Starting phenix.real_space_refine
on Sun Apr  5 01:26:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw5_54299/04_2026/9rw5_54299.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw5_54299/04_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_54299/04_2026/9rw5_54299.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw5_54299/04_2026/9rw5_54299.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rw5_54299/04_2026/9rw5_54299.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw5_54299/04_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-2.1rc1-6017/lib/python3.9/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: 1.78, per 1000 atoms: 0.26
  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: 0.84
  Conformation dependent library (CDL) restraints added in 232.8 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: 0.98
  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: 1.28

  Time building geometry restraints manager: 0.94 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=" N   GLU C   2 "
       pdb=" CA  GLU C   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.99e+00
  bond pdb=" N   CYS A 695 "
       pdb=" CA  CYS A 695 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.96e+00
  bond pdb=" N   GLU D   2 "
       pdb=" CA  GLU D   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.89e+00
  bond pdb=" N   CYS B 695 "
       pdb=" CA  CYS B 695 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.84e+00
  bond pdb=" N1    U F  40 "
       pdb=" C6    U F  40 "
    ideal  model  delta    sigma   weight residual
    1.375  1.397 -0.022 2.00e-02 2.50e+03 1.17e+00
  ... (remaining 7025 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.05: 9184
        1.05 -     2.10: 757
        2.10 -     3.15: 144
        3.15 -     4.20: 18
        4.20 -     5.25: 5
  Bond angle restraints: 10108
  Sorted by residual:
  angle pdb=" C4'   U F  39 "
        pdb=" C3'   U F  39 "
        pdb=" C2'   U F  39 "
      ideal   model   delta    sigma   weight residual
     102.60  105.87   -3.27 1.00e+00 1.00e+00 1.07e+01
  angle pdb=" N   GLU B 714 "
        pdb=" CA  GLU B 714 "
        pdb=" CB  GLU B 714 "
      ideal   model   delta    sigma   weight residual
     110.28  115.21   -4.93 1.55e+00 4.16e-01 1.01e+01
  angle pdb=" C5'   U F  39 "
        pdb=" C4'   U F  39 "
        pdb=" C3'   U F  39 "
      ideal   model   delta    sigma   weight residual
     116.00  111.43    4.57 1.50e+00 4.44e-01 9.29e+00
  angle pdb=" C5'   A F  43 "
        pdb=" C4'   A F  43 "
        pdb=" C3'   A F  43 "
      ideal   model   delta    sigma   weight residual
     116.00  112.06    3.94 1.50e+00 4.44e-01 6.89e+00
  angle pdb=" C4'   G F  37 "
        pdb=" C3'   G F  37 "
        pdb=" O3'   G F  37 "
      ideal   model   delta    sigma   weight residual
     113.00  109.08    3.92 1.50e+00 4.44e-01 6.83e+00
  ... (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 -    0.030: 892
       0.030 -    0.061: 321
       0.061 -    0.091: 95
       0.091 -    0.121: 76
       0.121 -    0.152: 12
  Chirality restraints: 1396
  Sorted by residual:
  chirality pdb=" C2'   U F  39 "
            pdb=" C3'   U F  39 "
            pdb=" O2'   U F  39 "
            pdb=" C1'   U F  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.60   -0.15 2.00e-01 2.50e+01 5.76e-01
  chirality pdb=" C4'   U F  35 "
            pdb=" C5'   U F  35 "
            pdb=" O4'   U F  35 "
            pdb=" C3'   U F  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.65    0.15 2.00e-01 2.50e+01 5.66e-01
  chirality pdb=" C1'   A E  13 "
            pdb=" O4'   A E  13 "
            pdb=" C2'   A E  13 "
            pdb=" N9    A E  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.32    0.14 2.00e-01 2.50e+01 4.89e-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:             0.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.740
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7118
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= 0.196
  Angle     :  0.647   5.251  10108  Z= 0.384
  Chirality :  0.041   0.152   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
  covalent geometry    : bond        0.00316 ( 7030)
  covalent geometry    : angle       0.64665 (10108)
  hydrogen bonds       : bond        0.12490 (  608)
  hydrogen bonds       : angle       6.02222 ( 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  : 0.205 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0307
  time to fit residues: 2.0813
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  : 0.228 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 106 optimal weight:    9.9990
   chunk 38 optimal weight:   20.0000
   overall best weight:    9.1990

