Starting phenix.real_space_refine
on Sun Apr  5 02:43:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw3_54297/04_2026/9rw3_54297.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw3_54297/04_2026/9rw3_54297.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rw3_54297/04_2026/9rw3_54297.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw3_54297/04_2026/9rw3_54297.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rw3_54297/04_2026/9rw3_54297.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw3_54297/04_2026/9rw3_54297.map"
  }
  resolution = 3.2
  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: 5
    Type Number    sf(0)   Gaussians
     P      84      5.49       5
     S      30      5.16       5
     C    4407      2.51       5
     N    1303      2.21       5
     O    1671      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  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: 7495
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 389
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 389
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 40
    Chain: "B"
      Number of atoms: 389
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 389
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 40
    Chain: "D"
      Number of atoms: 3654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 3654
          Classifications: {'peptide': 454}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 443}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      Number of atoms: 1255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1255
          Classifications: {'peptide': 157}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 152}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    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: 1.77, per 1000 atoms: 0.24
  Number of scatterers: 7495
  At special positions: 0
  Unit cell: (82.68, 96.46, 156.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P      84     15.00
     O    1671      8.00
     N    1303      7.00
     C    4407      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: 1.11
  Conformation dependent library (CDL) restraints added in 239.6 milliseconds
  

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1366

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 4 sheets defined
      72.2% alpha, 4.9% beta
      34 base pairs and 44 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 695 through 747
      removed outlier: 3.927A  pdb=" N   VAL A 699 " --> pdb=" O   CYS A 695 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ARG A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 747
      removed outlier: 3.613A  pdb=" N   ARG B 747 " --> pdb=" O   ASP B 743 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 25
      removed outlier: 4.010A  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 112
      removed outlier: 3.769A  pdb=" N   TYR D 111 " --> pdb=" O   LYS D 107 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   GLY D 112 " --> pdb=" O   MET D 108 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 125
      removed outlier: 3.699A  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: 4.019A  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 618 through 630
    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: 4.033A  pdb=" N   GLN D 680 " --> pdb=" O   PRO D 676 " (cutoff:3.500A)
      removed outlier: 3.581A  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 743
    Processing helix  chain 'D' and resid 746 through 773
      removed outlier: 3.500A  pdb=" N   THR D 773 " --> pdb=" O   LYS D 769 " (cutoff:3.500A)
    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 801
    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: 3.811A  pdb=" N   GLU C  99 " --> pdb=" O   ASP C  95 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   TYR C 111 " --> pdb=" O   LYS C 107 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   GLY C 112 " --> pdb=" O   MET C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 125
      removed outlier: 3.719A  pdb=" N   HIS C 125 " --> pdb=" O   SER C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 126 through 129
    Processing helix  chain 'C' and resid 130 through 137
    Processing helix  chain 'C' and resid 140 through 152
    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: 5.439A  pdb=" N   ILE D 573 " --> pdb=" O   ILE D 565 " (cutoff:3.500A)
      removed outlier: 6.194A  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: 6.677A  pdb=" N   ILE D 556 " --> pdb=" O   ILE D 612 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   VAL D 614 " --> pdb=" O   ILE D 556 " (cutoff:3.500A)
      removed outlier: 6.958A  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

    376 hydrogen bonds defined for protein.
    1089 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      82 hydrogen bonds
      156 hydrogen bond angles
      0 basepair planarities
      34 basepair parallelities
      44 stacking parallelities
  Total time for adding SS restraints: 1.22

