Starting phenix.real_space_refine
on Thu Jul  2 07:32:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw3_54297/07_2026/9rw3_54297.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw3_54297/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rw3_54297/07_2026/9rw3_54297.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw3_54297/07_2026/9rw3_54297.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rw3_54297/07_2026/9rw3_54297.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw3_54297/07_2026/9rw3_54297.cif"
  }
  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-dev-6108/lib/python3.11/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: 1.96, per 1000 atoms: 0.26
  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: 0.70
  Conformation dependent library (CDL) restraints added in 445.6 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: 0.92
  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: 1.24

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.18 -     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=" N1    C F  29 "
       pdb=" C6    C F  29 "
    ideal  model  delta    sigma   weight residual
    1.367  1.389 -0.022 6.00e-03 2.78e+04 1.34e+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=" N6    A F   8 "
        pdb=" C6    A F   8 "
        pdb=" N1    A F   8 "
      ideal   model   delta    sigma   weight residual
     118.60  114.74    3.86 6.00e-01 2.78e+00 4.14e+01
  angle pdb=" N6    A F  30 "
        pdb=" C6    A F  30 "
        pdb=" N1    A F  30 "
      ideal   model   delta    sigma   weight residual
     118.60  114.74    3.86 6.00e-01 2.78e+00 4.14e+01
  angle pdb=" N6    A F  13 "
        pdb=" C6    A F  13 "
        pdb=" N1    A F  13 "
      ideal   model   delta    sigma   weight residual
     118.60  115.32    3.28 6.00e-01 2.78e+00 2.99e+01
  angle pdb=" N6    A F  10 "
        pdb=" C6    A F  10 "
        pdb=" N1    A F  10 "
      ideal   model   delta    sigma   weight residual
     118.60  115.35    3.25 6.00e-01 2.78e+00 2.94e+01
  angle pdb=" C2    A F  30 "
        pdb=" N3    A F  30 "
        pdb=" C4    A F  30 "
      ideal   model   delta    sigma   weight residual
     110.60  112.97   -2.37 5.00e-01 4.00e+00 2.25e+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:             0.990
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.890
  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:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
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= 0.332
  Angle     :  0.668   6.729  10883  Z= 0.617
  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/Z
  covalent geometry    : bond        0.00420 /  0.33 ( 7783)
  covalent geometry    : angle       0.66753 /  0.62 (10883)
  hydrogen bonds       : bond        0.10425 /  6.98 (  458)
  hydrogen bonds       : angle       5.17395 /  4.08 ( 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  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 113
  average time/residue: 0.0939
  time to fit residues: 13.7617
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  : 0.258 
-------------------------------------------------------------------------------
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:    8.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.4188 r_free = 0.4188 target = 0.151238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.111449 restraints weight = 13156.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 2.32
r_work: 0.3289 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.1001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   7783  Z= 0.221
  Angle     :  0.566   7.681  10883  Z= 0.317
  Chirality :  0.039   0.189   1301
  Planarity :  0.004   0.057   1088
  Dihedral  : 18.723 109.599   2094
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 16.36 %
    Favored  : 80.47 %
  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:  1.96 (0.32), residues: 703
  helix:  2.11 (0.24), residues: 473
  sheet: -1.96 (0.97), residues: 27
  loop : -0.11 (0.44), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 785 
 TYR   0.015   0.002   TYR C  80 
 PHE   0.017   0.002   PHE D 147 
 TRP   0.003   0.001   TRP D 692 
 HIS   0.012   0.002   HIS D 714 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00483 /  0.22 ( 7783)
  covalent geometry    : angle       0.56647 /  0.32 (10883)
  hydrogen bonds       : bond        0.05829 /  4.14 (  458)
  hydrogen bonds       : angle       4.63296 /  3.54 ( 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
  134 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  735 GLN cc_start: 0.7668 (mp10) cc_final: 0.7201 (mp10)
REVERT: D  538 GLN cc_start: 0.8044 (pm20) cc_final: 0.7822 (pm20)
REVERT: D  596 MET cc_start: 0.6807 (ptm) cc_final: 0.6402 (ptp)
REVERT: D  680 GLN cc_start: 0.8314 (tm-30) cc_final: 0.8106 (tm-30)
REVERT: C   80 TYR cc_start: 0.9086 (OUTLIER) cc_final: 0.8376 (m-80)
  outliers start: 19
  outliers final: 10
  residues processed: 125
  average time/residue: 0.0883
  time to fit residues: 14.3832
Evaluate side-chains
