Starting phenix.real_space_refine
on Wed Mar  4 06:45:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wb1_32392/03_2026/7wb1_32392.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wb1_32392/03_2026/7wb1_32392.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wb1_32392/03_2026/7wb1_32392.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wb1_32392/03_2026/7wb1_32392.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wb1_32392/03_2026/7wb1_32392.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wb1_32392/03_2026/7wb1_32392.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     P     178      5.49       5
     S      28      5.16       5
     C    6661      2.51       5
     N    2059      2.21       5
     O    2598      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11524
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 614
          Classifications: {'DNA': 30}
          Link IDs: {'rna3p': 29}
    Chain: "C"
      Number of atoms: 547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 547
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "D"
      Number of atoms: 2577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 2577
          Classifications: {'RNA': 121}
          Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 59, 'rna3p_pyr': 48}
          Link IDs: {'rna2p': 14, 'rna3p': 106}
    Chain: "A"
      Number of atoms: 7786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 960, 7786
          Classifications: {'peptide': 960}
          Link IDs: {'PTRANS': 37, 'TRANS': 922}
          Chain breaks: 2
  Time building chain proxies: 2.46, per 1000 atoms: 0.21
  Number of scatterers: 11524
  At special positions: 0
  Unit cell: (101.52, 141, 121.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      28     16.00
     P     178     15.00
     O    2598      8.00
     N    2059      7.00
     C    6661      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.95
  Conformation dependent library (CDL) restraints added in 433.0 milliseconds
  

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1810

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 12 sheets defined
      49.4% alpha, 13.1% beta
      62 base pairs and 95 stacking pairs defined.
    Time for finding SS restraints: 1.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 17
    Processing helix  chain 'A' and resid 38 through 47
    Processing helix  chain 'A' and resid 60 through 92
      removed outlier: 3.735A  pdb=" N   ARG A  64 " --> pdb=" O   SER A  60 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ALA A  65 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ASN A  66 " --> pdb=" O   THR A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 100
    Processing helix  chain 'A' and resid 161 through 165
    Processing helix  chain 'A' and resid 195 through 201
      removed outlier: 3.552A  pdb=" N   ILE A 199 " --> pdb=" O   ASP A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 215
    Processing helix  chain 'A' and resid 222 through 271
      removed outlier: 3.577A  pdb=" N   ASP A 231 " --> pdb=" O   LYS A 227 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ALA A 236 " --> pdb=" O   ALA A 232 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   LEU A 249 " --> pdb=" O   GLN A 245 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   GLU A 250 " --> pdb=" O   ASP A 246 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   GLN A 252 " --> pdb=" O   ILE A 248 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   LYS A 260 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ARG A 261 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU A 262 " --> pdb=" O   ASN A 258 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ALA A 263 " --> pdb=" O   GLU A 259 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ASN A 264 " --> pdb=" O   LYS A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 309
    Processing helix  chain 'A' and resid 343 through 358
      removed outlier: 3.605A  pdb=" N   GLU A 357 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   LYS A 358 " --> pdb=" O   LEU A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 368
      removed outlier: 3.748A  pdb=" N   GLY A 362 " --> pdb=" O   LYS A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 378
      removed outlier: 3.755A  pdb=" N   GLU A 376 " --> pdb=" O   TYR A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 382
    Processing helix  chain 'A' and resid 384 through 390
      removed outlier: 3.807A  pdb=" N   LYS A 390 " --> pdb=" O   GLU A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 411
    Processing helix  chain 'A' and resid 413 through 443
      removed outlier: 4.041A  pdb=" N   VAL A 417 " --> pdb=" O   ASP A 413 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   TYR A 418 " --> pdb=" O   TRP A 414 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   ASP A 419 " --> pdb=" O   GLY A 415 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   ARG A 442 " --> pdb=" O   LEU A 438 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   ARG A 443 " --> pdb=" O   GLU A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 466
      removed outlier: 4.200A  pdb=" N   LYS A 450 " --> pdb=" O   ASP A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 469
