Starting phenix.real_space_refine
on Fri Aug 22 17:43:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mpw_48507/08_2025/9mpw_48507.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mpw_48507/08_2025/9mpw_48507.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.37
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mpw_48507/08_2025/9mpw_48507.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mpw_48507/08_2025/9mpw_48507.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mpw_48507/08_2025/9mpw_48507.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mpw_48507/08_2025/9mpw_48507.map"
  }
  resolution = 3.37
  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=   0.005
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
     S      28      5.16       5
     C    4002      2.51       5
     N    1054      2.21       5
     O    1252      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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6336
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "S"
      Number of atoms: 3083
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 3083
          Classifications: {'peptide': 402}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 17, 'TRANS': 384}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "H"
      Number of atoms: 1523
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1523
          Classifications: {'peptide': 204}
          Link IDs: {'PTRANS': 13, 'TRANS': 190}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1632
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "S"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "H"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.37, per 1000 atoms: 0.22
  Number of scatterers: 6336
  At special positions: 0
  Unit cell: (65.254, 99.946, 149.506, 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)
     S      28     16.00
     O    1252      8.00
     N    1054      7.00
     C    4002      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 738 " - pdb=" SG  CYS S 760 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 743 " - pdb=" SG  CYS S 749 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 970 " - pdb=" SG  CYS S 999 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S1032 " - pdb=" SG  CYS S1043 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 139 " - pdb=" SG  CYS H 195 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 135 " - pdb=" SG  CYS L 195 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
    NAG-ASN
      " NAG A   1 " - " ASN S1098 "
      " NAG H 301 " - " ASN H  81 "
      " NAG S1301 " - " ASN S1134 "
      " NAG S1302 " - " ASN S1074 "
      " NAG S1303 " - " ASN S 717 "
      " NAG S1304 " - " ASN S 801 "
  Time building additional restraints: 0.35
  Conformation dependent library (CDL) restraints added in 334.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1526

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 13 sheets defined
      26.8% alpha, 32.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'S' and resid 750 through 756
      removed outlier: 3.904A  pdb=" N   GLN S 755 " --> pdb=" O   ASN S 751 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 757 through 783
      removed outlier: 4.424A  pdb=" N   THR S 761 " --> pdb=" O   GLY S 757 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   GLN S 762 " --> pdb=" O   SER S 758 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LEU S 763 " --> pdb=" O   PHE S 759 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ALA S 766 " --> pdb=" O   GLN S 762 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 818 through 827
    Processing helix  chain 'S' and resid 832 through 842
      removed outlier: 3.884A  pdb=" N   GLY S 842 " --> pdb=" O   GLY S 838 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 844 through 846
      No H-bonds generated for 'chain 'S' and resid 844 through 846'
    Processing helix  chain 'S' and resid 847 through 852
      removed outlier: 3.592A  pdb=" N   ALA S 852 " --> pdb=" O   ASP S 848 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 866 through 878
    Processing helix  chain 'S' and resid 897 through 910
    Processing helix  chain 'S' and resid 912 through 919
      removed outlier: 4.343A  pdb=" N   LEU S 916 " --> pdb=" O   THR S 912 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 919 through 940
      removed outlier: 3.504A  pdb=" N   SER S 939 " --> pdb=" O   GLN S 935 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   SER S 940 " --> pdb=" O   ASP S 936 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 948 through 968
      removed outlier: 3.647A  pdb=" N   LEU S 962 " --> pdb=" O   ALA S 958 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL S 963 " --> pdb=" O   LEU S 959 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 989 through 1031
      removed outlier: 3.616A  pdb=" N   CYS S 999 " --> pdb=" O   ARG S 995 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU S1001 " --> pdb=" O   ILE S 997 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU S1004 " --> pdb=" O   ARG S1000 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ILE S1013 " --> pdb=" O   THR S1009 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   ARG S1014 " --> pdb=" O   GLN S1010 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 63 through 65
      No H-bonds generated for 'chain 'H' and resid 63 through 65'
    Processing helix  chain 'H' and resid 86 through 90
      removed outlier: 4.003A  pdb=" N   THR H  90 " --> pdb=" O   ALA H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 155 through 157
      No H-bonds generated for 'chain 'H' and resid 155 through 157'
    Processing helix  chain 'H' and resid 184 through 188
      removed outlier: 3.622A  pdb=" N   LEU H 188 " --> pdb=" O   SER H 185 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.514A  pdb=" N   ASP L  83 " --> pdb=" O   GLU L  80 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   PHE L  84 " --> pdb=" O   ALA L  81 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 80 through 84'
    Processing helix  chain 'L' and resid 122 through 129
    Processing helix  chain 'L' and resid 184 through 188
    Processing sheet with id=AA1, first strand: chain 'S' and resid 712 through 727
      removed outlier: 6.879A  pdb=" N   ALA S 713 " --> pdb=" O   ASN S1074 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ASN S1074 " --> pdb=" O   ALA S 713 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   GLU S1072 " --> pdb=" O   PRO S 715 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   TYR S1067 " --> pdb=" O   HIS S1048 " (cutoff:3.500A)
      removed outlier: 5.725A  pdb=" N   HIS S1048 " --> pdb=" O   TYR S1067 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'S' and resid 712 through 727
      removed outlier: 6.879A  pdb=" N   ALA S 713 " --> pdb=" O   ASN S1074 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ASN S1074 " --> pdb=" O   ALA S 713 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   GLU S1072 " --> pdb=" O   PRO S 715 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ALA S1078 " --> pdb=" O   PHE S1095 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   PHE S1095 " --> pdb=" O   ALA S1078 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'S' and resid 735 through 736
    Processing sheet with id=AA4, first strand: chain 'S' and resid 1120 through 1125
      removed outlier: 4.623A  pdb=" N   ALA S1087 " --> pdb=" O   SER S1123 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.632A  pdb=" N   LEU H  18 " --> pdb=" O   LEU H  82 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU H  82 " --> pdb=" O   LEU H  18 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.537A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 120 through 123
      removed outlier: 6.046A  pdb=" N   TYR H 175 " --> pdb=" O   ASP H 143 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 120 through 123
      removed outlier: 6.046A  pdb=" N   TYR H 175 " --> pdb=" O   ASP H 143 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 150 through 153
    Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 6
    Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.683A  pdb=" N   ALA L  85 " --> pdb=" O   VAL L 105 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   LEU L  34 " --> pdb=" O   PHE L  50 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   PHE L  50 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 116 through 119
      removed outlier: 3.922A  pdb=" N   ASN L 139 " --> pdb=" O   TYR L 174 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   TYR L 174 " --> pdb=" O   ASN L 139 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 146 through 151

    295 hydrogen bonds defined for protein.
