Starting phenix.real_space_refine
on Tue Aug  4 21:47:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw5_54299/08_2026/9rw5_54299.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw5_54299/08_2026/9rw5_54299.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rw5_54299/08_2026/9rw5_54299.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw5_54299/08_2026/9rw5_54299.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rw5_54299/08_2026/9rw5_54299.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw5_54299/08_2026/9rw5_54299.map"
  }
  resolution = 4.1
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     P      84      5.49       5
     C    3808      2.51       5
     N    1320      2.21       5
     O    1620      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6832
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 265
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 178
          Unresolved non-hydrogen angles: 222
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLU:plan': 10, 'TYR:plan': 1, 'GLN:plan1': 6, 'ASP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 111
    Chain: "B"
      Number of atoms: 265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 265
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 178
          Unresolved non-hydrogen angles: 222
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLU:plan': 10, 'TYR:plan': 1, 'GLN:plan1': 6, 'ASP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 111
    Chain: "D"
      Number of atoms: 2247
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 2247
          Classifications: {'peptide': 454}
          Incomplete info: {'truncation_to_alanine': 401}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 443}
          Chain breaks: 2
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 1475
          Unresolved non-hydrogen angles: 1865
          Unresolved non-hydrogen dihedrals: 1222
          Unresolved non-hydrogen chiralities: 129
          Planarities with less than four sites: {'GLU:plan': 30, 'TYR:plan': 19, 'ARG:plan': 23, 'ASN:plan1': 18, 'PHE:plan': 18, 'ASP:plan': 26, 'HIS:plan': 10, 'GLN:plan1': 31, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 800
    Chain: "C"
      Number of atoms: 2247
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 2247
          Classifications: {'peptide': 454}
          Incomplete info: {'truncation_to_alanine': 401}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 443}
          Chain breaks: 2
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 1475
          Unresolved non-hydrogen angles: 1865
          Unresolved non-hydrogen dihedrals: 1222
          Unresolved non-hydrogen chiralities: 129
          Planarities with less than four sites: {'GLU:plan': 30, 'TYR:plan': 19, 'ARG:plan': 23, 'ASN:plan1': 18, 'PHE:plan': 18, 'ASP:plan': 26, 'HIS:plan': 10, 'GLN:plan1': 31, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 800
    Chain: "E"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 904
          Classifications: {'RNA': 43}
          Modifications used: {'5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 19, 'rna3p_pyr': 22}
          Link IDs: {'rna2p': 2, 'rna3p': 40}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 904
          Classifications: {'RNA': 43}
          Modifications used: {'5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 19, 'rna3p_pyr': 22}
          Link IDs: {'rna2p': 2, 'rna3p': 40}
          Chain breaks: 1
  Time building chain proxies: 1.14, per 1000 atoms: 0.17
  Number of scatterers: 6832
  At special positions: 0
  Unit cell: (84.8, 109.18, 168.54, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     P      84     15.00
     O    1620      8.00
     N    1320      7.00
     C    3808      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: 0.47
  Conformation dependent library (CDL) restraints added in 313.4 milliseconds
  