      No H-bonds generated for 'chain 'A' and resid 467 through 469'
    Processing helix  chain 'A' and resid 472 through 493
    Processing helix  chain 'A' and resid 494 through 496
      No H-bonds generated for 'chain 'A' and resid 494 through 496'
    Processing helix  chain 'A' and resid 589 through 596
    Processing helix  chain 'A' and resid 697 through 717
      removed outlier: 3.602A  pdb=" N   LYS A 701 " --> pdb=" O   SER A 697 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ARG A 715 " --> pdb=" O   VAL A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 720 through 724
    Processing helix  chain 'A' and resid 725 through 750
    Processing helix  chain 'A' and resid 770 through 774
    Processing helix  chain 'A' and resid 776 through 789
    Processing helix  chain 'A' and resid 793 through 798
      removed outlier: 4.163A  pdb=" N   TYR A 797 " --> pdb=" O   PRO A 793 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 818 through 829
      removed outlier: 3.504A  pdb=" N   LYS A 828 " --> pdb=" O   ARG A 824 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 866 through 874
    Processing helix  chain 'A' and resid 875 through 877
      No H-bonds generated for 'chain 'A' and resid 875 through 877'
    Processing helix  chain 'A' and resid 881 through 885
    Processing helix  chain 'A' and resid 886 through 901
      removed outlier: 3.754A  pdb=" N   GLU A 892 " --> pdb=" O   GLY A 888 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 920 through 937
      removed outlier: 3.835A  pdb=" N   GLN A 924 " --> pdb=" O   HIS A 920 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA A 930 " --> pdb=" O   ALA A 926 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ARG A 937 " --> pdb=" O   TRP A 933 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 939 through 949
    Processing helix  chain 'A' and resid 954 through 971
      removed outlier: 3.805A  pdb=" N   PHE A 958 " --> pdb=" O   ASP A 954 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22
    Processing sheet with id=AA2, first strand: chain 'A' and resid 502 through 506
      removed outlier: 3.505A  pdb=" N   SER A 502 " --> pdb=" O   GLU A 618 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   GLY A 614 " --> pdb=" O   ILE A 506 " (cutoff:3.500A)
      removed outlier: 5.291A  pdb=" N   LEU A 611 " --> pdb=" O   GLU A 640 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   GLU A 640 " --> pdb=" O   LEU A 611 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ASN A 613 " --> pdb=" O   THR A 638 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   LEU A 633 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   VAL A  36 " --> pdb=" O   LEU A 633 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 587 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115
      removed outlier: 4.525A  pdb=" N   ILE A 114 " --> pdb=" O   LYS A 141 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   GLN A 135 " --> pdb=" O   CYS A 130 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   PHE A 128 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 115
      removed outlier: 4.525A  pdb=" N   ILE A 114 " --> pdb=" O   LYS A 141 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   TYR A 155 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 145
      removed outlier: 3.629A  pdb=" N   GLN A 144 " --> pdb=" O   HIS A 152 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   HIS A 152 " --> pdb=" O   GLN A 144 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 542 through 545
      removed outlier: 3.504A  pdb=" N   ARG A 542 " --> pdb=" O   ASN A 573 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ASN A 573 " --> pdb=" O   ARG A 542 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL A 572 " --> pdb=" O   PHE A 556 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   PHE A 556 " --> pdb=" O   VAL A 572 " (cutoff:3.500A)
      removed outlier: 5.393A  pdb=" N   VAL A 559 " --> pdb=" O   PHE A 517 " (cutoff:3.500A)
      removed outlier: 7.260A  pdb=" N   PHE A 517 " --> pdb=" O   VAL A 559 " (cutoff:3.500A)
      removed outlier: 10.291A  pdb=" N   ASN A 561 " --> pdb=" O   CYS A 515 " (cutoff:3.500A)
      removed outlier: 12.651A  pdb=" N   CYS A 515 " --> pdb=" O   ASN A 561 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 622 through 623
    Processing sheet with id=AA8, first strand: chain 'A' and resid 691 through 694
      removed outlier: 4.777A  pdb=" N   ALA A 756 " --> pdb=" O   ILE A 658 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   THR A 801 " --> pdb=" O   LEU A 753 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   PHE A 755 " --> pdb=" O   THR A 801 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 681 through 682
    Processing sheet with id=AB1, first strand: chain 'A' and resid 830 through 831
      removed outlier: 3.513A  pdb=" N   LYS A 830 " --> pdb=" O   MET A 837 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 850 through 853
      removed outlier: 4.192A  pdb=" N   TYR A 853 " --> pdb=" O   VAL A 862 " (cutoff:3.500A)
      removed outlier: 4.731A  pdb=" N   VAL A 862 " --> pdb=" O   TYR A 853 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 910 through 911

    382 hydrogen bonds defined for protein.