    807 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.86

  Time building geometry restraints manager: 0.48 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1999
        1.34 -     1.46: 1459
        1.46 -     1.58: 2972
        1.58 -     1.70: 0
        1.70 -     1.82: 36
  Bond restraints: 6466
  Sorted by residual:
  bond pdb=" CG  LEU S 767 "
       pdb=" CD1 LEU S 767 "
    ideal  model  delta    sigma   weight residual
    1.521  1.457  0.064 3.30e-02 9.18e+02 3.81e+00
  bond pdb=" C   SER S1055 "
       pdb=" N   ALA S1056 "
    ideal  model  delta    sigma   weight residual
    1.331  1.278  0.053 2.83e-02 1.25e+03 3.49e+00
  bond pdb=" C   SER L   7 "
       pdb=" N   PRO L   8 "
    ideal  model  delta    sigma   weight residual
    1.334  1.376 -0.042 2.34e-02 1.83e+03 3.17e+00
  bond pdb=" C   SER L  95 "
       pdb=" N   PRO L  96 "
    ideal  model  delta    sigma   weight residual
    1.334  1.373 -0.039 2.34e-02 1.83e+03 2.74e+00
  bond pdb=" CG1 ILE L  59 "
       pdb=" CD1 ILE L  59 "
    ideal  model  delta    sigma   weight residual
    1.513  1.449  0.064 3.90e-02 6.57e+02 2.72e+00
  ... (remaining 6461 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.68: 8658
        2.68 -     5.37: 119
        5.37 -     8.05: 18
        8.05 -    10.73: 0
       10.73 -    13.41: 1
  Bond angle restraints: 8796
  Sorted by residual:
  angle pdb=" C   CYS S 738 "
        pdb=" N   THR S 739 "
        pdb=" CA  THR S 739 "
      ideal   model   delta    sigma   weight residual
     123.05  129.20   -6.15 1.57e+00 4.06e-01 1.53e+01
  angle pdb=" CA  LEU H  63 "
        pdb=" CB  LEU H  63 "
        pdb=" CG  LEU H  63 "
      ideal   model   delta    sigma   weight residual
     116.30  129.71  -13.41 3.50e+00 8.16e-02 1.47e+01
  angle pdb=" N   LYS H 200 "
        pdb=" CA  LYS H 200 "
        pdb=" C   LYS H 200 "
      ideal   model   delta    sigma   weight residual
     109.81  116.63   -6.82 2.21e+00 2.05e-01 9.52e+00
  angle pdb=" N   PHE H 145 "
        pdb=" CA  PHE H 145 "
        pdb=" C   PHE H 145 "
      ideal   model   delta    sigma   weight residual
     109.81  116.56   -6.75 2.21e+00 2.05e-01 9.34e+00
  angle pdb=" C   SER H  74 "
        pdb=" N   LYS H  75 "
        pdb=" CA  LYS H  75 "
      ideal   model   delta    sigma   weight residual
     123.05  127.82   -4.77 1.57e+00 4.06e-01 9.23e+00
  ... (remaining 8791 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.72: 3577
       16.72 -    33.43: 310
       33.43 -    50.15: 64
       50.15 -    66.86: 13
       66.86 -    83.58: 5
  Dihedral angle restraints: 3969
    sinusoidal: 1602
      harmonic: 2367
  Sorted by residual:
  dihedral pdb=" CA  PRO H 148 "
           pdb=" C   PRO H 148 "
           pdb=" N   VAL H 149 "
           pdb=" CA  VAL H 149 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.46  -28.54     0      5.00e+00 4.00e-02 3.26e+01
  dihedral pdb=" CB  CYS H 139 "
           pdb=" SG  CYS H 139 "
           pdb=" SG  CYS H 195 "
           pdb=" CB  CYS H 195 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.60  -45.60     1      1.00e+01 1.00e-02 2.88e+01
  dihedral pdb=" CA  GLU H 147 "
           pdb=" C   GLU H 147 "
           pdb=" N   PRO H 148 "
           pdb=" CA  PRO H 148 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.74   23.26     0      5.00e+00 4.00e-02 2.16e+01
  ... (remaining 3966 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 711
       0.045 -    0.091: 235
       0.091 -    0.136: 69
       0.136 -    0.181: 21
       0.181 -    0.226: 5
  Chirality restraints: 1041
  Sorted by residual:
  chirality pdb=" CB  ILE L 118 "
            pdb=" CA  ILE L 118 "
            pdb=" CG1 ILE L 118 "
            pdb=" CG2 ILE L 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" C1  NAG S1303 "
            pdb=" ND2 ASN S 717 "
            pdb=" C2  NAG S1303 "
            pdb=" O5  NAG S1303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.19   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CB  ILE S 923 "
            pdb=" CA  ILE S 923 "
            pdb=" CG1 ILE S 923 "
            pdb=" CG2 ILE S 923 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.35e-01
  ... (remaining 1038 not shown)

  Planarity restraints: 1123