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1936

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 6 sheets defined
      71.8% alpha, 5.7% beta
      35 base pairs and 46 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 695 through 747
      removed outlier: 4.026A  pdb=" N   VAL A 699 " --> pdb=" O   CYS A 695 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ARG A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 747
      removed outlier: 3.805A  pdb=" N   ARG B 747 " --> pdb=" O   ASP B 743 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 25
      removed outlier: 4.002A  pdb=" N   LYS D  24 " --> pdb=" O   ARG D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 36
    Processing helix  chain 'D' and resid 37 through 39
      No H-bonds generated for 'chain 'D' and resid 37 through 39'
    Processing helix  chain 'D' and resid 43 through 51
    Processing helix  chain 'D' and resid 53 through 63
    Processing helix  chain 'D' and resid 95 through 110
    Processing helix  chain 'D' and resid 119 through 125
      removed outlier: 3.517A  pdb=" N   HIS D 125 " --> pdb=" O   SER D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 126 through 129
    Processing helix  chain 'D' and resid 130 through 137
    Processing helix  chain 'D' and resid 140 through 152
    Processing helix  chain 'D' and resid 521 through 530
    Processing helix  chain 'D' and resid 535 through 554
    Processing helix  chain 'D' and resid 594 through 600
      removed outlier: 3.837A  pdb=" N   THR D 598 " --> pdb=" O   PRO D 594 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 601 through 608
    Processing helix  chain 'D' and resid 617 through 630
      removed outlier: 4.806A  pdb=" N   ASP D 621 " --> pdb=" O   ASP D 617 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 639 through 652
    Processing helix  chain 'D' and resid 654 through 658
    Processing helix  chain 'D' and resid 662 through 670
    Processing helix  chain 'D' and resid 676 through 688
      removed outlier: 3.987A  pdb=" N   GLN D 680 " --> pdb=" O   PRO D 676 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLN D 683 " --> pdb=" O   ASP D 679 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ILE D 684 " --> pdb=" O   GLN D 680 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 689 through 693
    Processing helix  chain 'D' and resid 698 through 714
    Processing helix  chain 'D' and resid 714 through 723
    Processing helix  chain 'D' and resid 726 through 744
      removed outlier: 4.598A  pdb=" N   GLN D 744 " --> pdb=" O   GLN D 740 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 746 through 773
    Processing helix  chain 'D' and resid 780 through 787
    Processing helix  chain 'D' and resid 788 through 790
      No H-bonds generated for 'chain 'D' and resid 788 through 790'
    Processing helix  chain 'D' and resid 793 through 802
      removed outlier: 4.382A  pdb=" N   GLY D 802 " --> pdb=" O   GLU D 798 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 803 through 816
    Processing helix  chain 'C' and resid 3 through 25
    Processing helix  chain 'C' and resid 30 through 36
    Processing helix  chain 'C' and resid 43 through 50
    Processing helix  chain 'C' and resid 53 through 63
    Processing helix  chain 'C' and resid 95 through 112
      removed outlier: 3.612A  pdb=" N   GLU C  99 " --> pdb=" O   ASP C  95 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   TYR C 111 " --> pdb=" O   LYS C 107 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   GLY C 112 " --> pdb=" O   MET C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 125
      removed outlier: 3.621A  pdb=" N   HIS C 125 " --> pdb=" O   SER C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 126 through 128
      No H-bonds generated for 'chain 'C' and resid 126 through 128'
    Processing helix  chain 'C' and resid 130 through 137
    Processing helix  chain 'C' and resid 140 through 152
    Processing helix  chain 'C' and resid 521 through 530
    Processing helix  chain 'C' and resid 535 through 554
    Processing helix  chain 'C' and resid 594 through 600
      removed outlier: 4.007A  pdb=" N   THR C 598 " --> pdb=" O   PRO C 594 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 601 through 608
      removed outlier: 3.549A  pdb=" N   VAL C 605 " --> pdb=" O   GLY C 601 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 618 through 630
    Processing helix  chain 'C' and resid 639 through 652
    Processing helix  chain 'C' and resid 654 through 658
    Processing helix  chain 'C' and resid 662 through 670
    Processing helix  chain 'C' and resid 676 through 688
      removed outlier: 4.107A  pdb=" N   GLN C 680 " --> pdb=" O   PRO C 676 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 689 through 693
    Processing helix  chain 'C' and resid 698 through 714
    Processing helix  chain 'C' and resid 714 through 723
    Processing helix  chain 'C' and resid 726 through 744
      removed outlier: 4.519A  pdb=" N   GLN C 744 " --> pdb=" O   GLN C 740 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 746 through 773
      removed outlier: 3.666A  pdb=" N   VAL C 750 " --> pdb=" O   LYS C 746 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 780 through 788
      removed outlier: 4.230A  pdb=" N   ARG C 788 " --> pdb=" O   ILE C 784 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 793 through 801
    Processing helix  chain 'C' and resid 803 through 816
    Processing sheet with id=AA1, first strand: chain 'D' and resid 28 through 29
    Processing sheet with id=AA2, first strand: chain 'D' and resid 531 through 533
      removed outlier: 5.473A  pdb=" N   ILE D 573 " --> pdb=" O   ILE D 565 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   ILE D 565 " --> pdb=" O   ILE D 573 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 556 through 559
      removed outlier: 6.620A  pdb=" N   ILE D 556 " --> pdb=" O   ILE D 612 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   VAL D 614 " --> pdb=" O   ILE D 556 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   VAL D 558 " --> pdb=" O   VAL D 614 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 28 through 29
    Processing sheet with id=AA5, first strand: chain 'C' and resid 531 through 533
      removed outlier: 5.628A  pdb=" N   ILE C 573 " --> pdb=" O   ILE C 565 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ILE C 565 " --> pdb=" O   ILE C 573 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 556 through 559
      removed outlier: 6.744A  pdb=" N   ILE C 556 " --> pdb=" O   ILE C 612 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   VAL C 614 " --> pdb=" O   ILE C 556 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   VAL C 558 " --> pdb=" O   VAL C 614 " (cutoff:3.500A)