  116 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  705 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  562 CYS
Chi-restraints excluded: chain D residue  578 ILE
Chi-restraints excluded: chain D residue  666 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  137 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 28 optimal weight:    8.9990
   chunk 71 optimal weight:    6.9990
   chunk 47 optimal weight:    0.5980
   chunk 67 optimal weight:    6.9990
   chunk 77 optimal weight:   20.0000
   chunk 13 optimal weight:    0.9980
   chunk 41 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 18 optimal weight:    0.3980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 671 ASN
** D 714 HIS ** 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 = 0.4213 r_free = 0.4213 target = 0.153398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.114317 restraints weight = 12962.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 2.43
r_work: 0.3308 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.1331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7783  Z= 0.134
  Angle     :  0.505   7.267  10883  Z= 0.278
  Chirality :  0.035   0.175   1301
  Planarity :  0.004   0.059   1088
  Dihedral  : 18.726 106.813   2094
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 16.69 %
    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:  2.04 (0.32), residues: 703
  helix:  2.24 (0.24), residues: 470
  sheet: -2.17 (0.93), residues: 27
  loop : -0.19 (0.43), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 736 
 TYR   0.012   0.001   TYR C  80 
 PHE   0.013   0.002   PHE C 155 
 TRP   0.002   0.001   TRP D 692 
 HIS   0.005   0.001   HIS D 714 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.13 ( 7783)
  covalent geometry    : angle       0.50502 /  0.28 (10883)
  hydrogen bonds       : bond        0.04972 /  3.55 (  458)
  hydrogen bonds       : angle       4.34371 /  3.30 ( 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
  131 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  538 GLN cc_start: 0.8160 (pm20) cc_final: 0.7902 (pm20)
REVERT: D  634 ARG cc_start: 0.5755 (tpm170) cc_final: 0.5454 (tpm170)
REVERT: D  674 CYS cc_start: 0.6631 (t) cc_final: 0.5783 (p)
REVERT: D  680 GLN cc_start: 0.8259 (tm-30) cc_final: 0.8029 (tm-30)
REVERT: C   24 LYS cc_start: 0.7647 (tttt) cc_final: 0.7368 (tttt)
REVERT: C   80 TYR cc_start: 0.8942 (OUTLIER) cc_final: 0.8529 (m-80)
  outliers start: 19
  outliers final: 13
  residues processed: 121
  average time/residue: 0.0887
  time to fit residues: 14.3249
Evaluate side-chains
  120 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  705 LEU
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  562 CYS
Chi-restraints excluded: chain D residue  666 LEU
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  117 VAL
Chi-restraints excluded: chain C residue  137 SER
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:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 72 optimal weight:   10.0000
   chunk 14 optimal weight:    0.0070
   chunk 48 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0870
   chunk 69 optimal weight:    5.9990
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.4776

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 714 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 = 0.4224 r_free = 0.4224 target = 0.154400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.115669 restraints weight = 13131.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 2.39
r_work: 0.3347 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7783  Z= 0.114
  Angle     :  0.472   6.953  10883  Z= 0.260
  Chirality :  0.034   0.170   1301
  Planarity :  0.004   0.059   1088
  Dihedral  : 18.673 107.879   2092
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 17.36 %
    Favored  : 78.80 %
  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:  2.38 (0.24), residues: 470
  sheet: -2.10 (0.93), residues: 27
  loop : -0.16 (0.44), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 736 
 TYR   0.009   0.001   TYR C  80 
 PHE   0.012   0.002   PHE C 155 
 TRP   0.003   0.001   TRP D 522 
 HIS   0.004   0.001   HIS D 643 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00228 /  0.11 ( 7783)
  covalent geometry    : angle       0.47249 /  0.26 (10883)
  hydrogen bonds       : bond        0.04624 /  3.32 (  458)
  hydrogen bonds       : angle       4.22977 /  3.21 ( 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
  132 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  730 LYS cc_start: 0.8919 (tmtt) cc_final: 0.8479 (tttm)
REVERT: D  538 GLN cc_start: 0.8214 (pm20) cc_final: 0.8004 (mp10)
REVERT: D  588 PHE cc_start: 0.7250 (m-10) cc_final: 0.7019 (m-10)
REVERT: D  596 MET cc_start: 0.6313 (ptm) cc_final: 0.5950 (ptp)
REVERT: D  634 ARG cc_start: 0.5756 (tpm170) cc_final: 0.5463 (tpm170)
REVERT: D  674 CYS cc_start: 0.6377 (t) cc_final: 0.5454 (p)
REVERT: D  680 GLN cc_start: 0.8275 (tm-30) cc_final: 0.8049 (tm-30)
REVERT: C   24 LYS cc_start: 0.7636 (tttt) cc_final: 0.7402 (tttt)