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 147 "    0.051 5.00e-02 4.00e+02   7.64e-02 9.35e+00
        pdb=" N   PRO H 148 "   -0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO H 148 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO H 148 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN H  60 "   -0.037 5.00e-02 4.00e+02   5.71e-02 5.22e+00
        pdb=" N   PRO H  61 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO H  61 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO H  61 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS H  13 "    0.032 5.00e-02 4.00e+02   4.82e-02 3.72e+00
        pdb=" N   PRO H  14 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO H  14 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO H  14 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1120 not shown)

  Histogram of nonbonded interaction distances:
        2.55 -     3.02: 3133
        3.02 -     3.49: 5979
        3.49 -     3.96: 9604
        3.96 -     4.43: 10545
        4.43 -     4.90: 17999
  Nonbonded interactions: 47260
  Sorted by model distance:
  nonbonded pdb=" O5  NAG S1304 "
            pdb=" O6  NAG S1304 "
     model   vdw
     2.554 2.432
  nonbonded pdb=" N   GLU H  16 "
            pdb=" O   GLU H  16 "
     model   vdw
     2.609 2.496
  nonbonded pdb=" N   GLY S 946 "
            pdb=" N   LYS S 947 "
     model   vdw
     2.616 2.560
  nonbonded pdb=" N   ASN S1135 "
            pdb=" O   ASN S1135 "
     model   vdw
     2.631 2.496
  nonbonded pdb=" N   ASN L 211 "
            pdb=" O   ASN L 211 "
     model   vdw
     2.636 2.496
  ... (remaining 47255 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.840
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.670
  Find NCS groups from input model:        0.030
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
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      :  0.005   0.064   6481  Z= 0.210
  Angle     :  0.790  13.414   8833  Z= 0.414
  Chirality :  0.053   0.226   1041
  Planarity :  0.006   0.076   1117
  Dihedral  : 13.373  83.577   2419
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 2.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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 aren not related in a simple way.
  whole: -1.52 (0.27), residues: 802
  helix: -1.56 (0.31), residues: 193
  sheet:  0.26 (0.32), residues: 253
  loop : -1.58 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 212 
 TYR   0.015   0.002   TYR H  50 
 PHE   0.018   0.002   PHE S1121 
 TRP   0.011   0.002   TRP H 102 
 HIS   0.003   0.001   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 6466)
  covalent geometry    : angle       0.78256 ( 8796)
  SS BOND              : bond        0.00357 (    8)
  SS BOND              : angle       0.88706 (   16)
  hydrogen bonds       : bond        0.14125 (  270)
  hydrogen bonds       : angle       6.50240 (  807)
  link_BETA1-4         : bond        0.00524 (    1)
  link_BETA1-4         : angle       1.07761 (    3)
  link_NAG-ASN         : bond        0.00382 (    6)
  link_NAG-ASN         : angle       2.43655 (   18)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  144 TYR cc_start: 0.7602 (p90) cc_final: 0.7193 (p90)
REVERT: L  107 ILE cc_start: 0.9498 (mm) cc_final: 0.9213 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.1131
  time to fit residues: 20.9031
Evaluate side-chains
  68 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0970
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
S 895 GLN
S 954 GLN
S 992 GLN
** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 170 GLN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.066967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.051143 restraints weight = 21720.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.2882 rms_B_bonded: 4.52
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6481  Z= 0.140
  Angle     :  0.624   9.264   8833  Z= 0.321
  Chirality :  0.043   0.175   1041
  Planarity :  0.005   0.082   1117
  Dihedral  :  4.565  23.239   1013
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  9.40 %
    Favored  : 89.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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 aren not related in a simple way.