    524 hydrogen bonds defined for protein.
    1518 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      84 hydrogen bonds
      156 hydrogen bond angles
      0 basepair planarities
      35 basepair parallelities
      46 stacking parallelities
  Total time for adding SS restraints: 0.90

  Time building geometry restraints manager: 0.60 seconds

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

  Histogram of bond lengths:
        1.21 -     1.29: 1108
        1.29 -     1.37: 1407
        1.37 -     1.45: 844
        1.45 -     1.53: 3330
        1.53 -     1.61: 341
  Bond restraints: 7030
  Sorted by residual:
  bond pdb=" N1    C F  18 "
       pdb=" C6    C F  18 "
    ideal  model  delta    sigma   weight residual
    1.367  1.386 -0.019 6.00e-03 2.78e+04 9.65e+00
  bond pdb=" N1    C F  19 "
       pdb=" C6    C F  19 "
    ideal  model  delta    sigma   weight residual
    1.367  1.385 -0.018 6.00e-03 2.78e+04 9.19e+00
  bond pdb=" N1    C F  29 "
       pdb=" C6    C F  29 "
    ideal  model  delta    sigma   weight residual
    1.367  1.385 -0.018 6.00e-03 2.78e+04 8.64e+00
  bond pdb=" N1    C F  38 "
       pdb=" C6    C F  38 "
    ideal  model  delta    sigma   weight residual
    1.367  1.383 -0.016 6.00e-03 2.78e+04 6.90e+00
  bond pdb=" N1    C F  27 "
       pdb=" C6    C F  27 "
    ideal  model  delta    sigma   weight residual
    1.367  1.382 -0.015 6.00e-03 2.78e+04 6.15e+00
  ... (remaining 7025 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.05: 9014
        1.05 -     2.10: 837
        2.10 -     3.15: 209
        3.15 -     4.20: 38
        4.20 -     5.25: 10
  Bond angle restraints: 10108
  Sorted by residual:
  angle pdb=" N6    A F   8 "
        pdb=" C6    A F   8 "
        pdb=" N1    A F   8 "
      ideal   model   delta    sigma   weight residual
     118.60  114.72    3.88 6.00e-01 2.78e+00 4.19e+01
  angle pdb=" O5'   C F  38 "
        pdb=" C5'   C F  38 "
        pdb=" C4'   C F  38 "
      ideal   model   delta    sigma   weight residual
     109.40  114.03   -4.63 8.00e-01 1.56e+00 3.35e+01
  angle pdb=" N6    A F  30 "
        pdb=" C6    A F  30 "
        pdb=" N1    A F  30 "
      ideal   model   delta    sigma   weight residual
     118.60  115.44    3.16 6.00e-01 2.78e+00 2.77e+01
  angle pdb=" N6    A F  44 "
        pdb=" C6    A F  44 "
        pdb=" N1    A F  44 "
      ideal   model   delta    sigma   weight residual
     118.60  115.47    3.13 6.00e-01 2.78e+00 2.72e+01
  angle pdb=" C6    A F  13 "
        pdb=" C5    A F  13 "
        pdb=" C4    A F  13 "
      ideal   model   delta    sigma   weight residual
     117.00  114.47    2.53 5.00e-01 4.00e+00 2.55e+01
  ... (remaining 10103 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.62: 3985
       23.62 -    47.25: 142
       47.25 -    70.87: 107
       70.87 -    94.50: 20
       94.50 -   118.12: 6
  Dihedral angle restraints: 4260
    sinusoidal: 1318
      harmonic: 2942
  Sorted by residual:
  dihedral pdb=" C5'   U F  39 "
           pdb=" C4'   U F  39 "
           pdb=" C3'   U F  39 "
           pdb=" O3'   U F  39 "
      ideal   model   delta sinusoidal    sigma   weight residual
      82.00  107.82  -25.82     1      8.00e+00 1.56e-02 1.50e+01
  dihedral pdb=" C3'   U F  39 "
           pdb=" C4'   U F  39 "
           pdb=" O4'   U F  39 "
           pdb=" C1'   U F  39 "
      ideal   model   delta sinusoidal    sigma   weight residual
      20.00   -5.81   25.81     1      8.00e+00 1.56e-02 1.50e+01
  dihedral pdb=" O4'   U F  39 "
           pdb=" C4'   U F  39 "
           pdb=" C3'   U F  39 "
           pdb=" C2'   U F  39 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   -9.33  -25.67     1      8.00e+00 1.56e-02 1.48e+01
  ... (remaining 4257 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 879
       0.033 -    0.067: 283
       0.067 -    0.100: 130
       0.100 -    0.133: 85
       0.133 -    0.166: 19
  Chirality restraints: 1396
  Sorted by residual:
  chirality pdb=" C2'   C F  19 "
            pdb=" C3'   C F  19 "
            pdb=" O2'   C F  19 "
            pdb=" C1'   C F  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -2.78    0.17 2.00e-01 2.50e+01 6.91e-01
  chirality pdb=" C2'   U F  15 "
            pdb=" C3'   U F  15 "
            pdb=" O2'   U F  15 "
            pdb=" C1'   U F  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -2.78    0.16 2.00e-01 2.50e+01 6.49e-01
  chirality pdb=" C2'   G F  37 "
            pdb=" C3'   G F  37 "
            pdb=" O2'   G F  37 "
            pdb=" C1'   G F  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -2.78    0.16 2.00e-01 2.50e+01 6.22e-01
  ... (remaining 1393 not shown)