REVERT: C   80 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8532 (m-80)
  outliers start: 23
  outliers final: 15
  residues processed: 122
  average time/residue: 0.0984
  time to fit residues: 16.1016
Evaluate side-chains
  123 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  705 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  549 TYR
Chi-restraints excluded: chain D residue  562 CYS
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 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  157 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:   20.0000
   chunk 42 optimal weight:    5.9990
   chunk 36 optimal weight:    9.9990
   chunk 34 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 62 optimal weight:    0.9980
   chunk 70 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 714 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 = 0.4217 r_free = 0.4217 target = 0.153627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.113121 restraints weight = 13169.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 2.32
r_work: 0.3325 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1769

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= 0.145
  Angle     :  0.489   6.794  10883  Z= 0.266
  Chirality :  0.035   0.166   1301
  Planarity :  0.004   0.057   1088
  Dihedral  : 18.643 108.768   2092
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  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:  2.08 (0.32), residues: 703
  helix:  2.25 (0.24), residues: 473
  sheet: -1.95 (0.95), residues: 26
  loop : -0.21 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 736 
 TYR   0.012   0.001   TYR C  80 
 PHE   0.013   0.002   PHE D 147 
 TRP   0.002   0.001   TRP D 692 
 HIS   0.005   0.001   HIS D 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.14 ( 7783)
  covalent geometry    : angle       0.48920 /  0.27 (10883)
  hydrogen bonds       : bond        0.04579 /  3.28 (  458)
  hydrogen bonds       : angle       4.21775 /  3.19 ( 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
  130 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  538 GLN cc_start: 0.8235 (pm20) cc_final: 0.7984 (mp10)
REVERT: D  596 MET cc_start: 0.6426 (ptm) cc_final: 0.6036 (ptp)
REVERT: D  680 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7991 (tm-30)
REVERT: C   80 TYR cc_start: 0.8959 (OUTLIER) cc_final: 0.8480 (m-80)
  outliers start: 23
  outliers final: 17
  residues processed: 119
  average time/residue: 0.0910
  time to fit residues: 14.6293
Evaluate side-chains
  124 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  705 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  549 TYR
Chi-restraints excluded: chain D residue  562 CYS
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 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  117 VAL
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  157 VAL
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:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 72 optimal weight:   10.0000
   chunk 19 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 714 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 = 0.4221 r_free = 0.4221 target = 0.153931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.114034 restraints weight = 13208.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 2.27
r_work: 0.3334 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.1916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7783  Z= 0.130
  Angle     :  0.487   7.449  10883  Z= 0.264
  Chirality :  0.035   0.332   1301
  Planarity :  0.004   0.057   1088
  Dihedral  : 18.644 109.020   2092
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 18.03 %
    Favored  : 78.13 %
  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:  2.10 (0.32), residues: 703
  helix:  2.26 (0.24), residues: 473
  sheet: -1.80 (1.00), residues: 26
  loop : -0.22 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 736 
 TYR   0.013   0.001   TYR D 161 
 PHE   0.013   0.002   PHE D 147 
 TRP   0.003   0.001   TRP D 522 
 HIS   0.005   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.13 ( 7783)
  covalent geometry    : angle       0.48674 /  0.26 (10883)
  hydrogen bonds       : bond        0.04445 /  3.20 (  458)
  hydrogen bonds       : angle       4.16049 /  3.16 ( 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
  132 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  730 LYS cc_start: 0.8952 (tmtt) cc_final: 0.8525 (tttm)
REVERT: D  538 GLN cc_start: 0.8259 (pm20) cc_final: 0.7933 (pm20)
REVERT: D  596 MET cc_start: 0.6325 (ptm) cc_final: 0.5996 (ptp)
REVERT: D  786 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7655 (mp)
REVERT: C   24 LYS cc_start: 0.7510 (tttt) cc_final: 0.7264 (tttt)
REVERT: C   80 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.8476 (m-80)
  outliers start: 23
  outliers final: 19
  residues processed: 121
  average time/residue: 0.1023
  time to fit residues: 16.3470
Evaluate side-chains
  125 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain B residue  735 GLN