  whole: -0.67 (0.29), residues: 802
  helix:  0.36 (0.38), residues: 186
  sheet:  0.28 (0.32), residues: 252
  loop : -1.38 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG S 995 
 TYR   0.028   0.002   TYR L 141 
 PHE   0.013   0.001   PHE L  72 
 TRP   0.009   0.001   TRP H 153 
 HIS   0.002   0.001   HIS S1048 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6466)
  covalent geometry    : angle       0.61643 ( 8796)
  SS BOND              : bond        0.00201 (    8)
  SS BOND              : angle       0.66613 (   16)
  hydrogen bonds       : bond        0.03897 (  270)
  hydrogen bonds       : angle       5.00771 (  807)
  link_BETA1-4         : bond        0.00495 (    1)
  link_BETA1-4         : angle       0.98836 (    3)
  link_NAG-ASN         : bond        0.00247 (    6)
  link_NAG-ASN         : angle       2.24773 (   18)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: S  856 ASN cc_start: 0.8799 (m-40) cc_final: 0.8322 (m110)
REVERT: H   46 GLU cc_start: 0.8608 (tt0) cc_final: 0.7983 (tt0)
REVERT: H  191 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7848 (tm-30)
REVERT: H  193 TYR cc_start: 0.7921 (m-10) cc_final: 0.7585 (m-10)
REVERT: L   78 ARG cc_start: 0.8427 (mmm-85) cc_final: 0.8153 (mmm-85)
REVERT: L   80 GLU cc_start: 0.8166 (mp0) cc_final: 0.7931 (mp0)
REVERT: L   82 GLU cc_start: 0.8912 (mp0) cc_final: 0.8498 (pm20)
REVERT: L  106 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7261 (tm-30)
REVERT: L  123 ASP cc_start: 0.9216 (p0) cc_final: 0.8818 (p0)
REVERT: L  124 GLU cc_start: 0.9295 (mt-10) cc_final: 0.8912 (mp0)
REVERT: L  144 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7758 (tm-30)
REVERT: L  189 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8979 (mtmt)
  outliers start: 8
  outliers final: 3
  residues processed: 82
  average time/residue: 0.1106
  time to fit residues: 11.5542
Evaluate side-chains
  69 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  100 ASP
Chi-restraints excluded: chain H residue  111 SER
Chi-restraints excluded: chain L residue  159 ASN
Chi-restraints excluded: chain L residue  189 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 55 optimal weight:    0.4980
   chunk 62 optimal weight:    0.6980
   chunk 53 optimal weight:    6.9990
   chunk 32 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 24 optimal weight:    9.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
H 170 GLN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.065184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.049099 restraints weight = 21548.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.2820 rms_B_bonded: 4.48
r_work: 0.2656 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6481  Z= 0.198
  Angle     :  0.607   6.423   8833  Z= 0.313
  Chirality :  0.043   0.184   1041
  Planarity :  0.005   0.078   1117
  Dihedral  :  4.378  19.956   1013
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 11.11 %
    Favored  : 87.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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 aren not related in a simple way.
  whole: -0.28 (0.30), residues: 802
  helix:  0.95 (0.39), residues: 195
  sheet:  0.21 (0.31), residues: 273
  loop : -1.17 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG L  18 
 TYR   0.016   0.002   TYR S1067 
 PHE   0.022   0.001   PHE H 145 
 TRP   0.010   0.001   TRP H 153 
 HIS   0.004   0.001   HIS S1048 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 6466)
  covalent geometry    : angle       0.59971 ( 8796)
  SS BOND              : bond        0.00191 (    8)
  SS BOND              : angle       0.67367 (   16)
  hydrogen bonds       : bond        0.03675 (  270)
  hydrogen bonds       : angle       4.77279 (  807)
  link_BETA1-4         : bond        0.00173 (    1)
  link_BETA1-4         : angle       1.02548 (    3)
  link_NAG-ASN         : bond        0.00108 (    6)
  link_NAG-ASN         : angle       2.07863 (   18)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: S  869 MET cc_start: 0.9203 (mtt) cc_final: 0.8906 (mpp)
REVERT: H   13 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8696 (mmmt)
REVERT: H   46 GLU cc_start: 0.9101 (tt0) cc_final: 0.8530 (tt0)
REVERT: H  104 GLN cc_start: 0.8665 (pm20) cc_final: 0.8443 (pm20)
REVERT: H  191 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7885 (tm-30)
REVERT: H  207 ASP cc_start: 0.8851 (m-30) cc_final: 0.8384 (m-30)
REVERT: H  209 ARG cc_start: 0.8268 (mmm-85) cc_final: 0.7819 (tpt90)
REVERT: L   78 ARG cc_start: 0.8580 (mmm-85) cc_final: 0.8358 (mmm-85)
REVERT: L   80 GLU cc_start: 0.8291 (mp0) cc_final: 0.8031 (mp0)
REVERT: L   82 GLU cc_start: 0.9135 (mp0) cc_final: 0.8721 (pm20)
REVERT: L  106 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7646 (tm-30)
REVERT: L  144 GLU cc_start: 0.8492 (tm-30) cc_final: 0.7915 (tm-30)
  outliers start: 9
  outliers final: 4
  residues processed: 73
  average time/residue: 0.1146
  time to fit residues: 10.4483
Evaluate side-chains
  64 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue 1050 MET
Chi-restraints excluded: chain S residue 1055 SER
Chi-restraints excluded: chain H residue  111 SER
Chi-restraints excluded: chain L residue  159 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 48 optimal weight:    0.3980
   chunk 67 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.065030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.049078 restraints weight = 21495.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 4.33
r_work: 0.2671 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.3118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6481  Z= 0.179
  Angle     :  0.586   6.559   8833  Z= 0.302
  Chirality :  0.043   0.185   1041
  Planarity :  0.004   0.065   1117
  Dihedral  :  4.279  18.913   1013
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 13.11 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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 aren not related in a simple way.