  Planarity restraints: 1092
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G F  34 "   -0.057 2.00e-02 2.50e+03   2.22e-02 1.48e+01
        pdb=" N9    G F  34 "    0.030 2.00e-02 2.50e+03
        pdb=" C8    G F  34 "    0.021 2.00e-02 2.50e+03
        pdb=" N7    G F  34 "    0.011 2.00e-02 2.50e+03
        pdb=" C5    G F  34 "    0.003 2.00e-02 2.50e+03
        pdb=" C6    G F  34 "   -0.009 2.00e-02 2.50e+03
        pdb=" O6    G F  34 "   -0.025 2.00e-02 2.50e+03
        pdb=" N1    G F  34 "   -0.008 2.00e-02 2.50e+03
        pdb=" C2    G F  34 "    0.002 2.00e-02 2.50e+03
        pdb=" N2    G F  34 "    0.014 2.00e-02 2.50e+03
        pdb=" N3    G F  34 "    0.009 2.00e-02 2.50e+03
        pdb=" C4    G F  34 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C F  16 "    0.040 2.00e-02 2.50e+03   2.36e-02 1.25e+01
        pdb=" N1    C F  16 "    0.004 2.00e-02 2.50e+03
        pdb=" C2    C F  16 "   -0.005 2.00e-02 2.50e+03
        pdb=" O2    C F  16 "   -0.022 2.00e-02 2.50e+03
        pdb=" N3    C F  16 "    0.000 2.00e-02 2.50e+03
        pdb=" C4    C F  16 "   -0.016 2.00e-02 2.50e+03
        pdb=" N4    C F  16 "    0.041 2.00e-02 2.50e+03
        pdb=" C5    C F  16 "   -0.022 2.00e-02 2.50e+03
        pdb=" C6    C F  16 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U F  39 "   -0.044 2.00e-02 2.50e+03   2.28e-02 1.16e+01
        pdb=" N1    U F  39 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    U F  39 "    0.012 2.00e-02 2.50e+03
        pdb=" O2    U F  39 "    0.028 2.00e-02 2.50e+03
        pdb=" N3    U F  39 "   -0.016 2.00e-02 2.50e+03
        pdb=" C4    U F  39 "   -0.007 2.00e-02 2.50e+03
        pdb=" O4    U F  39 "   -0.021 2.00e-02 2.50e+03
        pdb=" C5    U F  39 "    0.021 2.00e-02 2.50e+03
        pdb=" C6    U F  39 "    0.024 2.00e-02 2.50e+03
  ... (remaining 1089 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2220
        2.82 -     3.34: 7091
        3.34 -     3.86: 11965
        3.86 -     4.38: 11608
        4.38 -     4.90: 17537
  Nonbonded interactions: 50421
  Sorted by model distance:
  nonbonded pdb=" O   PRO C 118 "
            pdb=" N   ARG C 120 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" O2'   U E  35 "
            pdb=" O5'   U E  36 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" O   PRO D 118 "
            pdb=" N   ARG D 120 "
     model   vdw
     2.365 3.120
  nonbonded pdb=" O   ILE D  67 "
            pdb=" N   ASN D  78 "
     model   vdw
     2.408 3.120
  nonbonded pdb=" O2'   U E  36 "
            pdb=" O5'   G E  37 "
     model   vdw
     2.431 3.040
  ... (remaining 50416 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}