  Time building geometry restraints manager: 1.34 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1082
        1.31 -     1.43: 2448
        1.43 -     1.56: 4036
        1.56 -     1.69: 166
        1.69 -     1.81: 51
  Bond restraints: 7783
  Sorted by residual:
  bond pdb=" CA  MET C  46 "
       pdb=" C   MET C  46 "
    ideal  model  delta    sigma   weight residual
    1.524  1.453  0.070 1.29e-02 6.01e+03 2.97e+01
  bond pdb=" N   ILE D 578 "
       pdb=" CA  ILE D 578 "
    ideal  model  delta    sigma   weight residual
    1.459  1.398  0.062 1.29e-02 6.01e+03 2.28e+01
  bond pdb=" C   ILE D 578 "
       pdb=" O   ILE D 578 "
    ideal  model  delta    sigma   weight residual
    1.234  1.180  0.054 1.16e-02 7.43e+03 2.19e+01
  bond pdb=" C   MET C  46 "
       pdb=" O   MET C  46 "
    ideal  model  delta    sigma   weight residual
    1.237  1.181  0.056 1.19e-02 7.06e+03 2.18e+01
  bond pdb=" C   GLU C 143 "
       pdb=" O   GLU C 143 "
    ideal  model  delta    sigma   weight residual
    1.237  1.197  0.040 1.19e-02 7.06e+03 1.11e+01
  ... (remaining 7778 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 10225
        1.35 -     2.69: 561
        2.69 -     4.04: 84
        4.04 -     5.38: 11
        5.38 -     6.73: 2
  Bond angle restraints: 10883
  Sorted by residual:
  angle pdb=" N   ILE D 578 "
        pdb=" CA  ILE D 578 "
        pdb=" C   ILE D 578 "
      ideal   model   delta    sigma   weight residual
     108.06  102.93    5.13 1.28e+00 6.10e-01 1.61e+01
  angle pdb=" N   ILE D 578 "
        pdb=" CA  ILE D 578 "
        pdb=" CB  ILE D 578 "
      ideal   model   delta    sigma   weight residual
     111.19  116.57   -5.38 1.35e+00 5.49e-01 1.59e+01
  angle pdb=" CA  ILE D 578 "
        pdb=" C   ILE D 578 "
        pdb=" O   ILE D 578 "
      ideal   model   delta    sigma   weight residual
     120.96  117.32    3.64 9.40e-01 1.13e+00 1.50e+01
  angle pdb=" CA  ILE D 578 "
        pdb=" C   ILE D 578 "
        pdb=" N   GLY D 579 "
      ideal   model   delta    sigma   weight residual
     115.80  120.46   -4.66 1.33e+00 5.65e-01 1.23e+01
  angle pdb=" C   MET C  46 "
        pdb=" CA  MET C  46 "
        pdb=" CB  MET C  46 "
      ideal   model   delta    sigma   weight residual
     110.85  105.12    5.73 1.70e+00 3.46e-01 1.14e+01
  ... (remaining 10878 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.70: 4284
       23.70 -    47.40: 428
       47.40 -    71.10: 128
       71.10 -    94.80: 22
       94.80 -   118.50: 5
  Dihedral angle restraints: 4867
    sinusoidal: 2764
      harmonic: 2103
  Sorted by residual:
  dihedral pdb=" CA  ALA C  79 "
           pdb=" C   ALA C  79 "
           pdb=" N   TYR C  80 "
           pdb=" CA  TYR C  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.90  -24.10     0      5.00e+00 4.00e-02 2.32e+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   -2.57   22.57     1      8.00e+00 1.56e-02 1.15e+01
  dihedral pdb=" CA  ASN C  78 "
           pdb=" C   ASN C  78 "
           pdb=" N   ALA C  79 "
           pdb=" CA  ALA C  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.16   16.84     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 4864 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 996
       0.041 -    0.082: 234
       0.082 -    0.123: 61
       0.123 -    0.164: 8
       0.164 -    0.205: 2
  Chirality restraints: 1301
  Sorted by residual:
  chirality pdb=" CB  ILE D 578 "
            pdb=" CA  ILE D 578 "
            pdb=" CG1 ILE D 578 "
            pdb=" CG2 ILE D 578 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" C3'   G F  26 "
            pdb=" C4'   G F  26 "
            pdb=" O3'   G F  26 "
            pdb=" C2'   G F  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.66    0.18 2.00e-01 2.50e+01 8.20e-01
  chirality pdb=" C3'   C F  27 "
            pdb=" C4'   C F  27 "
            pdb=" O3'   C F  27 "
            pdb=" C2'   C F  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.64    0.16 2.00e-01 2.50e+01 6.23e-01
  ... (remaining 1298 not shown)