  whole: -0.11 (0.30), residues: 802
  helix:  1.24 (0.39), residues: 195
  sheet:  0.26 (0.31), residues: 268
  loop : -1.11 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H   5 
 TYR   0.017   0.001   TYR S1067 
 PHE   0.017   0.001   PHE H 145 
 TRP   0.008   0.001   TRP H 102 
 HIS   0.003   0.001   HIS S1048 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 6466)
  covalent geometry    : angle       0.57942 ( 8796)
  SS BOND              : bond        0.00177 (    8)
  SS BOND              : angle       0.60517 (   16)
  hydrogen bonds       : bond        0.03450 (  270)
  hydrogen bonds       : angle       4.65256 (  807)
  link_BETA1-4         : bond        0.00231 (    1)
  link_BETA1-4         : angle       0.99937 (    3)
  link_NAG-ASN         : bond        0.00128 (    6)
  link_NAG-ASN         : angle       1.99290 (   18)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S  869 MET cc_start: 0.9219 (mtt) cc_final: 0.8928 (mpp)
REVERT: H   46 GLU cc_start: 0.9063 (tt0) cc_final: 0.8519 (tt0)
REVERT: H  104 GLN cc_start: 0.8666 (pm20) cc_final: 0.8444 (pm20)
REVERT: H  191 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8287 (tm-30)
REVERT: H  205 LYS cc_start: 0.9056 (mptt) cc_final: 0.8795 (mptt)
REVERT: H  207 ASP cc_start: 0.8816 (m-30) cc_final: 0.8366 (m-30)
REVERT: H  209 ARG cc_start: 0.8315 (mmm-85) cc_final: 0.7862 (tpt90)
REVERT: L   78 ARG cc_start: 0.8567 (mmm-85) cc_final: 0.8321 (mmm-85)
REVERT: L   80 GLU cc_start: 0.8265 (mp0) cc_final: 0.8039 (mp0)
REVERT: L   82 GLU cc_start: 0.9130 (mp0) cc_final: 0.8731 (pm20)
REVERT: L  106 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7593 (tm-30)
REVERT: L  144 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7860 (tm-30)
  outliers start: 9
  outliers final: 7
  residues processed: 74
  average time/residue: 0.1123
  time to fit residues: 10.4817
Evaluate side-chains
  66 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  742 ILE
Chi-restraints excluded: chain S residue  931 ILE
Chi-restraints excluded: chain S residue 1050 MET
Chi-restraints excluded: chain S residue 1055 SER
Chi-restraints excluded: chain H residue  111 SER
Chi-restraints excluded: chain L residue  159 ASN
Chi-restraints excluded: chain L residue  192 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 6 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 72 optimal weight:    3.9990
   chunk 17 optimal weight:    0.4980
   chunk 7 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3242 r_free = 0.3242 target = 0.065718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.049769 restraints weight = 21768.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 4.39
r_work: 0.2687 rms_B_bonded: 4.86 restraints_weight: 0.5000
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.3288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6481  Z= 0.134
  Angle     :  0.562   7.039   8833  Z= 0.288
  Chirality :  0.042   0.188   1041
  Planarity :  0.004   0.067   1117
  Dihedral  :  4.114  19.101   1013
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 13.96 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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 aren not related in a simple way.
  whole:  0.08 (0.30), residues: 802
  helix:  1.60 (0.39), residues: 188
  sheet:  0.37 (0.32), residues: 256
  loop : -1.02 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H   5 
 TYR   0.015   0.001   TYR S1067 
 PHE   0.015   0.001   PHE H 145 
 TRP   0.007   0.001   TRP H 102 
 HIS   0.002   0.001   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6466)
  covalent geometry    : angle       0.55574 ( 8796)
  SS BOND              : bond        0.00151 (    8)
  SS BOND              : angle       0.56371 (   16)
  hydrogen bonds       : bond        0.03186 (  270)
  hydrogen bonds       : angle       4.57917 (  807)
  link_BETA1-4         : bond        0.00340 (    1)
  link_BETA1-4         : angle       0.94393 (    3)
  link_NAG-ASN         : bond        0.00196 (    6)
  link_NAG-ASN         : angle       1.91017 (   18)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S  869 MET cc_start: 0.9236 (mtt) cc_final: 0.8942 (mpp)
REVERT: H   46 GLU cc_start: 0.9069 (tt0) cc_final: 0.8535 (tt0)
REVERT: H  104 GLN cc_start: 0.8730 (pm20) cc_final: 0.8483 (pm20)
REVERT: H  191 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8203 (tm-30)
REVERT: H  193 TYR cc_start: 0.8104 (m-80) cc_final: 0.7640 (m-80)
REVERT: H  207 ASP cc_start: 0.8783 (m-30) cc_final: 0.8336 (m-30)
REVERT: L   78 ARG cc_start: 0.8571 (mmm-85) cc_final: 0.8336 (mmm-85)
REVERT: L  106 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7636 (tm-30)
REVERT: L  144 GLU cc_start: 0.8428 (tm-30) cc_final: 0.7821 (tm-30)
  outliers start: 8
  outliers final: 5
  residues processed: 72
  average time/residue: 0.1125
  time to fit residues: 10.3173
Evaluate side-chains
  66 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue 1050 MET
Chi-restraints excluded: chain S residue 1055 SER
Chi-restraints excluded: chain H residue  111 SER
Chi-restraints excluded: chain L residue  159 ASN
Chi-restraints excluded: chain L residue  192 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0010
   chunk 54 optimal weight:    0.0670
   chunk 57 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.4726

-------------------------------------------------------------------------------
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 = 0.3268 r_free = 0.3268 target = 0.066844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.050941 restraints weight = 21631.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.2874 rms_B_bonded: 4.47
r_work: 0.2716 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.3424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6481  Z= 0.102
  Angle     :  0.555   8.680   8833  Z= 0.282
  Chirality :  0.042   0.175   1041
  Planarity :  0.004   0.061   1117
  Dihedral  :  3.971  20.323   1013
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 13.82 %
    Favored  : 84.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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 aren not related in a simple way.
