET cc_start: 0.7175 (tmm) cc_final: 0.6561 (tmm)
REVERT: A  479 MET cc_start: 0.8490 (mpp) cc_final: 0.8165 (mpp)
REVERT: A  719 MET cc_start: 0.8747 (mmm) cc_final: 0.8086 (mmm)
REVERT: A  756 MET cc_start: 0.8288 (ttp) cc_final: 0.7697 (ttm)
REVERT: A  900 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7344 (tp)
REVERT: A  956 PHE cc_start: 0.5326 (OUTLIER) cc_final: 0.3424 (p90)
  outliers start: 24
  outliers final: 20
  residues processed: 115
  average time/residue: 0.1518
  time to fit residues: 25.5794
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  : 0.954 
-------------------------------------------------------------------------------
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  342 LEU
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  653 THR
Chi-restraints excluded: chain A residue  715 ILE
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 5 optimal weight:    0.2980
   chunk 57 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.4231 r_free = 0.4231 target = 0.203053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.161507 restraints weight = 8010.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 1.82
r_work: 0.3630 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3486 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
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      :  0.003   0.040   7749  Z= 0.206
  Angle     :  0.557   7.194  10514  Z= 0.280
  Chirality :  0.042   0.169   1242
  Planarity :  0.004   0.037   1335
  Dihedral  :  3.895  16.801   1040
  Min Nonbonded Distance : 1.845

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 19.57 %
    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: -0.33 (0.27), residues: 973
  helix:  1.16 (0.24), residues: 452
  sheet: -1.60 (0.51), residues: 92
  loop : -1.41 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 854 
 HIS   0.002   0.000   HIS A  15 
 PHE   0.025   0.002   PHE A 759 
 TYR   0.014   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
  114 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.743 
Fit side-chains
REVERT: A  138 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7856 (pm20)
REVERT: A  198 ARG cc_start: 0.8242 (ttm170) cc_final: 0.7247 (tmt170)
REVERT: A  246 ARG cc_start: 0.7554 (mtp85) cc_final: 0.6897 (mtm-85)
REVERT: A  452 MET cc_start: 0.7211 (tmm) cc_final: 0.6841 (tmm)
REVERT: A  479 MET cc_start: 0.8529 (mpp) cc_final: 0.8127 (mpp)
REVERT: A  719 MET cc_start: 0.8739 (mmm) cc_final: 0.8077 (mmm)
REVERT: A  756 MET cc_start: 0.8277 (ttp) cc_final: 0.7683 (ttm)
REVERT: A  900 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7353 (tp)
REVERT: A  956 PHE cc_start: 0.5234 (OUTLIER) cc_final: 0.3332 (p90)
  outliers start: 23
  outliers final: 20
  residues processed: 109
  average time/residue: 0.1499
  time to fit residues: 24.3067
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  : 0.734 
-------------------------------------------------------------------------------
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  342 LEU
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  715 ILE
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  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 1023 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 4 optimal weight:   30.0000
   chunk 83 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.4227 r_free = 0.4227 target = 0.202622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.161024 restraints weight = 7950.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3777 rms_B_bonded: 1.81
r_work: 0.3628 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3485 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7749  Z= 0.214
  Angle     :  0.567   8.452  10514  Z= 0.282
  Chirality :  0.042   0.169   1242
  Planarity :  0.004   0.035   1335
  Dihedral  :  3.928  16.566   1040
  Min Nonbonded Distance : 1.831

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 19.33 %
    Favored  : 77.33 %
  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:  1.20 (0.24), residues: 451
  sheet: -1.63 (0.51), residues: 92
  loop : -1.41 (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  15 
 PHE   0.025   0.002   PHE A 759 
 TYR   0.014   0.001   TYR A 990 
 ARG   0.003   0.000   ARG A 523 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4108.36 seconds
wall clock time: 71 minutes 8.74 seconds (4268.74 seconds total)