  Planarity restraints: 1088
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C F  16 "    0.072 2.00e-02 2.50e+03   3.61e-02 2.93e+01
        pdb=" N1    C F  16 "   -0.023 2.00e-02 2.50e+03
        pdb=" C2    C F  16 "   -0.012 2.00e-02 2.50e+03
        pdb=" O2    C F  16 "   -0.024 2.00e-02 2.50e+03
        pdb=" N3    C F  16 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    C F  16 "   -0.019 2.00e-02 2.50e+03
        pdb=" N4    C F  16 "    0.060 2.00e-02 2.50e+03
        pdb=" C5    C F  16 "   -0.025 2.00e-02 2.50e+03
        pdb=" C6    C F  16 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G F  34 "   -0.073 2.00e-02 2.50e+03   2.94e-02 2.59e+01
        pdb=" N9    G F  34 "    0.030 2.00e-02 2.50e+03
        pdb=" C8    G F  34 "    0.033 2.00e-02 2.50e+03
        pdb=" N7    G F  34 "    0.021 2.00e-02 2.50e+03
        pdb=" C5    G F  34 "    0.005 2.00e-02 2.50e+03
        pdb=" C6    G F  34 "   -0.015 2.00e-02 2.50e+03
        pdb=" O6    G F  34 "   -0.032 2.00e-02 2.50e+03
        pdb=" N1    G F  34 "   -0.015 2.00e-02 2.50e+03
        pdb=" C2    G F  34 "   -0.003 2.00e-02 2.50e+03
        pdb=" N2    G F  34 "    0.029 2.00e-02 2.50e+03
        pdb=" N3    G F  34 "    0.011 2.00e-02 2.50e+03
        pdb=" C4    G F  34 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U F   6 "   -0.064 2.00e-02 2.50e+03   2.99e-02 2.01e+01
        pdb=" N1    U F   6 "    0.026 2.00e-02 2.50e+03
        pdb=" C2    U F   6 "    0.007 2.00e-02 2.50e+03
        pdb=" O2    U F   6 "    0.029 2.00e-02 2.50e+03
        pdb=" N3    U F   6 "   -0.008 2.00e-02 2.50e+03
        pdb=" C4    U F   6 "   -0.009 2.00e-02 2.50e+03
        pdb=" O4    U F   6 "   -0.029 2.00e-02 2.50e+03
        pdb=" C5    U F   6 "    0.016 2.00e-02 2.50e+03
        pdb=" C6    U F   6 "    0.034 2.00e-02 2.50e+03
  ... (remaining 1085 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 193
        2.67 -     3.22: 7439
        3.22 -     3.78: 12846
        3.78 -     4.34: 16537
        4.34 -     4.90: 25832
  Nonbonded interactions: 62847
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP D 589 "
            pdb=" OG  SER D 592 "
     model   vdw
     2.107 3.040
  nonbonded pdb=" O   MET D 149 "
            pdb=" OG1 THR D 152 "
     model   vdw
     2.125 3.040
  nonbonded pdb=" OD1 ASN D 620 "
            pdb=" O2'   U E  39 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" OG1 THR C  43 "
            pdb=" OE1 GLU C  45 "
     model   vdw
     2.150 3.040
  nonbonded pdb=" OG1 THR D 793 "
            pdb=" OD1 ASP D 795 "
     model   vdw
     2.211 3.040
  ... (remaining 62842 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 '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 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:             1.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.220
  Find NCS groups from input model:        0.050
  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:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
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      :  0.004   0.070   7783  Z= 0.237
  Angle     :  0.667   6.729  10883  Z= 0.371
  Chirality :  0.039   0.205   1301
  Planarity :  0.005   0.056   1088
  Dihedral  : 19.449 118.500   3501
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  : 17.53 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  2.12 (0.33), residues: 703
  helix:  2.30 (0.24), residues: 461
  sheet: -1.86 (1.04), residues: 27
  loop : -0.10 (0.44), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 785 
 TYR   0.014   0.001   TYR C  80 
 PHE   0.010   0.001   PHE D 147 
 TRP   0.002   0.001   TRP D 692 
 HIS   0.005   0.001   HIS D 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 7783)
  covalent geometry    : angle       0.66745 (10883)
  hydrogen bonds       : bond        0.10425 (  458)
  hydrogen bonds       : angle       5.17395 ( 1245)

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

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

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 113
  average time/residue: 0.1066
  time to fit residues: 15.5796
Evaluate side-chains
  104 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  578 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 708 GLN
D 151 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.150795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.111449 restraints weight = 13094.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 2.47
r_work: 0.3271 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.1476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7783  Z= 0.226
  Angle     :  0.590   8.376  10883  Z= 0.305
  Chirality :  0.038   0.148   1301
  Planarity :  0.004   0.058   1088
  Dihedral  : 18.743 107.817   2094
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 17.03 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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 (0.32), residues: 703
  helix:  2.09 (0.24), residues: 472
  sheet: -1.97 (0.99), residues: 27
  loop : -0.12 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 785 
 TYR   0.017   0.002   TYR C  80 
 PHE   0.017   0.003   PHE D 147 
 TRP   0.004   0.001   TRP D 692 
 HIS   0.007   0.002   HIS D 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 7783)
  covalent geometry    : angle       0.59043 (10883)
  hydrogen bonds       : bond        0.04995 (  458)
  hydrogen bonds       : angle       4.48363 ( 1245)