    1095 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      150 hydrogen bonds
      276 hydrogen bond angles
      0 basepair planarities
      62 basepair parallelities
      95 stacking parallelities
  Total time for adding SS restraints: 2.87

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2385
        1.33 -     1.45: 3515
        1.45 -     1.57: 5830
        1.57 -     1.69: 353
        1.69 -     1.81: 41
  Bond restraints: 12124
  Sorted by residual:
  bond pdb=" CG  LEU A  70 "
       pdb=" CD2 LEU A  70 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.69e+00
  bond pdb=" N1    C D 103 "
       pdb=" C2    C D 103 "
    ideal  model  delta    sigma   weight residual
    1.397  1.422 -0.025 2.00e-02 2.50e+03 1.59e+00
  bond pdb=" C2    C D 104 "
       pdb=" O2    C D 104 "
    ideal  model  delta    sigma   weight residual
    1.240  1.216  0.024 2.00e-02 2.50e+03 1.50e+00
  bond pdb=" O4'  DG B  19 "
       pdb=" C1'  DG B  19 "
    ideal  model  delta    sigma   weight residual
    1.414  1.395  0.019 2.00e-02 2.50e+03 9.34e-01
  bond pdb=" CG  ARG A 967 "
       pdb=" CD  ARG A 967 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.98e-01
  ... (remaining 12119 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 16501
        1.32 -     2.64: 542
        2.64 -     3.96: 102
        3.96 -     5.28: 15
        5.28 -     6.60: 11
  Bond angle restraints: 17171
  Sorted by residual:
  angle pdb=" N   TYR A 854 "
        pdb=" CA  TYR A 854 "
        pdb=" C   TYR A 854 "
      ideal   model   delta    sigma   weight residual
     107.32  112.15   -4.83 1.65e+00 3.67e-01 8.57e+00
  angle pdb=" C   GLU A 439 "
        pdb=" N   GLU A 440 "
        pdb=" CA  GLU A 440 "
      ideal   model   delta    sigma   weight residual
     121.94  116.41    5.53 2.00e+00 2.50e-01 7.63e+00
  angle pdb=" C2'   G D  73 "
        pdb=" C1'   G D  73 "
        pdb=" N9    G D  73 "
      ideal   model   delta    sigma   weight residual
     112.00  115.74   -3.74 1.50e+00 4.44e-01 6.23e+00
  angle pdb=" C   TYR A 966 "
        pdb=" N   ARG A 967 "
        pdb=" CA  ARG A 967 "
      ideal   model   delta    sigma   weight residual
     121.14  116.80    4.34 1.75e+00 3.27e-01 6.14e+00
  angle pdb=" O3'   G D  45 "
        pdb=" C3'   G D  45 "
        pdb=" C2'   G D  45 "
      ideal   model   delta    sigma   weight residual
     113.70  117.36   -3.66 1.50e+00 4.44e-01 5.95e+00
  ... (remaining 17166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.91: 6686
       35.91 -    71.82: 558
       71.82 -   107.73: 49
      107.73 -   143.64: 3
      143.64 -   179.55: 6
  Dihedral angle restraints: 7302
    sinusoidal: 4500
      harmonic: 2802
  Sorted by residual:
  dihedral pdb=" O4'   U D  11 "
           pdb=" C1'   U D  11 "
           pdb=" N1    U D  11 "
           pdb=" C2    U D  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   51.55 -179.55     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U D  17 "
           pdb=" C1'   U D  17 "
           pdb=" N1    U D  17 "
           pdb=" C2    U D  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   50.22 -178.22     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U D   9 "
           pdb=" C1'   U D   9 "
           pdb=" N1    U D   9 "
           pdb=" C2    U D   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00 -100.01  -59.99     1      1.50e+01 4.44e-03 2.13e+01
  ... (remaining 7299 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1634
       0.045 -    0.089: 268
       0.089 -    0.134: 68
       0.134 -    0.178: 8
       0.178 -    0.223: 1
  Chirality restraints: 1979
  Sorted by residual:
  chirality pdb=" C1'   G D  73 "
            pdb=" O4'   G D  73 "
            pdb=" C2'   G D  73 "
            pdb=" N9    G D  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.23    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" C3'   C D  41 "
            pdb=" C4'   C D  41 "
            pdb=" O3'   C D  41 "
            pdb=" C2'   C D  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.30   -0.18 2.00e-01 2.50e+01 7.72e-01
  chirality pdb=" C3'   G D  45 "
            pdb=" C4'   G D  45 "
            pdb=" O3'   G D  45 "
            pdb=" C2'   G D  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.30   -0.17 2.00e-01 2.50e+01 7.50e-01
  ... (remaining 1976 not shown)

  Planarity restraints: 1546
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C D 104 "    0.009 2.00e-02 2.50e+03   2.56e-02 1.47e+01
        pdb=" N1    C D 104 "   -0.006 2.00e-02 2.50e+03
        pdb=" C2    C D 104 "   -0.063 2.00e-02 2.50e+03
        pdb=" O2    C D 104 "    0.039 2.00e-02 2.50e+03
        pdb=" N3    C D 104 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    C D 104 "   -0.005 2.00e-02 2.50e+03
        pdb=" N4    C D 104 "    0.010 2.00e-02 2.50e+03
        pdb=" C5    C D 104 "    0.010 2.00e-02 2.50e+03
        pdb=" C6    C D 104 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C D 118 "    0.022 2.00e-02 2.50e+03   1.66e-02 6.17e+00
        pdb=" N1    C D 118 "   -0.033 2.00e-02 2.50e+03
        pdb=" C2    C D 118 "    0.007 2.00e-02 2.50e+03
        pdb=" O2    C D 118 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3    C D 118 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4    C D 118 "    0.025 2.00e-02 2.50e+03
        pdb=" N4    C D 118 "   -0.010 2.00e-02 2.50e+03