  whole:  0.20 (0.30), residues: 802
  helix:  1.79 (0.39), residues: 189
  sheet:  0.43 (0.33), residues: 249
  loop : -0.96 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 143 
 TYR   0.013   0.001   TYR S1067 
 PHE   0.013   0.001   PHE H 145 
 TRP   0.006   0.001   TRP H 102 
 HIS   0.003   0.001   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 6466)
  covalent geometry    : angle       0.54890 ( 8796)
  SS BOND              : bond        0.00249 (    8)
  SS BOND              : angle       0.61100 (   16)
  hydrogen bonds       : bond        0.02887 (  270)
  hydrogen bonds       : angle       4.42435 (  807)
  link_BETA1-4         : bond        0.00474 (    1)
  link_BETA1-4         : angle       0.90160 (    3)
  link_NAG-ASN         : bond        0.00261 (    6)
  link_NAG-ASN         : angle       1.81520 (   18)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S  869 MET cc_start: 0.9236 (mtt) cc_final: 0.8940 (mpp)
REVERT: S  994 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8731 (tm-30)
REVERT: H   46 GLU cc_start: 0.9040 (tt0) cc_final: 0.8524 (tt0)
REVERT: H  104 GLN cc_start: 0.8733 (pm20) cc_final: 0.8443 (pm20)
REVERT: H  191 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8216 (tm-30)
REVERT: H  193 TYR cc_start: 0.8078 (m-80) cc_final: 0.7690 (m-80)
REVERT: H  205 LYS cc_start: 0.9191 (mptt) cc_final: 0.8989 (mmtt)
REVERT: H  207 ASP cc_start: 0.8764 (m-30) cc_final: 0.8337 (m-30)
REVERT: L   80 GLU cc_start: 0.8145 (pm20) cc_final: 0.7944 (pm20)
REVERT: L  106 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7652 (tm-30)
REVERT: L  144 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8157 (tm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 80
  average time/residue: 0.1080
  time to fit residues: 11.0612
Evaluate side-chains
  69 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  931 ILE
Chi-restraints excluded: chain S residue  994 GLN
Chi-restraints excluded: chain S residue 1055 SER
Chi-restraints excluded: chain H residue  109 THR
Chi-restraints excluded: chain H residue  111 SER
Chi-restraints excluded: chain L residue  159 ASN
Chi-restraints excluded: chain L residue  192 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 37 optimal weight:    0.0050
   chunk 40 optimal weight:    3.9990
   chunk 80 optimal weight:    0.0370
   chunk 51 optimal weight:   10.0000
   chunk 65 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 74 optimal weight:    0.3980
   chunk 25 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.4274

-------------------------------------------------------------------------------
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 = 0.3268 r_free = 0.3268 target = 0.066877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.051108 restraints weight = 21403.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.2882 rms_B_bonded: 4.43
r_work: 0.2723 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6481  Z= 0.107
  Angle     :  0.566   8.186   8833  Z= 0.289
  Chirality :  0.042   0.176   1041
  Planarity :  0.004   0.063   1117
  Dihedral  :  3.870  20.456   1013
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 15.38 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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 aren not related in a simple way.
  whole:  0.36 (0.30), residues: 802
  helix:  1.91 (0.39), residues: 189
  sheet:  0.51 (0.33), residues: 249
  loop : -0.84 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 143 
 TYR   0.012   0.001   TYR S1067 
 PHE   0.012   0.001   PHE H 145 
 TRP   0.005   0.001   TRP H 102 
 HIS   0.003   0.001   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 6466)
  covalent geometry    : angle       0.56116 ( 8796)
  SS BOND              : bond        0.00163 (    8)
  SS BOND              : angle       0.58618 (   16)
  hydrogen bonds       : bond        0.02954 (  270)
  hydrogen bonds       : angle       4.43547 (  807)
  link_BETA1-4         : bond        0.00469 (    1)
  link_BETA1-4         : angle       0.88960 (    3)
  link_NAG-ASN         : bond        0.00266 (    6)
  link_NAG-ASN         : angle       1.74107 (   18)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S  869 MET cc_start: 0.9241 (mtt) cc_final: 0.8955 (mpp)
REVERT: S  994 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8688 (tm-30)
REVERT: H   46 GLU cc_start: 0.9039 (tt0) cc_final: 0.8531 (tt0)
REVERT: H  191 GLN cc_start: 0.8469 (tm-30) cc_final: 0.8228 (tm-30)
REVERT: H  205 LYS cc_start: 0.9188 (mptt) cc_final: 0.8981 (mmtt)
REVERT: H  207 ASP cc_start: 0.8752 (m-30) cc_final: 0.8331 (m-30)
REVERT: L   55 ARG cc_start: 0.8740 (mtm-85) cc_final: 0.8375 (ttm-80)
REVERT: L  106 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7626 (tm-30)
REVERT: L  144 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7835 (tm-30)
  outliers start: 9
  outliers final: 6
  residues processed: 76
  average time/residue: 0.1139
  time to fit residues: 11.0433
Evaluate side-chains
  71 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  931 ILE
Chi-restraints excluded: chain S residue  994 GLN
Chi-restraints excluded: chain S residue 1050 MET
Chi-restraints excluded: chain S residue 1055 SER
Chi-restraints excluded: chain H residue  111 SER
Chi-restraints excluded: chain L residue  159 ASN
Chi-restraints excluded: chain L residue  192 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 78 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
S1010 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.064447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.048529 restraints weight = 21805.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.2814 rms_B_bonded: 4.35
r_work: 0.2655 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.3666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6481  Z= 0.207
  Angle     :  0.625   8.482   8833  Z= 0.321
  Chirality :  0.043   0.190   1041
  Planarity :  0.004   0.063   1117
  Dihedral  :  4.072  20.945   1013
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 15.95 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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 aren not related in a simple way.