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

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

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  735 GLN cc_start: 0.7797 (mp10) cc_final: 0.7562 (mp10)
REVERT: D  538 GLN cc_start: 0.8199 (pm20) cc_final: 0.7948 (pm20)
REVERT: D  596 MET cc_start: 0.6851 (ptm) cc_final: 0.6519 (ptp)
REVERT: C   80 TYR cc_start: 0.9128 (OUTLIER) cc_final: 0.8573 (m-80)
REVERT: C  105 LYS cc_start: 0.7938 (ptmt) cc_final: 0.7573 (pptt)
  outliers start: 17
  outliers final: 12
  residues processed: 120
  average time/residue: 0.1073
  time to fit residues: 16.5909
Evaluate side-chains
  117 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  162 VAL
Chi-restraints excluded: chain D residue  562 CYS
Chi-restraints excluded: chain D residue  578 ILE
Chi-restraints excluded: chain D residue  603 LYS
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  667 CYS
Chi-restraints excluded: chain C residue    4 MET
Chi-restraints excluded: chain C residue   80 TYR
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  152 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 77 optimal weight:    8.9990
   chunk 13 optimal weight:    0.6980
   chunk 41 optimal weight:    7.9990
   chunk 50 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
D 714 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.152107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.113270 restraints weight = 12869.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 2.37
r_work: 0.3306 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7783  Z= 0.157
  Angle     :  0.527   7.471  10883  Z= 0.268
  Chirality :  0.034   0.142   1301
  Planarity :  0.004   0.057   1088
  Dihedral  : 18.693 107.599   2094
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 15.36 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  2.07 (0.32), residues: 703
  helix:  2.21 (0.24), residues: 471
  sheet: -2.02 (0.98), residues: 27
  loop : -0.06 (0.44), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 785 
 TYR   0.014   0.001   TYR C  80 
 PHE   0.014   0.002   PHE D 147 
 TRP   0.003   0.001   TRP D 522 
 HIS   0.006   0.001   HIS D 643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7783)
  covalent geometry    : angle       0.52696 (10883)
  hydrogen bonds       : bond        0.04346 (  458)
  hydrogen bonds       : angle       4.25421 ( 1245)

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

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

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 110
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  735 GLN cc_start: 0.7865 (mp10) cc_final: 0.7537 (mp10)
REVERT: D  538 GLN cc_start: 0.8194 (pm20) cc_final: 0.7972 (mp10)
REVERT: D  674 CYS cc_start: 0.6253 (t) cc_final: 0.5363 (p)
REVERT: D  786 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7587 (mp)
REVERT: C   73 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7817 (t0)
REVERT: C   80 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.8636 (m-80)
  outliers start: 30
  outliers final: 15
  residues processed: 128
  average time/residue: 0.0918
  time to fit residues: 15.2855
Evaluate side-chains
  123 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  162 VAL
Chi-restraints excluded: chain D residue  549 TYR
Chi-restraints excluded: chain D residue  562 CYS
Chi-restraints excluded: chain D residue  603 LYS
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  702 MET
Chi-restraints excluded: chain D residue  736 LEU
Chi-restraints excluded: chain D residue  780 SER
Chi-restraints excluded: chain D residue  786 LEU
Chi-restraints excluded: chain C residue    4 MET
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   80 TYR
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  157 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 48 optimal weight:    8.9990
   chunk 12 optimal weight:    0.8980
   chunk 34 optimal weight:    6.9990
   chunk 18 optimal weight:    0.0010
   chunk 69 optimal weight:    9.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.6386

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

Flipped N/Q/H residues before XYZ refinement:
** C 125 HIS ** 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 = 0.4226 r_free = 0.4226 target = 0.154301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.115773 restraints weight = 13155.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 2.35
r_work: 0.3352 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7783  Z= 0.117
  Angle     :  0.509   8.607  10883  Z= 0.256
  Chirality :  0.033   0.171   1301
  Planarity :  0.004   0.057   1088
  Dihedral  : 18.602 107.277   2092
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 17.53 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  2.30 (0.32), residues: 703
  helix:  2.37 (0.24), residues: 472
  sheet: -2.05 (0.95), residues: 26
  loop :  0.04 (0.44), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 785 
 TYR   0.013   0.001   TYR D 161 
 PHE   0.012   0.002   PHE D 718 
 TRP   0.004   0.001   TRP D 522 
 HIS   0.005   0.001   HIS D 643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 7783)
  covalent geometry    : angle       0.50946 (10883)
  hydrogen bonds       : bond        0.03916 (  458)
  hydrogen bonds       : angle       4.09679 ( 1245)