        pdb=" C5    C D 118 "    0.004 2.00e-02 2.50e+03
        pdb=" C6    C D 118 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  56 "   -0.006 2.00e-02 2.50e+03   1.42e-02 5.57e+00
        pdb=" N9    A D  56 "   -0.000 2.00e-02 2.50e+03
        pdb=" C8    A D  56 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    A D  56 "    0.004 2.00e-02 2.50e+03
        pdb=" C5    A D  56 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    A D  56 "    0.007 2.00e-02 2.50e+03
        pdb=" N6    A D  56 "    0.000 2.00e-02 2.50e+03
        pdb=" N1    A D  56 "   -0.033 2.00e-02 2.50e+03
        pdb=" C2    A D  56 "    0.031 2.00e-02 2.50e+03
        pdb=" N3    A D  56 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4    A D  56 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1543 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 183
        2.62 -     3.19: 9664
        3.19 -     3.76: 19864
        3.76 -     4.33: 25399
        4.33 -     4.90: 38127
  Nonbonded interactions: 93237
  Sorted by model distance:
  nonbonded pdb=" N2    G D  59 "
            pdb=" O2    C D  94 "
     model   vdw
     2.046 2.496
  nonbonded pdb=" OP2   G D 101 "
            pdb=" NH2 ARG A 591 "
     model   vdw
     2.182 3.120
  nonbonded pdb=" NZ  LYS A 521 "
            pdb=" OE2 GLU A 605 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" O6   DG B  22 "
            pdb=" NZ  LYS A 227 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" OG1 THR A 202 "
            pdb=" OE1 GLU A 204 "
     model   vdw
     2.263 3.040
  ... (remaining 93232 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.580
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
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   0.043  12124  Z= 0.139
  Angle     :  0.590   6.604  17171  Z= 0.317
  Chirality :  0.037   0.223   1979
  Planarity :  0.004   0.044   1546
  Dihedral  : 22.125 179.554   5492
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.72 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.28), residues: 954
  helix:  1.86 (0.26), residues: 412
  sheet: -0.69 (0.45), residues: 140
  loop : -0.80 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 764 
 TYR   0.017   0.001   TYR A 857 
 PHE   0.016   0.001   PHE A 332 
 TRP   0.009   0.001   TRP A 962 
 HIS   0.015   0.002   HIS A 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (12124)
  covalent geometry    : angle       0.59037 (17171)
  hydrogen bonds       : bond        0.17607 (  531)
  hydrogen bonds       : angle       5.88496 ( 1371)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A   29 MET cc_start: 0.6905 (ppp) cc_final: 0.5886 (ppp)
REVERT: A  375 GLN cc_start: 0.7736 (mm110) cc_final: 0.7534 (tp40)
REVERT: A  570 MET cc_start: 0.7668 (tpt) cc_final: 0.7458 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0936
  time to fit residues: 11.7343
Evaluate side-chains
  58 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    9.9990
   chunk 100 optimal weight:   10.0000
   chunk 106 optimal weight:    2.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 152 HIS
A 251 HIS
A 520 GLN
A 729 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.092850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.067062 restraints weight = 43965.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.069122 restraints weight = 23698.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.070409 restraints weight = 16666.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.071135 restraints weight = 13643.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 62)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.071601 restraints weight = 12228.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.1304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12124  Z= 0.191
  Angle     :  0.646   8.473  17171  Z= 0.342
  Chirality :  0.040   0.222   1979
  Planarity :  0.005   0.045   1546
  Dihedral  : 24.779 179.584   3482
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  8.34 %
    Favored  : 90.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.28), residues: 954
  helix:  1.65 (0.25), residues: 421
  sheet: -1.05 (0.41), residues: 154
  loop : -0.81 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 615 
 TYR   0.018   0.002   TYR A 857 
 PHE   0.026   0.002   PHE A 399 
 TRP   0.016   0.002   TRP A 366 
 HIS   0.007   0.002   HIS A 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 (12124)
  covalent geometry    : angle       0.64630 (17171)
  hydrogen bonds       : bond        0.07388 (  531)
  hydrogen bonds       : angle       4.65283 ( 1371)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  134 CYS cc_start: 0.8259 (m) cc_final: 0.8050 (m)
REVERT: A  486 TRP cc_start: 0.6974 (m-10) cc_final: 0.6766 (m-10)
REVERT: A  570 MET cc_start: 0.7996 (tpt) cc_final: 0.7720 (mmm)
  outliers start: 11
  outliers final: 8
  residues processed: 64
  average time/residue: 0.0858
  time to fit residues: 8.7578
Evaluate side-chains
  62 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 MET
Chi-restraints excluded: chain A residue  152 HIS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  653 MET
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  934 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 3 optimal weight:    7.9990
   chunk 55 optimal weight:    9.9990
   chunk 15 optimal weight:    7.9990
   chunk 43 optimal weight:    9.9990