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:             0.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.230
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
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   0.033   7030  Z= 0.323
  Angle     :  0.718   5.251  10108  Z= 0.705
  Chirality :  0.048   0.166   1396
  Planarity :  0.003   0.024   1092
  Dihedral  : 18.204 118.121   2324
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  0.68 (0.26), residues: 998
  helix:  1.24 (0.20), residues: 656
  sheet: -2.23 (0.61), residues: 52
  loop : -0.73 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE D  16 
 TRP   0.000   0.000   TRP D 522 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.32 ( 7030)
  covalent geometry    : angle       0.71837 /  0.71 (10108)
  hydrogen bonds       : bond        0.12490 /  9.55 (  608)
  hydrogen bonds       : angle       6.02222 /  4.81 ( 1674)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.180 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0213
  time to fit residues: 1.4634
Evaluate side-chains
  32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:   10.0000
   chunk 106 optimal weight:   20.0000
   chunk 38 optimal weight:   20.0000
   overall best weight:    9.3994

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.087097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.071816 restraints weight = 45326.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.070977 restraints weight = 55801.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 84)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.069472 restraints weight = 53722.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.069214 restraints weight = 57535.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 71)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.068679 restraints weight = 51664.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   7030  Z= 0.365
  Angle     :  0.752   8.872  10108  Z= 0.451
  Chirality :  0.050   0.209   1396
  Planarity :  0.005   0.022   1092
  Dihedral  : 18.520 112.647   2324
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  0.32 (0.25), residues: 998
  helix:  0.94 (0.19), residues: 660
  sheet: -2.18 (0.64), residues: 52
  loop : -0.86 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE D  16 
 TRP   0.000   0.000   TRP D 522 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00491 /  0.37 ( 7030)
  covalent geometry    : angle       0.75164 /  0.45 (10108)
  hydrogen bonds       : bond        0.07762 /  5.83 (  608)
  hydrogen bonds       : angle       5.73322 /  4.58 ( 1674)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.154 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0240
  time to fit residues: 1.6190
Evaluate side-chains
  32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 85 optimal weight:    5.9990
   chunk 67 optimal weight:    9.9990
   chunk 36 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 10 optimal weight:   10.0000
   chunk 22 optimal weight:    0.8980
   chunk 93 optimal weight:   20.0000
   chunk 0 optimal weight:   50.0000
   overall best weight:    3.1788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.088473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.073313 restraints weight = 45116.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.072688 restraints weight = 53605.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 83)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.071582 restraints weight = 48352.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.071282 restraints weight = 49832.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.071121 restraints weight = 44336.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   7030  Z= 0.154
  Angle     :  0.424   5.101  10108  Z= 0.267
  Chirality :  0.037   0.134   1396
  Planarity :  0.002   0.012   1092
  Dihedral  : 18.332 110.975   2324
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.96 (0.27), residues: 998
  helix:  2.30 (0.20), residues: 662
  sheet: -2.18 (0.63), residues: 52
  loop : -0.39 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE D  16 
 TRP   0.000   0.000   TRP D 522 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00201 /  0.15 ( 7030)
  covalent geometry    : angle       0.42354 /  0.27 (10108)
  hydrogen bonds       : bond        0.05123 /  3.81 (  608)