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

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

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  730 LYS cc_start: 0.8947 (tmtt) cc_final: 0.8512 (tttm)
REVERT: B  735 GLN cc_start: 0.7901 (mp10) cc_final: 0.7392 (mp10)
REVERT: D  538 GLN cc_start: 0.8187 (pm20) cc_final: 0.7976 (mp10)
REVERT: D  588 PHE cc_start: 0.7612 (m-10) cc_final: 0.7379 (m-80)
REVERT: D  596 MET cc_start: 0.6751 (ptm) cc_final: 0.6410 (ptp)
REVERT: D  674 CYS cc_start: 0.5899 (t) cc_final: 0.5072 (p)
REVERT: C   24 LYS cc_start: 0.7471 (tttt) cc_final: 0.7174 (tttt)
REVERT: C   80 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.8534 (m-80)
  outliers start: 17
  outliers final: 12
  residues processed: 118
  average time/residue: 0.1045
  time to fit residues: 15.9860
Evaluate side-chains
  117 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  738 GLU
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  549 TYR
Chi-restraints excluded: chain D residue  702 MET
Chi-restraints excluded: chain D residue  736 LEU
Chi-restraints excluded: chain D residue  780 SER
Chi-restraints excluded: chain C residue    4 MET
Chi-restraints excluded: chain C residue   80 TYR
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  108 MET
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  152 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:   10.0000
   chunk 42 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** C 125 HIS ** 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 = 0.4204 r_free = 0.4204 target = 0.152685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.114138 restraints weight = 13201.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3658 rms_B_bonded: 2.40
r_work: 0.3315 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7783  Z= 0.149
  Angle     :  0.534  10.558  10883  Z= 0.266
  Chirality :  0.034   0.143   1301
  Planarity :  0.004   0.052   1088
  Dihedral  : 18.546 106.794   2092
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 17.86 %
    Favored  : 78.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  2.19 (0.32), residues: 703
  helix:  2.30 (0.24), residues: 472
  sheet: -2.14 (0.98), residues: 27
  loop : -0.01 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 736 
 TYR   0.022   0.001   TYR D 704 
 PHE   0.014   0.002   PHE D 147 
 TRP   0.002   0.001   TRP D 692 
 HIS   0.005   0.001   HIS D 643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 7783)
  covalent geometry    : angle       0.53354 (10883)
  hydrogen bonds       : bond        0.04120 (  458)
  hydrogen bonds       : angle       4.12328 ( 1245)

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

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

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  736 ARG cc_start: 0.8377 (ttp80) cc_final: 0.8060 (ttm-80)
REVERT: B  730 LYS cc_start: 0.9003 (tmtt) cc_final: 0.8558 (tttm)
REVERT: B  735 GLN cc_start: 0.7927 (mp10) cc_final: 0.7457 (mp10)
REVERT: D  538 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7857 (pm20)
REVERT: D  588 PHE cc_start: 0.7454 (m-10) cc_final: 0.7242 (m-80)
REVERT: D  596 MET cc_start: 0.6581 (ptm) cc_final: 0.6159 (ptp)
REVERT: D  701 MET cc_start: 0.6298 (ptp) cc_final: 0.5998 (ptp)
REVERT: D  786 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7625 (mp)
REVERT: C   24 LYS cc_start: 0.7528 (tttt) cc_final: 0.7220 (tttt)
REVERT: C   80 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.8581 (m-80)
REVERT: C  134 ARG cc_start: 0.7850 (mtt90) cc_final: 0.7571 (mtt90)
  outliers start: 23
  outliers final: 15
  residues processed: 123
  average time/residue: 0.1007
  time to fit residues: 16.2721
Evaluate side-chains
  122 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  162 VAL
Chi-restraints excluded: chain D residue  538 GLN
Chi-restraints excluded: chain D residue  549 TYR
Chi-restraints excluded: chain D residue  562 CYS
Chi-restraints excluded: chain D residue  632 LEU
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  702 MET
Chi-restraints excluded: chain D residue  736 LEU
Chi-restraints excluded: chain D residue  780 SER
Chi-restraints excluded: chain D residue  786 LEU
Chi-restraints excluded: chain C residue    4 MET
Chi-restraints excluded: chain C residue   80 TYR
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  108 MET
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  152 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 53 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0060
   chunk 72 optimal weight:    6.9990
   chunk 19 optimal weight:    0.5980
   chunk 54 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
C 125 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.154592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.116654 restraints weight = 13268.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 2.39
r_work: 0.3357 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7783  Z= 0.112
  Angle     :  0.518  11.402  10883  Z= 0.256
  Chirality :  0.033   0.155   1301
  Planarity :  0.004   0.048   1088
  Dihedral  : 18.462 105.069   2092
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 18.36 %
    Favored  : 78.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  2.35 (0.33), residues: 703
  helix:  2.40 (0.24), residues: 472
  sheet: -1.70 (1.03), residues: 26
  loop :  0.06 (0.44), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 736 
 TYR   0.021   0.001   TYR D 704 
 PHE   0.011   0.001   PHE D 147 
 TRP   0.003   0.001   TRP D 522 
 HIS   0.004   0.001   HIS D 643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 7783)
  covalent geometry    : angle       0.51783 (10883)
  hydrogen bonds       : bond        0.03733 (  458)
  hydrogen bonds       : angle       4.02959 ( 1245)