   chunk 75 optimal weight:    6.9990
   chunk 41 optimal weight:    8.9990
   chunk 14 optimal weight:    9.9990
   chunk 87 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 160 ASN
A 284 GLN
A 306 ASN
A 375 GLN
A 804 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.090461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.064439 restraints weight = 44436.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.066520 restraints weight = 23407.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 73)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.067805 restraints weight = 16381.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 66)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.068563 restraints weight = 13401.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.068919 restraints weight = 11993.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  12124  Z= 0.275
  Angle     :  0.744  12.290  17171  Z= 0.391
  Chirality :  0.043   0.221   1979
  Planarity :  0.006   0.047   1546
  Dihedral  : 24.912 179.226   3482
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 11.08 %
    Favored  : 87.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.27), residues: 954
  helix:  1.05 (0.24), residues: 418
  sheet: -1.48 (0.43), residues: 133
  loop : -1.23 (0.30), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 642 
 TYR   0.021   0.002   TYR A 138 
 PHE   0.023   0.002   PHE A 399 
 TRP   0.013   0.002   TRP A 782 
 HIS   0.025   0.003   HIS A 152 

Details of bonding type rmsd
  covalent geometry    : bond        0.00581 (12124)
  covalent geometry    : angle       0.74412 (17171)
  hydrogen bonds       : bond        0.07978 (  531)
  hydrogen bonds       : angle       4.77557 ( 1371)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A  134 CYS cc_start: 0.8274 (m) cc_final: 0.7771 (t)
REVERT: A  486 TRP cc_start: 0.7050 (m-10) cc_final: 0.6804 (m-10)
REVERT: A  570 MET cc_start: 0.7916 (tpt) cc_final: 0.7587 (mmm)
REVERT: A  744 TYR cc_start: 0.8706 (t80) cc_final: 0.8489 (t80)
  outliers start: 15
  outliers final: 11
  residues processed: 65
  average time/residue: 0.0786
  time to fit residues: 8.3207
Evaluate side-chains
  61 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  233 CYS
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  653 MET
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  934 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 99 optimal weight:   10.0000
   chunk 85 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 48 optimal weight:    7.9990
   chunk 90 optimal weight:    9.9990
   chunk 68 optimal weight:    2.9990
   chunk 49 optimal weight:    8.9990
   overall best weight:    2.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.091741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.065845 restraints weight = 44153.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.067959 restraints weight = 23443.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.069244 restraints weight = 16393.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.070048 restraints weight = 13460.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.070446 restraints weight = 11960.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  12124  Z= 0.194
  Angle     :  0.649   8.692  17171  Z= 0.343
  Chirality :  0.040   0.221   1979
  Planarity :  0.005   0.051   1546
  Dihedral  : 24.764 178.721   3482
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 13.47 %
    Favored  : 84.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.27), residues: 954
  helix:  1.27 (0.25), residues: 420
  sheet: -1.28 (0.42), residues: 143
  loop : -1.22 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 261 
 TYR   0.020   0.002   TYR A 138 
 PHE   0.019   0.002   PHE A 399 
 TRP   0.015   0.002   TRP A 782 
 HIS   0.006   0.002   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (12124)
  covalent geometry    : angle       0.64871 (17171)
  hydrogen bonds       : bond        0.06780 (  531)
  hydrogen bonds       : angle       4.47735 ( 1371)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 CYS cc_start: 0.8229 (m) cc_final: 0.7758 (t)
REVERT: A  486 TRP cc_start: 0.7053 (m-10) cc_final: 0.6739 (m-10)
REVERT: A  570 MET cc_start: 0.7924 (tpt) cc_final: 0.7628 (mmm)
  outliers start: 19
  outliers final: 11
  residues processed: 74
  average time/residue: 0.0828
  time to fit residues: 9.7560
Evaluate side-chains
  68 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  251 HIS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  653 MET
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  732 ASP
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  970 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 99 optimal weight:    6.9990
   chunk 81 optimal weight:    5.9990
   chunk 14 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 16 optimal weight:   10.0000
   chunk 102 optimal weight:    3.9990
   chunk 107 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 286 HIS
A 654 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.089728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.063851 restraints weight = 44879.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.065893 restraints weight = 23684.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 72)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.067148 restraints weight = 16590.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.067813 restraints weight = 13604.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.068252 restraints weight = 12261.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.2703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  12124  Z= 0.274