  hydrogen bonds       : angle       4.64004 /  3.70 ( 1674)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.227 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0286
  time to fit residues: 1.9420
Evaluate side-chains
  32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 50 optimal weight:   20.0000
   chunk 45 optimal weight:    7.9990
   chunk 3 optimal weight:   20.0000
   chunk 35 optimal weight:   20.0000
   chunk 28 optimal weight:   60.0000
   chunk 25 optimal weight:    6.9990
   chunk 93 optimal weight:   30.0000
   chunk 86 optimal weight:    0.8980
   chunk 10 optimal weight:   10.0000
   chunk 30 optimal weight:    0.8980
   chunk 19 optimal weight:    7.9990
   overall best weight:    4.9586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.087325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.072180 restraints weight = 45264.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.071328 restraints weight = 54639.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.071356 restraints weight = 53209.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.070851 restraints weight = 51117.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.070969 restraints weight = 44920.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.3111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7030  Z= 0.206
  Angle     :  0.484   5.844  10108  Z= 0.300
  Chirality :  0.039   0.164   1396
  Planarity :  0.003   0.016   1092
  Dihedral  : 18.329 112.515   2324
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.67 (0.27), residues: 998
  helix:  2.08 (0.20), residues: 662
  sheet: -2.42 (0.61), residues: 52
  loop : -0.48 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE D  16 
 TRP   0.000   0.000   TRP D 522 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.21 ( 7030)
  covalent geometry    : angle       0.48361 /  0.30 (10108)
  hydrogen bonds       : bond        0.05589 /  4.19 (  608)
  hydrogen bonds       : angle       4.71692 /  3.76 ( 1674)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.134 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0221
  time to fit residues: 1.5343
Evaluate side-chains
  32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 96 optimal weight:   40.0000
   chunk 53 optimal weight:   50.0000
   chunk 63 optimal weight:    0.8980
   chunk 10 optimal weight:   10.0000
   chunk 88 optimal weight:    8.9990
   chunk 1 optimal weight:   20.0000
   overall best weight:    4.9788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.087056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.071251 restraints weight = 45196.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.070213 restraints weight = 57379.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 112)---------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.069494 restraints weight = 46985.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.069032 restraints weight = 53589.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 68)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.068970 restraints weight = 47408.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.3619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7030  Z= 0.190
  Angle     :  0.463   5.759  10108  Z= 0.285
  Chirality :  0.039   0.147   1396
  Planarity :  0.003   0.013   1092
  Dihedral  : 18.329 115.191   2324
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.27), residues: 998
  helix:  2.19 (0.20), residues: 662
  sheet: -2.55 (0.59), residues: 52
  loop : -0.57 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE D  16 
 TRP   0.000   0.000   TRP D 522 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.19 ( 7030)
  covalent geometry    : angle       0.46341 /  0.29 (10108)
  hydrogen bonds       : bond        0.05244 /  3.92 (  608)
  hydrogen bonds       : angle       4.57752 /  3.64 ( 1674)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.125 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0250
  time to fit residues: 1.6709
Evaluate side-chains
  32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 70 optimal weight:   40.0000
   chunk 103 optimal weight:   30.0000
   chunk 44 optimal weight:   30.0000
   chunk 86 optimal weight:   50.0000
   chunk 21 optimal weight:    0.4980
   chunk 30 optimal weight:    4.9990
   chunk 18 optimal weight:    8.9990
   chunk 8 optimal weight:   20.0000
   chunk 87 optimal weight:   40.0000
   chunk 46 optimal weight:    0.0070
   chunk 74 optimal weight:    6.9990
   overall best weight:    4.3004