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

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

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  736 ARG cc_start: 0.8374 (ttp80) cc_final: 0.8065 (ttm-80)
REVERT: B  730 LYS cc_start: 0.8952 (tmtt) cc_final: 0.8541 (tttm)
REVERT: D  538 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7922 (mp10)
REVERT: D  577 GLU cc_start: 0.7467 (pt0) cc_final: 0.7036 (pt0)
REVERT: D  596 MET cc_start: 0.6461 (ptm) cc_final: 0.6052 (ptp)
REVERT: D  680 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7917 (tm-30)
REVERT: D  701 MET cc_start: 0.6250 (ptp) cc_final: 0.5993 (ptp)
REVERT: D  786 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7599 (mp)
REVERT: C   73 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7773 (t0)
REVERT: C   80 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.8497 (m-80)
REVERT: C  134 ARG cc_start: 0.7840 (mtt90) cc_final: 0.7564 (mtt90)
  outliers start: 20
  outliers final: 14
  residues processed: 117
  average time/residue: 0.0972
  time to fit residues: 14.8867
Evaluate side-chains
  119 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  162 VAL
Chi-restraints excluded: chain D residue  538 GLN
Chi-restraints excluded: chain D residue  549 TYR
Chi-restraints excluded: chain D residue  562 CYS
Chi-restraints excluded: chain D residue  632 LEU
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  702 MET
Chi-restraints excluded: chain D residue  736 LEU
Chi-restraints excluded: chain D residue  780 SER
Chi-restraints excluded: chain D residue  786 LEU
Chi-restraints excluded: chain C residue    4 MET
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   80 TYR
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  152 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 58 optimal weight:    0.8980
   chunk 38 optimal weight:    7.9990
   chunk 28 optimal weight:    5.9990
   chunk 76 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0970
   chunk 45 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
C  98 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.152865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.112709 restraints weight = 13149.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 2.33
r_work: 0.3304 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7783  Z= 0.137
  Angle     :  0.535  11.414  10883  Z= 0.266
  Chirality :  0.034   0.175   1301
  Planarity :  0.004   0.050   1088
  Dihedral  : 18.424 104.921   2092
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 18.53 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  2.24 (0.33), residues: 703
  helix:  2.30 (0.24), residues: 472
  sheet: -1.58 (1.03), residues: 26
  loop :  0.02 (0.45), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 120 
 TYR   0.015   0.001   TYR D 704 
 PHE   0.013   0.002   PHE D 147 
 TRP   0.002   0.001   TRP D 522 
 HIS   0.005   0.001   HIS D 643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7783)
  covalent geometry    : angle       0.53467 (10883)
  hydrogen bonds       : bond        0.03924 (  458)
  hydrogen bonds       : angle       4.06084 ( 1245)

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

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

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 100
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  736 ARG cc_start: 0.8385 (ttp80) cc_final: 0.8078 (ttm-80)
REVERT: B  730 LYS cc_start: 0.8983 (tmtt) cc_final: 0.8539 (tttm)
REVERT: D  538 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7799 (pm20)
REVERT: D  603 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7780 (mtmm)
REVERT: D  680 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7901 (tm-30)
REVERT: D  701 MET cc_start: 0.6227 (ptp) cc_final: 0.6021 (ptp)
REVERT: D  786 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7657 (mp)
REVERT: C   73 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7765 (t0)
REVERT: C   80 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.8505 (m-80)
REVERT: C  134 ARG cc_start: 0.7848 (mtt90) cc_final: 0.7567 (mtt180)
  outliers start: 25
  outliers final: 16
  residues processed: 115
  average time/residue: 0.0928
  time to fit residues: 14.0362
Evaluate side-chains
  121 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  162 VAL
Chi-restraints excluded: chain D residue  538 GLN
Chi-restraints excluded: chain D residue  549 TYR
Chi-restraints excluded: chain D residue  562 CYS
Chi-restraints excluded: chain D residue  603 LYS
Chi-restraints excluded: chain D residue  632 LEU
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  681 LEU
Chi-restraints excluded: chain D residue  702 MET
Chi-restraints excluded: chain D residue  736 LEU
Chi-restraints excluded: chain D residue  780 SER
Chi-restraints excluded: chain D residue  786 LEU
Chi-restraints excluded: chain C residue    4 MET
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   80 TYR
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  152 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 75 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0980
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 = 0.4217 r_free = 0.4217 target = 0.153888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.113578 restraints weight = 13175.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 2.36
r_work: 0.3327 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7783  Z= 0.120
  Angle     :  0.529  10.458  10883  Z= 0.262
  Chirality :  0.033   0.184   1301
  Planarity :  0.003   0.049   1088
  Dihedral  : 18.404 103.746   2092
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 18.86 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  2.25 (0.32), residues: 703
  helix:  2.28 (0.24), residues: 474
  sheet: -1.44 (1.05), residues: 26
  loop :  0.06 (0.45), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 126 
 TYR   0.013   0.001   TYR D 161 
 PHE   0.012   0.001   PHE D 147 
 TRP   0.003   0.001   TRP D 522 
 HIS   0.004   0.001   HIS D 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 7783)
  covalent geometry    : angle       0.52937 (10883)
  hydrogen bonds       : bond        0.03752 (  458)
  hydrogen bonds       : angle       4.02124 ( 1245)