-------------------------------------------------------------------------------
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 = 0.3770 r_free = 0.3770 target = 0.084913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.069165 restraints weight = 45173.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.068253 restraints weight = 57264.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.067854 restraints weight = 51916.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.067431 restraints weight = 50803.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 154)---------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.067076 restraints weight = 51536.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.4058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051   7030  Z= 0.422
  Angle     :  0.801   7.593  10108  Z= 0.451
  Chirality :  0.047   0.278   1396
  Planarity :  0.004   0.019   1092
  Dihedral  : 18.931 121.510   2324
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  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:  0.49 (0.26), residues: 998
  helix:  1.03 (0.19), residues: 658
  sheet: -2.70 (0.60), residues: 52
  loop : -0.53 (0.37), residues: 288

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
  covalent geometry    : bond        0.00688 ( 7030)
  covalent geometry    : angle       0.80149 (10108)
  hydrogen bonds       : bond        0.07016 (  608)
  hydrogen bonds       : angle       5.96670 ( 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  : 0.205 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0300
  time to fit residues: 2.0498
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  : 0.124 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   chunk 85 optimal weight:    8.9990
   chunk 67 optimal weight:    6.9990
   chunk 36 optimal weight:   30.0000
   chunk 83 optimal weight:    6.9990
   chunk 10 optimal weight:   10.0000
   chunk 22 optimal weight:    8.9990
   chunk 93 optimal weight:    0.9990
   chunk 0 optimal weight:   50.0000
   overall best weight:    3.5788

-------------------------------------------------------------------------------
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 = 0.3816 r_free = 0.3816 target = 0.086911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.071121 restraints weight = 45151.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.070591 restraints weight = 52049.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 69)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.069308 restraints weight = 46148.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 71)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.069093 restraints weight = 47003.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.068792 restraints weight = 47998.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.3992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   7030  Z= 0.178
  Angle     :  0.477   5.790  10108  Z= 0.266
  Chirality :  0.036   0.181   1396
  Planarity :  0.002   0.012   1092
  Dihedral  : 18.346 110.134   2324
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    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:  1.93 (0.27), residues: 998
  helix:  2.32 (0.20), residues: 662
  sheet: -2.81 (0.54), residues: 52
  loop : -0.39 (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
  covalent geometry    : bond        0.00283 ( 7030)
  covalent geometry    : angle       0.47724 (10108)
  hydrogen bonds       : bond        0.04620 (  608)
  hydrogen bonds       : angle       4.53713 ( 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  : 0.180 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0285
  time to fit residues: 1.9553
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  : 0.194 
-------------------------------------------------------------------------------
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:   30.0000
   chunk 45 optimal weight:   40.0000
   chunk 3 optimal weight:   20.0000
   chunk 35 optimal weight:   20.0000
   chunk 28 optimal weight:   60.0000
   chunk 25 optimal weight:   30.0000
   chunk 93 optimal weight:   20.0000
   chunk 86 optimal weight:   50.0000
   chunk 10 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:   12.1996

-------------------------------------------------------------------------------
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 = 0.3730 r_free = 0.3730 target = 0.082817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.067651 restraints weight = 45181.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.066548 restraints weight = 64030.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.066254 restraints weight = 59347.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.065479 restraints weight = 64821.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.065551 restraints weight = 57350.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.5814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.071   7030  Z= 0.551
  Angle     :  0.944   7.721  10108  Z= 0.539
  Chirality :  0.052   0.337   1396
  Planarity :  0.005   0.028   1092
  Dihedral  : 19.337 121.605   2324
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.81 %
    Favored  : 93.09 %
  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: -0.81 (0.26), residues: 998
  helix:  0.18 (0.19), residues: 666
  sheet: -4.70 (0.59), residues: 24
  loop : -1.58 (0.34), residues: 308

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
  covalent geometry    : bond        0.00903 ( 7030)
  covalent geometry    : angle       0.94382 (10108)
  hydrogen bonds       : bond        0.08343 (  608)
  hydrogen bonds       : angle       6.73135 ( 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  : 0.199 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0309
  time to fit residues: 2.0507
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 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 43 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9990
   chunk 6 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   chunk 96 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 63 optimal weight:    0.8980
   chunk 10 optimal weight:   10.0000
   chunk 88 optimal weight:   10.0000
   chunk 1 optimal weight:   20.0000
   overall best weight:    3.9788

-------------------------------------------------------------------------------
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 = 0.3798 r_free = 0.3798 target = 0.085571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.070151 restraints weight = 44729.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.069093 restraints weight = 55920.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.068593 restraints weight = 48933.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 81)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.068206 restraints weight = 45848.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 131)---------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.065930 restraints weight = 46351.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.5552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7030  Z= 0.197
  Angle     :  0.518   6.155  10108  Z= 0.289
  Chirality :  0.037   0.213   1396
  Planarity :  0.003   0.012   1092
  Dihedral  : 18.558 110.778   2324
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  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:  0.81 (0.27), residues: 998
  helix:  1.55 (0.20), residues: 660
  sheet: -4.77 (0.56), residues: 24
  loop : -1.20 (0.35), residues: 314