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.086916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.072489 restraints weight = 45438.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.071550 restraints weight = 60796.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.071683 restraints weight = 59045.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.071187 restraints weight = 55608.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.071445 restraints weight = 47997.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.3960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7030  Z= 0.176
  Angle     :  0.442   5.588  10108  Z= 0.273
  Chirality :  0.038   0.138   1396
  Planarity :  0.003   0.015   1092
  Dihedral  : 18.190 113.789   2324
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.81 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  2.05 (0.27), residues: 998
  helix:  2.41 (0.20), residues: 662
  sheet: -2.91 (0.64), residues: 36
  loop : -0.48 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE D  16 
 TRP   0.000   0.000   TRP D 522 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.18 ( 7030)
  covalent geometry    : angle       0.44246 /  0.27 (10108)
  hydrogen bonds       : bond        0.05181 /  3.88 (  608)
  hydrogen bonds       : angle       4.50268 /  3.57 ( 1674)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.217 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0223
  time to fit residues: 1.5663
Evaluate side-chains
  32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 42 optimal weight:    5.9990
   chunk 54 optimal weight:   30.0000
   chunk 74 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 25 optimal weight:   20.0000
   chunk 88 optimal weight:   40.0000
   chunk 24 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 34 optimal weight:   10.0000
   chunk 66 optimal weight:    7.9990
   overall best weight:    3.3588

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.087228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.072138 restraints weight = 44563.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.071132 restraints weight = 62038.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.071409 restraints weight = 57597.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.071044 restraints weight = 47805.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.071220 restraints weight = 45047.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.4118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   7030  Z= 0.146
  Angle     :  0.403   5.126  10108  Z= 0.250
  Chirality :  0.036   0.132   1396
  Planarity :  0.002   0.012   1092
  Dihedral  : 18.130 114.390   2324
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  2.40 (0.27), residues: 998
  helix:  2.68 (0.20), residues: 662
  sheet: -3.05 (0.62), residues: 36
  loop : -0.34 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE D  16 
 TRP   0.000   0.000   TRP D 522 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00190 /  0.15 ( 7030)
  covalent geometry    : angle       0.40299 /  0.25 (10108)
  hydrogen bonds       : bond        0.04727 /  3.52 (  608)
  hydrogen bonds       : angle       4.26108 /  3.37 ( 1674)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.212 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0290
  time to fit residues: 2.0129
Evaluate side-chains
  32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 84 optimal weight:   30.0000
   chunk 54 optimal weight:   30.0000
   chunk 39 optimal weight:   10.0000
   chunk 62 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   chunk 31 optimal weight:   50.0000
   chunk 50 optimal weight:    5.9990
   chunk 79 optimal weight:   10.0000
   chunk 47 optimal weight:   30.0000
   chunk 19 optimal weight:    6.9990
   chunk 90 optimal weight:   20.0000
   overall best weight:    6.9992

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.085334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.069671 restraints weight = 45548.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.068806 restraints weight = 57186.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.068278 restraints weight = 54007.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.067847 restraints weight = 52817.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.067437 restraints weight = 60359.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.4605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7030  Z= 0.273
  Angle     :  0.589   6.683  10108  Z= 0.357
  Chirality :  0.044   0.188   1396
  Planarity :  0.003   0.018   1092
  Dihedral  : 18.161 117.648   2324
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.31 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.27), residues: 998
  helix:  1.65 (0.20), residues: 662
  sheet: -3.49 (0.60), residues: 36
  loop : -0.79 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE D  16 
 TRP   0.000   0.000   TRP D 522 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.27 ( 7030)
  covalent geometry    : angle       0.58876 /  0.36 (10108)
  hydrogen bonds       : bond        0.06537 /  4.93 (  608)
  hydrogen bonds       : angle       5.12241 /  4.06 ( 1674)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.191 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0237
  time to fit residues: 1.5747
Evaluate side-chains
  32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 95 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 51 optimal weight:    8.9990
   chunk 82 optimal weight:   20.0000
   chunk 94 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   chunk 72 optimal weight:    8.9990
   chunk 53 optimal weight:   50.0000
   chunk 66 optimal weight:    0.2980
   chunk 67 optimal weight:   10.0000
   chunk 105 optimal weight:   20.0000
   overall best weight:    6.4588