  whole:  0.46 (0.31), residues: 802
  helix:  2.08 (0.39), residues: 187
  sheet:  0.54 (0.33), residues: 251
  loop : -0.80 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H   5 
 TYR   0.015   0.001   TYR H 144 
 PHE   0.015   0.001   PHE H 145 
 TRP   0.009   0.001   TRP H 102 
 HIS   0.004   0.001   HIS L 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 6466)
  covalent geometry    : angle       0.62036 ( 8796)
  SS BOND              : bond        0.00187 (    8)
  SS BOND              : angle       0.59684 (   16)
  hydrogen bonds       : bond        0.03429 (  270)
  hydrogen bonds       : angle       4.63645 (  807)
  link_BETA1-4         : bond        0.00170 (    1)
  link_BETA1-4         : angle       1.06657 (    3)
  link_NAG-ASN         : bond        0.00139 (    6)
  link_NAG-ASN         : angle       1.74964 (   18)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S  869 MET cc_start: 0.9260 (mtt) cc_final: 0.8975 (mpp)
REVERT: S  994 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8935 (tp40)
REVERT: H   32 TYR cc_start: 0.8986 (m-10) cc_final: 0.8769 (m-10)
REVERT: H   46 GLU cc_start: 0.9064 (tt0) cc_final: 0.8541 (tt0)
REVERT: H  104 GLN cc_start: 0.8715 (pm20) cc_final: 0.8491 (pm20)
REVERT: H  191 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8185 (tm-30)
REVERT: H  205 LYS cc_start: 0.9138 (mptt) cc_final: 0.8926 (mmtt)
REVERT: H  207 ASP cc_start: 0.8741 (m-30) cc_final: 0.8307 (m-30)
REVERT: L   80 GLU cc_start: 0.8372 (pm20) cc_final: 0.7865 (pm20)
REVERT: L  106 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7498 (tm-30)
REVERT: L  144 GLU cc_start: 0.8445 (tm-30) cc_final: 0.7882 (tm-30)
  outliers start: 10
  outliers final: 7
  residues processed: 71
  average time/residue: 0.1064
  time to fit residues: 9.8181
Evaluate side-chains
  69 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  931 ILE
Chi-restraints excluded: chain S residue  994 GLN
Chi-restraints excluded: chain S residue 1050 MET
Chi-restraints excluded: chain S residue 1055 SER
Chi-restraints excluded: chain H residue  111 SER
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  159 ASN
Chi-restraints excluded: chain L residue  192 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 72 optimal weight:    0.4980
   chunk 17 optimal weight:    0.5980
   chunk 4 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.3222 r_free = 0.3222 target = 0.064861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.048974 restraints weight = 21983.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.2825 rms_B_bonded: 4.37
r_work: 0.2668 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.2668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.3711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6481  Z= 0.155
  Angle     :  0.599   8.135   8833  Z= 0.307
  Chirality :  0.042   0.184   1041
  Planarity :  0.004   0.062   1117
  Dihedral  :  4.082  20.750   1013
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 16.52 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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 aren not related in a simple way.
  whole:  0.58 (0.31), residues: 802
  helix:  2.22 (0.39), residues: 188
  sheet:  0.62 (0.33), residues: 258
  loop : -0.80 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 143 
 TYR   0.016   0.001   TYR H 144 
 PHE   0.015   0.001   PHE H 145 
 TRP   0.008   0.001   TRP H 102 
 HIS   0.002   0.001   HIS S1048 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 6466)
  covalent geometry    : angle       0.59395 ( 8796)
  SS BOND              : bond        0.00282 (    8)
  SS BOND              : angle       0.60005 (   16)
  hydrogen bonds       : bond        0.03215 (  270)
  hydrogen bonds       : angle       4.51399 (  807)
  link_BETA1-4         : bond        0.00324 (    1)
  link_BETA1-4         : angle       1.02536 (    3)
  link_NAG-ASN         : bond        0.00177 (    6)
  link_NAG-ASN         : angle       1.71580 (   18)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S  869 MET cc_start: 0.9245 (mtt) cc_final: 0.8952 (mpp)
REVERT: S  994 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.8734 (tm-30)
REVERT: H   46 GLU cc_start: 0.9013 (tt0) cc_final: 0.8491 (tt0)
REVERT: H  104 GLN cc_start: 0.8736 (pm20) cc_final: 0.8496 (pm20)
REVERT: H  191 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8086 (tm-30)
REVERT: H  205 LYS cc_start: 0.9157 (mptt) cc_final: 0.8926 (mmtt)
REVERT: H  207 ASP cc_start: 0.8694 (m-30) cc_final: 0.8264 (m-30)
REVERT: H  209 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.7750 (tpt90)
REVERT: L  106 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7465 (tm-30)
REVERT: L  144 GLU cc_start: 0.8440 (tm-30) cc_final: 0.7896 (tm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 70
  average time/residue: 0.1091
  time to fit residues: 9.7604
Evaluate side-chains
  69 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  931 ILE
Chi-restraints excluded: chain S residue  994 GLN
Chi-restraints excluded: chain S residue 1050 MET
Chi-restraints excluded: chain S residue 1055 SER
Chi-restraints excluded: chain H residue  111 SER
Chi-restraints excluded: chain L residue  159 ASN
Chi-restraints excluded: chain L residue  192 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 79 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
S1101 HIS
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.062584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.046541 restraints weight = 22126.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.2755 rms_B_bonded: 4.35
r_work: 0.2596 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.2596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.3948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.071   6481  Z= 0.289
  Angle     :  0.698   9.299   8833  Z= 0.357
  Chirality :  0.044   0.198   1041
  Planarity :  0.005   0.069   1117
  Dihedral  :  4.527  21.004   1013
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 16.81 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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 aren not related in a simple way.