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
  covalent geometry    : bond        0.00311 ( 7030)
  covalent geometry    : angle       0.51833 (10108)
  hydrogen bonds       : bond        0.05107 (  608)
  hydrogen bonds       : angle       4.99650 ( 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  : 0.219 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0293
  time to fit residues: 1.9488
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  : 0.192 
-------------------------------------------------------------------------------
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:    0.0870
   chunk 103 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 86 optimal weight:    0.1980
   chunk 21 optimal weight:    8.9990
   chunk 30 optimal weight:   40.0000
   chunk 18 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   chunk 87 optimal weight:   20.0000
   chunk 46 optimal weight:    0.4980
   chunk 74 optimal weight:    9.9990
   overall best weight:    1.5562

-------------------------------------------------------------------------------
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 = 0.3849 r_free = 0.3849 target = 0.087927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.073060 restraints weight = 45178.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.072601 restraints weight = 57473.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.072070 restraints weight = 49581.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.072062 restraints weight = 49976.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.072062 restraints weight = 42407.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.5454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   7030  Z= 0.102
  Angle     :  0.402   5.387  10108  Z= 0.218
  Chirality :  0.034   0.180   1396
  Planarity :  0.002   0.011   1092
  Dihedral  : 18.035 105.983   2324
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  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:  2.50 (0.28), residues: 998
  helix:  2.94 (0.20), residues: 662
  sheet: -4.09 (0.54), residues: 36
  loop : -0.62 (0.38), 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
  covalent geometry    : bond        0.00158 ( 7030)
  covalent geometry    : angle       0.40211 (10108)
  hydrogen bonds       : bond        0.03813 (  608)
  hydrogen bonds       : angle       3.88933 ( 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  : 0.202 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0289
  time to fit residues: 1.9474
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  : 0.179 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 42 optimal weight:   50.0000
   chunk 54 optimal weight:   30.0000
   chunk 74 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 88 optimal weight:    7.9990
   chunk 24 optimal weight:   20.0000
   chunk 43 optimal weight:   40.0000
   chunk 34 optimal weight:    7.9990
   chunk 66 optimal weight:    8.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 = 0.3801 r_free = 0.3801 target = 0.085814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.069765 restraints weight = 44208.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.068734 restraints weight = 50416.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.067781 restraints weight = 42202.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.067971 restraints weight = 40233.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.068001 restraints weight = 34608.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.5702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7030  Z= 0.210
  Angle     :  0.500   5.709  10108  Z= 0.278
  Chirality :  0.037   0.224   1396
  Planarity :  0.002   0.012   1092
  Dihedral  : 18.115 108.650   2324
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  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:  1.98 (0.28), residues: 998
  helix:  2.51 (0.20), residues: 662
  sheet: -4.19 (0.53), residues: 36
  loop : -0.75 (0.38), 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
  covalent geometry    : bond        0.00341 ( 7030)
  covalent geometry    : angle       0.50009 (10108)
  hydrogen bonds       : bond        0.04861 (  608)
  hydrogen bonds       : angle       4.47763 ( 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  : 0.148 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0295
  time to fit residues: 2.0762
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 84 optimal weight:    0.8980
   chunk 54 optimal weight:   30.0000
   chunk 39 optimal weight:   30.0000
   chunk 62 optimal weight:    5.9990
   chunk 20 optimal weight:    0.2980
   chunk 31 optimal weight:   50.0000
   chunk 50 optimal weight:   20.0000
   chunk 79 optimal weight:   50.0000
   chunk 47 optimal weight:   20.0000
   chunk 19 optimal weight:    5.9990
   chunk 90 optimal weight:   40.0000
   overall best weight:    6.6388

-------------------------------------------------------------------------------
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 = 0.3767 r_free = 0.3767 target = 0.084168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 108)---------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.067705 restraints weight = 45070.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.065435 restraints weight = 52988.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.064418 restraints weight = 44903.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.064680 restraints weight = 40187.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.064627 restraints weight = 36337.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.6308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7030  Z= 0.315
  Angle     :  0.621   6.371  10108  Z= 0.353
  Chirality :  0.041   0.272   1396
  Planarity :  0.003   0.015   1092
  Dihedral  : 18.570 111.959   2324
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  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:  0.92 (0.27), residues: 998
  helix:  1.70 (0.20), residues: 674
  sheet: -3.75 (0.64), residues: 36
  loop : -1.43 (0.37), residues: 288