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.085871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.070683 restraints weight = 44834.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.070280 restraints weight = 59544.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.069587 restraints weight = 50769.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.069139 restraints weight = 54570.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.069347 restraints weight = 47750.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.4983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7030  Z= 0.240
  Angle     :  0.520   6.679  10108  Z= 0.316
  Chirality :  0.041   0.165   1396
  Planarity :  0.003   0.017   1092
  Dihedral  : 18.281 118.611   2324
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.27), residues: 998
  helix:  1.71 (0.20), residues: 662
  sheet: -4.26 (0.68), residues: 24
  loop : -1.04 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE D  16 
 TRP   0.000   0.000   TRP D 522 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.24 ( 7030)
  covalent geometry    : angle       0.52036 /  0.32 (10108)
  hydrogen bonds       : bond        0.05729 /  4.30 (  608)
  hydrogen bonds       : angle       4.95852 /  3.93 ( 1674)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.172 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0236
  time to fit residues: 1.6344
Evaluate side-chains
  32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 64 optimal weight:   20.0000
   chunk 46 optimal weight:    6.9990
   chunk 102 optimal weight:   30.0000
   chunk 73 optimal weight:   50.0000
   chunk 18 optimal weight:    0.7980
   chunk 49 optimal weight:    9.9990
   chunk 32 optimal weight:   50.0000
   chunk 9 optimal weight:    9.9990
   chunk 53 optimal weight:    9.9990
   chunk 95 optimal weight:    8.9990
   chunk 88 optimal weight:   50.0000
   overall best weight:    7.3588

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.084988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.070242 restraints weight = 44760.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.069287 restraints weight = 57833.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.068955 restraints weight = 53370.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.068620 restraints weight = 46900.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 102)---------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.068252 restraints weight = 53974.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.5321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7030  Z= 0.280
  Angle     :  0.603   7.225  10108  Z= 0.366
  Chirality :  0.044   0.183   1396
  Planarity :  0.003   0.017   1092
  Dihedral  : 18.383 118.955   2324
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  0.58 (0.27), residues: 998
  helix:  1.32 (0.20), residues: 662
  sheet: -4.36 (0.72), residues: 24
  loop : -1.22 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE D  16 
 TRP   0.000   0.000   TRP D 522 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.28 ( 7030)
  covalent geometry    : angle       0.60297 /  0.37 (10108)
  hydrogen bonds       : bond        0.06535 /  4.92 (  608)
  hydrogen bonds       : angle       5.33696 /  4.23 ( 1674)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.128 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0208
  time to fit residues: 1.4574
Evaluate side-chains
  32 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 104 optimal weight:   10.0000
   chunk 13 optimal weight:    7.9990
   chunk 92 optimal weight:    0.7980
   chunk 11 optimal weight:   10.0000
   chunk 77 optimal weight:   50.0000
   chunk 28 optimal weight:   70.0000
   chunk 86 optimal weight:    0.0970
   chunk 100 optimal weight:   20.0000
   chunk 58 optimal weight:    3.9990
   chunk 82 optimal weight:   20.0000
   chunk 56 optimal weight:   10.0000
   overall best weight:    4.5786

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.085868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.070792 restraints weight = 44220.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.069727 restraints weight = 57982.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.069227 restraints weight = 55284.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.068932 restraints weight = 49610.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.068661 restraints weight = 52013.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.5349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7030  Z= 0.186
  Angle     :  0.473   6.290  10108  Z= 0.289
  Chirality :  0.039   0.160   1396
  Planarity :  0.003   0.014   1092
  Dihedral  : 18.311 116.763   2324
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.27), residues: 998
  helix:  1.89 (0.20), residues: 662
  sheet: -4.29 (0.73), residues: 24
  loop : -1.06 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A 698 
 PHE   0.000   0.000   PHE D  16 
 TRP   0.000   0.000   TRP D 522 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.19 ( 7030)
  covalent geometry    : angle       0.47327 /  0.29 (10108)
  hydrogen bonds       : bond        0.05421 /  4.06 (  608)
  hydrogen bonds       : angle       4.85476 /  3.84 ( 1674)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 970.98 seconds
wall clock time: 17 minutes 13.55 seconds (1033.55 seconds total)