  whole:  0.41 (0.31), residues: 802
  helix:  1.97 (0.39), residues: 194
  sheet:  0.39 (0.31), residues: 273
  loop : -0.81 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L 143 
 TYR   0.022   0.002   TYR H 144 
 PHE   0.019   0.002   PHE H 145 
 TRP   0.010   0.002   TRP H  47 
 HIS   0.006   0.001   HIS L 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00651 ( 6466)
  covalent geometry    : angle       0.69303 ( 8796)
  SS BOND              : bond        0.00247 (    8)
  SS BOND              : angle       0.70164 (   16)
  hydrogen bonds       : bond        0.03892 (  270)
  hydrogen bonds       : angle       4.83544 (  807)
  link_BETA1-4         : bond        0.00037 (    1)
  link_BETA1-4         : angle       1.32483 (    3)
  link_NAG-ASN         : bond        0.00202 (    6)
  link_NAG-ASN         : angle       1.85449 (   18)

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: S  869 MET cc_start: 0.9262 (mtt) cc_final: 0.8957 (mpp)
REVERT: S  994 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8952 (tp40)
REVERT: H   46 GLU cc_start: 0.9064 (tt0) cc_final: 0.8524 (tt0)
REVERT: H  104 GLN cc_start: 0.8824 (pm20) cc_final: 0.8613 (pm20)
REVERT: H  191 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8067 (tm-30)
REVERT: H  205 LYS cc_start: 0.9122 (mptt) cc_final: 0.8906 (mmtt)
REVERT: H  207 ASP cc_start: 0.8713 (m-30) cc_final: 0.8304 (m-30)
REVERT: H  209 ARG cc_start: 0.8273 (mmm-85) cc_final: 0.7834 (tpt90)
REVERT: L   92 TYR cc_start: 0.9324 (p90) cc_final: 0.9068 (p90)
REVERT: L  106 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7518 (tm-30)
REVERT: L  144 GLU cc_start: 0.8471 (tm-30) cc_final: 0.7930 (tm-30)
  outliers start: 8
  outliers final: 7
  residues processed: 68
  average time/residue: 0.1000
  time to fit residues: 8.8353
Evaluate side-chains
  67 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  931 ILE
Chi-restraints excluded: chain S residue  994 GLN
Chi-restraints excluded: chain S residue 1050 MET
Chi-restraints excluded: chain S residue 1055 SER
Chi-restraints excluded: chain H residue  111 SER
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  159 ASN
Chi-restraints excluded: chain L residue  192 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   chunk 65 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 71 optimal weight:    6.9990
   chunk 47 optimal weight:    0.0870
   chunk 64 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.7560

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

Flipped N/Q/H residues before XYZ refinement:
S 992 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.064734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.048897 restraints weight = 21707.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.2821 rms_B_bonded: 4.34
r_work: 0.2666 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.3901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6481  Z= 0.135
  Angle     :  0.625   9.082   8833  Z= 0.321
  Chirality :  0.043   0.184   1041
  Planarity :  0.005   0.118   1117
  Dihedral  :  4.253  21.060   1013
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 16.81 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    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 aren not related in a simple way.
  whole:  0.61 (0.31), residues: 802
  helix:  2.24 (0.39), residues: 190
  sheet:  0.61 (0.33), residues: 249
  loop : -0.74 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H   5 
 TYR   0.029   0.002   TYR H 175 
 PHE   0.010   0.001   PHE L  72 
 TRP   0.008   0.001   TRP H 102 
 HIS   0.003   0.001   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6466)
  covalent geometry    : angle       0.61968 ( 8796)
  SS BOND              : bond        0.00173 (    8)
  SS BOND              : angle       0.64303 (   16)
  hydrogen bonds       : bond        0.03279 (  270)
  hydrogen bonds       : angle       4.55560 (  807)
  link_BETA1-4         : bond        0.00457 (    1)
  link_BETA1-4         : angle       1.08680 (    3)
  link_NAG-ASN         : bond        0.00208 (    6)
  link_NAG-ASN         : angle       1.78000 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1671.30 seconds
wall clock time: 29 minutes 24.45 seconds (1764.45 seconds total)