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

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

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  736 ARG cc_start: 0.8409 (ttp80) cc_final: 0.8097 (ttm-80)
REVERT: B  730 LYS cc_start: 0.8961 (tmtt) cc_final: 0.8542 (tttm)
REVERT: D  527 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7050 (pp)
REVERT: D  538 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7789 (pm20)
REVERT: D  680 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7832 (tm-30)
REVERT: D  786 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7615 (mp)
REVERT: C   73 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7782 (t0)
REVERT: C   80 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.8537 (m-80)
REVERT: C  134 ARG cc_start: 0.7850 (mtt90) cc_final: 0.7554 (mtt180)
  outliers start: 23
  outliers final: 16
  residues processed: 117
  average time/residue: 0.0975
  time to fit residues: 14.8627
Evaluate side-chains
  124 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  162 VAL
Chi-restraints excluded: chain D residue  527 LEU
Chi-restraints excluded: chain D residue  538 GLN
Chi-restraints excluded: chain D residue  549 TYR
Chi-restraints excluded: chain D residue  562 CYS
Chi-restraints excluded: chain D residue  632 LEU
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  681 LEU
Chi-restraints excluded: chain D residue  702 MET
Chi-restraints excluded: chain D residue  736 LEU
Chi-restraints excluded: chain D residue  780 SER
Chi-restraints excluded: chain D residue  786 LEU
Chi-restraints excluded: chain C residue    4 MET
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   80 TYR
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  152 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 58 optimal weight:    0.0970
   chunk 9 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 13 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 19 optimal weight:    0.3980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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 = 0.4227 r_free = 0.4227 target = 0.154677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.115341 restraints weight = 13047.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 2.39
r_work: 0.3333 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.2998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7783  Z= 0.114
  Angle     :  0.532   9.877  10883  Z= 0.263
  Chirality :  0.033   0.192   1301
  Planarity :  0.003   0.049   1088
  Dihedral  : 18.371 103.234   2092
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 19.70 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  2.26 (0.32), residues: 703
  helix:  2.28 (0.24), residues: 474
  sheet: -1.48 (1.04), residues: 26
  loop :  0.07 (0.44), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 120 
 TYR   0.010   0.001   TYR D 704 
 PHE   0.012   0.001   PHE D 147 
 TRP   0.005   0.001   TRP D 692 
 HIS   0.004   0.001   HIS D 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 7783)
  covalent geometry    : angle       0.53213 (10883)
  hydrogen bonds       : bond        0.03639 (  458)
  hydrogen bonds       : angle       3.99883 ( 1245)