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  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  720 ASN
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  157 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 58 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 76 optimal weight:   20.0000
   chunk 61 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    1.3388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 714 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 = 0.4208 r_free = 0.4208 target = 0.152913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.112246 restraints weight = 13190.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 2.33
r_work: 0.3311 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7783  Z= 0.163
  Angle     :  0.509   8.946  10883  Z= 0.274
  Chirality :  0.036   0.257   1301
  Planarity :  0.004   0.056   1088
  Dihedral  : 18.631 109.447   2092
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 18.03 %
    Favored  : 77.63 %
  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:  2.01 (0.32), residues: 703
  helix:  2.18 (0.24), residues: 472
  sheet: -1.80 (1.04), residues: 26
  loop : -0.21 (0.44), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 619 
 TYR   0.015   0.001   TYR C  80 
 PHE   0.016   0.002   PHE D 588 
 TRP   0.003   0.001   TRP D 692 
 HIS   0.006   0.001   HIS D 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.16 ( 7783)
  covalent geometry    : angle       0.50886 /  0.27 (10883)
  hydrogen bonds       : bond        0.04598 /  3.29 (  458)
  hydrogen bonds       : angle       4.19245 /  3.19 ( 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
  133 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  730 LYS cc_start: 0.8989 (tmtt) cc_final: 0.8547 (tttm)
REVERT: D  527 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6943 (pp)
REVERT: D  538 GLN cc_start: 0.8347 (pm20) cc_final: 0.7993 (pm20)
REVERT: D  596 MET cc_start: 0.6273 (ptm) cc_final: 0.5964 (ptp)
REVERT: D  786 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7722 (mp)
REVERT: C   24 LYS cc_start: 0.7551 (tttt) cc_final: 0.7280 (tttt)
REVERT: C   80 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.8519 (m-80)
REVERT: C  103 TYR cc_start: 0.7848 (t80) cc_final: 0.7537 (t80)
  outliers start: 26
  outliers final: 18
  residues processed: 122
  average time/residue: 0.1017
  time to fit residues: 16.3817
Evaluate side-chains
  126 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain B residue  735 GLN
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  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   45 GLU
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  117 VAL
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  157 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 5 optimal weight:    0.4980
   chunk 20 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 30 optimal weight:    4.9990
   chunk 28 optimal weight:    6.9990
   chunk 42 optimal weight:    8.9990
   chunk 11 optimal weight:    0.7980
   chunk 75 optimal weight:   20.0000
   chunk 21 optimal weight:    0.0270
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.5638

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 708 GLN
** D 714 HIS ** 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 = 0.4225 r_free = 0.4225 target = 0.154341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.116415 restraints weight = 13189.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 2.38
r_work: 0.3352 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   7783  Z= 0.117
  Angle     :  0.513  11.504  10883  Z= 0.270
  Chirality :  0.035   0.316   1301
  Planarity :  0.004   0.057   1088
  Dihedral  : 18.650 108.967   2092
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 18.53 %
    Favored  : 77.63 %
  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:  2.12 (0.33), residues: 703
  helix:  2.24 (0.24), residues: 473
  sheet: -1.64 (1.05), residues: 26
  loop : -0.11 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 120 
 TYR   0.010   0.001   TYR C  80 
 PHE   0.025   0.002   PHE D 588 
 TRP   0.003   0.001   TRP D 522 
 HIS   0.004   0.001   HIS D 643 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.12 ( 7783)
  covalent geometry    : angle       0.51320 /  0.27 (10883)
  hydrogen bonds       : bond        0.04237 /  3.06 (  458)
  hydrogen bonds       : angle       4.09682 /  3.11 ( 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
  128 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  730 LYS cc_start: 0.8947 (tmtt) cc_final: 0.8526 (tttm)
REVERT: D  527 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6926 (pp)
REVERT: D  538 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8046 (pm20)
REVERT: D  596 MET cc_start: 0.6183 (ptm) cc_final: 0.5715 (ptp)
REVERT: D  674 CYS cc_start: 0.6176 (t) cc_final: 0.5229 (p)
REVERT: D  786 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7648 (mp)
REVERT: C   80 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8537 (m-80)
  outliers start: 23
  outliers final: 17
  residues processed: 118