  Angle     :  0.749  12.652  17171  Z= 0.392
  Chirality :  0.043   0.221   1979
  Planarity :  0.006   0.050   1546
  Dihedral  : 24.949 179.553   3482
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 14.30 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.27), residues: 954
  helix:  0.78 (0.24), residues: 415
  sheet: -1.46 (0.43), residues: 143
  loop : -1.45 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 642 
 TYR   0.026   0.002   TYR A 138 
 PHE   0.031   0.002   PHE A 399 
 TRP   0.012   0.002   TRP A  86 
 HIS   0.007   0.002   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00578 (12124)
  covalent geometry    : angle       0.74877 (17171)
  hydrogen bonds       : bond        0.07786 (  531)
  hydrogen bonds       : angle       4.74569 ( 1371)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 59
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A  134 CYS cc_start: 0.8339 (m) cc_final: 0.7854 (t)
REVERT: A  231 ASP cc_start: 0.8905 (p0) cc_final: 0.8649 (p0)
REVERT: A  486 TRP cc_start: 0.7112 (m-10) cc_final: 0.6774 (m-10)
REVERT: A  489 ASP cc_start: 0.8041 (m-30) cc_final: 0.7749 (m-30)
  outliers start: 29
  outliers final: 21
  residues processed: 78
  average time/residue: 0.0841
  time to fit residues: 10.7343
Evaluate side-chains
  76 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 55
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  152 HIS
Chi-restraints excluded: chain A residue  233 CYS
Chi-restraints excluded: chain A residue  251 HIS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  621 LEU
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  653 MET
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  732 ASP
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue  970 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 75 optimal weight:    3.9990
   chunk 65 optimal weight:    6.9990
   chunk 99 optimal weight:   20.0000
   chunk 23 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 98 optimal weight:   20.0000
   chunk 109 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   overall best weight:    1.5386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.092873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.067177 restraints weight = 43767.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.069251 restraints weight = 23503.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.070502 restraints weight = 16548.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.071273 restraints weight = 13599.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.071639 restraints weight = 12152.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12124  Z= 0.140
  Angle     :  0.595   8.505  17171  Z= 0.316
  Chirality :  0.038   0.220   1979
  Planarity :  0.004   0.051   1546
  Dihedral  : 24.626 179.038   3482
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 16.45 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.28), residues: 954
  helix:  1.42 (0.26), residues: 420
  sheet: -1.31 (0.42), residues: 150
  loop : -1.15 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 740 
 TYR   0.012   0.001   TYR A 138 
 PHE   0.015   0.001   PHE A 463 
 TRP   0.012   0.001   TRP A 366 
 HIS   0.004   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (12124)
  covalent geometry    : angle       0.59548 (17171)
  hydrogen bonds       : bond        0.06011 (  531)
  hydrogen bonds       : angle       4.25761 ( 1371)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A   29 MET cc_start: 0.6775 (ppp) cc_final: 0.5940 (ppp)
REVERT: A  134 CYS cc_start: 0.8248 (m) cc_final: 0.7764 (t)
REVERT: A  489 ASP cc_start: 0.7788 (m-30) cc_final: 0.7442 (m-30)
  outliers start: 17
  outliers final: 8
  residues processed: 80
  average time/residue: 0.0765
  time to fit residues: 10.0681
Evaluate side-chains
  68 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 HIS
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  732 ASP
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  857 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 76 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 71 optimal weight:    0.0030
   chunk 90 optimal weight:    5.9990
   chunk 68 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   overall best weight:    2.1596

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.092182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.066429 restraints weight = 44193.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.068497 restraints weight = 23660.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.069743 restraints weight = 16634.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 61)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.070512 restraints weight = 13671.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.070876 restraints weight = 12196.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12124  Z= 0.161
  Angle     :  0.619   9.319  17171  Z= 0.325
  Chirality :  0.038   0.218   1979
  Planarity :  0.004   0.049   1546
  Dihedral  : 24.667 178.593   3482