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

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

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  736 ARG cc_start: 0.8355 (ttp80) cc_final: 0.8058 (ttm-80)
REVERT: B  730 LYS cc_start: 0.8953 (tmtt) cc_final: 0.8519 (tttm)
REVERT: D  527 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7091 (pp)
REVERT: D  538 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7866 (pm20)
REVERT: D  588 PHE cc_start: 0.7330 (m-10) cc_final: 0.7077 (m-80)
REVERT: D  596 MET cc_start: 0.6606 (ptm) cc_final: 0.6276 (ptp)
REVERT: D  626 TYR cc_start: 0.8013 (t80) cc_final: 0.7800 (t80)
REVERT: D  680 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7859 (tm-30)
REVERT: D  772 GLN cc_start: 0.7843 (pp30) cc_final: 0.7560 (pp30)
REVERT: D  786 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7620 (mp)
REVERT: C   73 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7814 (t0)
REVERT: C   80 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8469 (m-80)
REVERT: C  134 ARG cc_start: 0.7829 (mtt90) cc_final: 0.7523 (mtt180)
  outliers start: 22
  outliers final: 15
  residues processed: 118
  average time/residue: 0.1000
  time to fit residues: 15.5425
Evaluate side-chains
  124 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  127 SER
Chi-restraints excluded: chain D residue  162 VAL
Chi-restraints excluded: chain D residue  527 LEU
Chi-restraints excluded: chain D residue  538 GLN
Chi-restraints excluded: chain D residue  549 TYR
Chi-restraints excluded: chain D residue  562 CYS
Chi-restraints excluded: chain D residue  632 LEU
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  681 LEU
Chi-restraints excluded: chain D residue  736 LEU
Chi-restraints excluded: chain D residue  780 SER
Chi-restraints excluded: chain D residue  786 LEU
Chi-restraints excluded: chain C residue    4 MET
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   80 TYR
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  152 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   chunk 56 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4213 r_free = 0.4213 target = 0.153728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.114250 restraints weight = 12993.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 2.24
r_work: 0.3349 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.3067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7783  Z= 0.126
  Angle     :  0.537   9.707  10883  Z= 0.266
  Chirality :  0.033   0.184   1301
  Planarity :  0.004   0.049   1088
  Dihedral  : 18.352 102.687   2092
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 20.03 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  2.21 (0.32), residues: 703
  helix:  2.25 (0.24), residues: 474
  sheet: -1.53 (1.03), residues: 26
  loop :  0.05 (0.44), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 619 
 TYR   0.012   0.001   TYR C  80 
 PHE   0.013   0.001   PHE D 147 
 TRP   0.003   0.001   TRP D 692 
 HIS   0.004   0.001   HIS D 643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 7783)
  covalent geometry    : angle       0.53663 (10883)
  hydrogen bonds       : bond        0.03740 (  458)
  hydrogen bonds       : angle       4.00199 ( 1245)

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

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

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  736 ARG cc_start: 0.8340 (ttp80) cc_final: 0.8083 (ttm-80)
REVERT: B  730 LYS cc_start: 0.8954 (tmtt) cc_final: 0.8499 (tttm)
REVERT: D  527 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7125 (pp)
REVERT: D  538 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7850 (pm20)
REVERT: D  588 PHE cc_start: 0.7341 (m-10) cc_final: 0.7113 (m-80)
REVERT: D  626 TYR cc_start: 0.8019 (t80) cc_final: 0.7785 (t80)
REVERT: D  680 GLN cc_start: 0.8251 (tm-30) cc_final: 0.7830 (tm-30)
REVERT: D  772 GLN cc_start: 0.7817 (pp30) cc_final: 0.7541 (pp30)
REVERT: D  786 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7697 (mp)
REVERT: C   73 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7753 (t0)
REVERT: C   80 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.8444 (m-80)
REVERT: C   97 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7273 (mp)
REVERT: C  134 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7657 (mtt180)
REVERT: C  149 MET cc_start: 0.7027 (mmp) cc_final: 0.6241 (ptp)
  outliers start: 20
  outliers final: 14
  residues processed: 115
  average time/residue: 0.0989
  time to fit residues: 14.9471
Evaluate side-chains
  123 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  127 SER
Chi-restraints excluded: chain D residue  162 VAL
Chi-restraints excluded: chain D residue  527 LEU
Chi-restraints excluded: chain D residue  538 GLN
Chi-restraints excluded: chain D residue  549 TYR
Chi-restraints excluded: chain D residue  562 CYS
Chi-restraints excluded: chain D residue  632 LEU
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  681 LEU
Chi-restraints excluded: chain D residue  736 LEU
Chi-restraints excluded: chain D residue  780 SER
Chi-restraints excluded: chain D residue  786 LEU
Chi-restraints excluded: chain C residue    4 MET
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue   80 TYR
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  152 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 72 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 0 optimal weight:   20.0000
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.4223 r_free = 0.4223 target = 0.154564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.115368 restraints weight = 13174.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 2.28
r_work: 0.3343 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7783  Z= 0.126
  Angle     :  0.540   9.504  10883  Z= 0.268
  Chirality :  0.033   0.176   1301
  Planarity :  0.004   0.063   1088
  Dihedral  : 18.348 102.327   2092
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 19.70 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    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:  2.21 (0.32), residues: 703
  helix:  2.24 (0.24), residues: 474
  sheet: -1.49 (1.04), residues: 26
  loop :  0.05 (0.45), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 120 
 TYR   0.011   0.001   TYR C  80 
 PHE   0.012   0.001   PHE D 147 
 TRP   0.004   0.001   TRP D 692 
 HIS   0.005   0.001   HIS D 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 7783)
  covalent geometry    : angle       0.54002 (10883)
  hydrogen bonds       : bond        0.03731 (  458)
  hydrogen bonds       : angle       3.99874 ( 1245)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1879.43 seconds
wall clock time: 32 minutes 52.48 seconds (1972.48 seconds total)