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
  covalent geometry    : bond        0.00517 ( 7030)
  covalent geometry    : angle       0.62133 (10108)
  hydrogen bonds       : bond        0.05943 (  608)
  hydrogen bonds       : angle       5.22352 ( 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  : 0.184 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0292
  time to fit residues: 1.9853
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  : 0.188 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 9 optimal weight:    7.9990
   chunk 51 optimal weight:    9.9990
   chunk 82 optimal weight:    4.9990
   chunk 94 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 72 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 66 optimal weight:    8.9990
   chunk 67 optimal weight:    1.9990
   chunk 105 optimal weight:    8.9990
   overall best weight:    6.1990

-------------------------------------------------------------------------------
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 = 0.3769 r_free = 0.3769 target = 0.084168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.069019 restraints weight = 44669.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.068332 restraints weight = 60106.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.068704 restraints weight = 53253.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.068288 restraints weight = 47354.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.068412 restraints weight = 44264.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.6779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7030  Z= 0.291
  Angle     :  0.591   6.058  10108  Z= 0.333
  Chirality :  0.040   0.258   1396
  Planarity :  0.003   0.015   1092
  Dihedral  : 18.550 108.353   2324
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  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:  0.75 (0.27), residues: 998
  helix:  1.59 (0.20), residues: 674
  sheet: -3.98 (0.63), residues: 42
  loop : -1.45 (0.37), residues: 282

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
  covalent geometry    : bond        0.00474 ( 7030)
  covalent geometry    : angle       0.59145 (10108)
  hydrogen bonds       : bond        0.05628 (  608)
  hydrogen bonds       : angle       5.12445 ( 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  : 0.126 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0296
  time to fit residues: 1.9933
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  : 0.160 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 102 optimal weight:   10.0000
   chunk 73 optimal weight:   70.0000
   chunk 18 optimal weight:    9.9990
   chunk 49 optimal weight:   20.0000
   chunk 32 optimal weight:    0.0370
   chunk 9 optimal weight:    8.9990
   chunk 53 optimal weight:   50.0000
   chunk 95 optimal weight:   10.0000
   chunk 88 optimal weight:    5.9990
   overall best weight:    7.0068

-------------------------------------------------------------------------------
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 = 0.3759 r_free = 0.3759 target = 0.083796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.069368 restraints weight = 44705.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.068617 restraints weight = 63323.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.068366 restraints weight = 57187.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.067882 restraints weight = 54022.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.067980 restraints weight = 51740.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.6852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   7030  Z= 0.321
  Angle     :  0.628   6.511  10108  Z= 0.355
  Chirality :  0.041   0.265   1396
  Planarity :  0.003   0.017   1092
  Dihedral  : 18.603 108.026   2324
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  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:  0.42 (0.27), residues: 998
  helix:  1.37 (0.20), residues: 672
  sheet: -3.98 (0.66), residues: 42
  loop : -1.69 (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
  covalent geometry    : bond        0.00523 ( 7030)
  covalent geometry    : angle       0.62780 (10108)
  hydrogen bonds       : bond        0.06060 (  608)
  hydrogen bonds       : angle       5.33375 ( 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  : 0.221 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0299
  time to fit residues: 2.0630
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  : 0.196 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 13 optimal weight:    9.9990
   chunk 92 optimal weight:    0.9980
   chunk 11 optimal weight:   10.0000
   chunk 77 optimal weight:   50.0000
   chunk 28 optimal weight:   70.0000
   chunk 86 optimal weight:    0.4980
   chunk 100 optimal weight:    6.9990
   chunk 58 optimal weight:    8.9990
   chunk 82 optimal weight:   40.0000
   chunk 56 optimal weight:   10.0000
   overall best weight:    4.6986

-------------------------------------------------------------------------------
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 = 0.3777 r_free = 0.3777 target = 0.084629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.069342 restraints weight = 44402.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.068805 restraints weight = 55069.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.068167 restraints weight = 46608.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.067980 restraints weight = 48216.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.068140 restraints weight = 39219.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.6901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7030  Z= 0.221
  Angle     :  0.528   5.614  10108  Z= 0.295
  Chirality :  0.038   0.253   1396
  Planarity :  0.003   0.018   1092
  Dihedral  : 18.417 104.535   2324
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  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:  0.96 (0.27), residues: 998
  helix:  1.82 (0.20), residues: 674
  sheet: -3.96 (0.67), residues: 42
  loop : -1.56 (0.37), residues: 282

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
  covalent geometry    : bond        0.00359 ( 7030)
  covalent geometry    : angle       0.52764 (10108)
  hydrogen bonds       : bond        0.05211 (  608)
  hydrogen bonds       : angle       4.87785 ( 1674)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1215.08 seconds
wall clock time: 21 minutes 24.92 seconds (1284.92 seconds total)