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.57 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.28), residues: 954
  helix:  1.44 (0.26), residues: 420
  sheet: -1.38 (0.40), residues: 160
  loop : -1.18 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 764 
 TYR   0.013   0.001   TYR A 138 
 PHE   0.014   0.001   PHE A 958 
 TRP   0.011   0.001   TRP A 782 
 HIS   0.005   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (12124)
  covalent geometry    : angle       0.61906 (17171)
  hydrogen bonds       : bond        0.06118 (  531)
  hydrogen bonds       : angle       4.31963 ( 1371)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 59
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.6715 (ppp) cc_final: 0.5857 (ppp)
REVERT: A  113 LEU cc_start: 0.6004 (OUTLIER) cc_final: 0.5746 (pt)
REVERT: A  134 CYS cc_start: 0.8276 (m) cc_final: 0.7798 (t)
REVERT: A  489 ASP cc_start: 0.7740 (m-30) cc_final: 0.7383 (m-30)
REVERT: A  710 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7953 (mt-10)
  outliers start: 20
  outliers final: 13
  residues processed: 75
  average time/residue: 0.0790
  time to fit residues: 9.7495
Evaluate side-chains
  72 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  251 HIS
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  621 LEU
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  732 ASP
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  857 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 102 optimal weight:    8.9990
   chunk 43 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 103 optimal weight:    0.1980
   chunk 3 optimal weight:    7.9990
   overall best weight:    1.8186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.092727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.066950 restraints weight = 44235.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.069027 restraints weight = 23782.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 74)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.070315 restraints weight = 16726.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.071066 restraints weight = 13666.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.071404 restraints weight = 12221.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12124  Z= 0.146
  Angle     :  0.599   9.064  17171  Z= 0.314
  Chirality :  0.037   0.219   1979
  Planarity :  0.004   0.049   1546
  Dihedral  : 24.648 178.867   3482
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 17.28 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.28), residues: 954
  helix:  1.52 (0.26), residues: 419
  sheet: -1.23 (0.41), residues: 160
  loop : -1.15 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 764 
 TYR   0.012   0.001   TYR A 138 
 PHE   0.013   0.001   PHE A 958 
 TRP   0.011   0.001   TRP A 782 
 HIS   0.004   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (12124)
  covalent geometry    : angle       0.59860 (17171)
  hydrogen bonds       : bond        0.05901 (  531)
  hydrogen bonds       : angle       4.22395 ( 1371)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.6572 (ppp) cc_final: 0.5920 (ppp)
REVERT: A  113 LEU cc_start: 0.5924 (OUTLIER) cc_final: 0.5678 (pt)
REVERT: A  134 CYS cc_start: 0.8287 (m) cc_final: 0.7785 (t)
REVERT: A  489 ASP cc_start: 0.7701 (m-30) cc_final: 0.7338 (m-30)
REVERT: A  710 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7918 (mt-10)
  outliers start: 17
  outliers final: 14
  residues processed: 75
  average time/residue: 0.0804
  time to fit residues: 9.9380
Evaluate side-chains
  73 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  251 HIS
Chi-restraints excluded: chain A residue  284 GLN
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  621 LEU
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  732 ASP
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  857 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0470
   chunk 86 optimal weight:    0.0170
   chunk 83 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9980
   chunk 14 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 55 optimal weight:    1.9990
   chunk 111 optimal weight:    4.9990
   chunk 78 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.7918

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

Flipped N/Q/H residues before XYZ refinement:
A 804 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.095013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.069470 restraints weight = 43748.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.071546 restraints weight = 24084.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.072802 restraints weight = 17035.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.073513 restraints weight = 14041.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.074005 restraints weight = 12581.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  12124  Z= 0.116
  Angle     :  0.562   8.629  17171  Z= 0.295
  Chirality :  0.036   0.217   1979
  Planarity :  0.004   0.052   1546
  Dihedral  : 24.574 178.748   3482
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 18.12 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.29), residues: 954
  helix:  1.78 (0.26), residues: 428
  sheet: -0.84 (0.43), residues: 152
  loop : -0.96 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 203 
 TYR   0.008   0.001   TYR A 822 
 PHE   0.012   0.001   PHE A 958 
 TRP   0.014   0.001   TRP A 598 
 HIS   0.004   0.001   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (12124)
  covalent geometry    : angle       0.56249 (17171)
  hydrogen bonds       : bond        0.05396 (  531)
  hydrogen bonds       : angle       4.06728 ( 1371)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.6406 (ppp) cc_final: 0.6041 (ppp)
REVERT: A   76 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8122 (tp30)
REVERT: A  134 CYS cc_start: 0.8086 (m) cc_final: 0.7547 (t)
REVERT: A  204 GLU cc_start: 0.7347 (mp0) cc_final: 0.7092 (mp0)
REVERT: A  489 ASP cc_start: 0.7710 (m-30) cc_final: 0.7382 (m-30)
REVERT: A  500 GLU cc_start: 0.6068 (tp30) cc_final: 0.5469 (tm-30)
REVERT: A  781 ASP cc_start: 0.7486 (p0) cc_final: 0.7266 (p0)
  outliers start: 13
  outliers final: 9
  residues processed: 79
  average time/residue: 0.0851
  time to fit residues: 10.4633
Evaluate side-chains
  73 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 MET
Chi-restraints excluded: chain A residue  251 HIS
Chi-restraints excluded: chain A residue  284 GLN
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  732 ASP
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  967 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 95 optimal weight:    9.9990
   chunk 3 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 86 optimal weight:    4.9990
   chunk 57 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0470
   overall best weight:    3.2086

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

Flipped N/Q/H residues before XYZ refinement:
A 804 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.091876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.066105 restraints weight = 44371.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.068149 restraints weight = 24008.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.069418 restraints weight = 16862.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.070190 restraints weight = 13882.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.070539 restraints weight = 12355.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12124  Z= 0.202
  Angle     :  0.655   9.739  17171  Z= 0.343
  Chirality :  0.039   0.216   1979
  Planarity :  0.005   0.049   1546
  Dihedral  : 24.754 179.726   3482
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 18.95 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.28), residues: 954
  helix:  1.38 (0.26), residues: 425
  sheet: -0.94 (0.45), residues: 145
  loop : -1.16 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 736 
 TYR   0.016   0.002   TYR A 138 
 PHE   0.034   0.002   PHE A 399 
 TRP   0.011   0.002   TRP A  86 
 HIS   0.006   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (12124)
  covalent geometry    : angle       0.65480 (17171)
  hydrogen bonds       : bond        0.06472 (  531)
  hydrogen bonds       : angle       4.33907 ( 1371)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 MET cc_start: 0.6656 (ppp) cc_final: 0.5907 (ppp)
REVERT: A  134 CYS cc_start: 0.8224 (m) cc_final: 0.7668 (t)
REVERT: A  500 GLU cc_start: 0.6346 (tp30) cc_final: 0.5754 (tm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 70
  average time/residue: 0.0887
  time to fit residues: 9.8767
Evaluate side-chains
  69 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 HIS
Chi-restraints excluded: chain A residue  284 GLN
Chi-restraints excluded: chain A residue  314 LYS
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  732 ASP
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  840 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 77 optimal weight:    9.9990
   chunk 40 optimal weight:    4.9990
   chunk 86 optimal weight:    4.9990
   chunk 79 optimal weight:    5.9990
   chunk 50 optimal weight:    0.5980
   chunk 75 optimal weight:    0.8980
   chunk 16 optimal weight:    9.9990
   chunk 23 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 37 optimal weight:    4.9990
   overall best weight:    3.0986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.091537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.065869 restraints weight = 44208.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.067913 restraints weight = 23715.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.069174 restraints weight = 16668.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.069937 restraints weight = 13651.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.070285 restraints weight = 12196.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12124  Z= 0.198
  Angle     :  0.665  10.289  17171  Z= 0.349
  Chirality :  0.039   0.223   1979
  Planarity :  0.005   0.047   1546
  Dihedral  : 24.849 178.473   3482
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 19.43 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.28), residues: 954
  helix:  1.15 (0.25), residues: 426
  sheet: -0.98 (0.47), residues: 135
  loop : -1.28 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 967 
 TYR   0.018   0.002   TYR A 138 
 PHE   0.039   0.002   PHE A 399 
 TRP   0.012   0.002   TRP A 782 
 HIS   0.005   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 (12124)
  covalent geometry    : angle       0.66523 (17171)
  hydrogen bonds       : bond        0.06631 (  531)
  hydrogen bonds       : angle       4.43281 ( 1371)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2292.50 seconds
wall clock time: 40 minutes 17.14 seconds (2417.14 seconds total)