  average time/residue: 0.1044
  time to fit residues: 16.4400
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  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  708 GLN
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain B residue  735 GLN
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  632 LEU
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  702 MET
Chi-restraints excluded: chain D residue  720 ASN
Chi-restraints excluded: chain D residue  736 LEU
Chi-restraints excluded: chain D residue  786 LEU
Chi-restraints excluded: chain C residue    4 MET
Chi-restraints excluded: chain C residue   45 GLU
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  157 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0970
   chunk 53 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 714 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 = 0.4224 r_free = 0.4224 target = 0.154295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.115927 restraints weight = 13123.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 2.43
r_work: 0.3342 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7783  Z= 0.121
  Angle     :  0.526  12.918  10883  Z= 0.274
  Chirality :  0.035   0.285   1301
  Planarity :  0.004   0.057   1088
  Dihedral  : 18.620 108.921   2092
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 19.20 %
    Favored  : 76.96 %
  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:  2.16 (0.33), residues: 703
  helix:  2.26 (0.24), residues: 473
  sheet: -1.65 (1.04), residues: 26
  loop : -0.08 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 707 
 TYR   0.014   0.001   TYR C 103 
 PHE   0.022   0.002   PHE D 588 
 TRP   0.003   0.001   TRP D 522 
 HIS   0.004   0.001   HIS D 643 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.12 ( 7783)
  covalent geometry    : angle       0.52561 /  0.27 (10883)
  hydrogen bonds       : bond        0.04239 /  3.06 (  458)
  hydrogen bonds       : angle       4.07820 /  3.10 ( 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
  126 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  708 GLN cc_start: 0.8001 (pt0) cc_final: 0.7671 (pm20)
REVERT: B  730 LYS cc_start: 0.8950 (tmtt) cc_final: 0.8546 (tttm)
REVERT: D  527 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6934 (pp)
REVERT: D  538 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7973 (pm20)
REVERT: D  596 MET cc_start: 0.6299 (ptm) cc_final: 0.5963 (ptp)
REVERT: D  674 CYS cc_start: 0.6118 (t) cc_final: 0.5188 (p)
REVERT: D  786 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7679 (mp)
REVERT: C   80 TYR cc_start: 0.8892 (OUTLIER) cc_final: 0.8471 (m-80)
  outliers start: 23
  outliers final: 18
  residues processed: 118
  average time/residue: 0.0974
  time to fit residues: 15.3675
Evaluate side-chains
  125 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain B residue  735 GLN
Chi-restraints excluded: chain D residue  110 GLN
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  632 LEU
Chi-restraints excluded: chain D residue  666 LEU
Chi-restraints excluded: chain D residue  702 MET
Chi-restraints excluded: chain D residue  720 ASN
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   45 GLU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 42 optimal weight:    6.9990
   chunk 56 optimal weight:    0.5980
   chunk 29 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4207 r_free = 0.4207 target = 0.152909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.114648 restraints weight = 13080.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 2.35
r_work: 0.3317 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7783  Z= 0.161
  Angle     :  0.543  13.836  10883  Z= 0.285
  Chirality :  0.036   0.267   1301
  Planarity :  0.004   0.057   1088
  Dihedral  : 18.603 109.318   2092
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 19.53 %
    Favored  : 76.96 %
  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:  2.03 (0.33), residues: 703
  helix:  2.16 (0.24), residues: 472
  sheet: -1.95 (1.01), residues: 26
  loop : -0.08 (0.44), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 736 
 TYR   0.016   0.001   TYR D 704 
 PHE   0.015   0.002   PHE D 147 
 TRP   0.003   0.001   TRP D 692 
 HIS   0.007   0.002   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.16 ( 7783)
  covalent geometry    : angle       0.54349 /  0.28 (10883)
  hydrogen bonds       : bond        0.04432 /  3.19 (  458)
  hydrogen bonds       : angle       4.13905 /  3.14 ( 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
  126 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  708 GLN cc_start: 0.7964 (pt0) cc_final: 0.7593 (pm20)
REVERT: B  730 LYS cc_start: 0.8994 (tmtt) cc_final: 0.8532 (tttm)
REVERT: D  527 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6948 (pp)
REVERT: D  538 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7920 (pm20)
REVERT: D  596 MET cc_start: 0.6241 (ptm) cc_final: 0.5929 (ptp)
REVERT: D  674 CYS cc_start: 0.6171 (t) cc_final: 0.5247 (p)
REVERT: D  786 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7634 (mp)
REVERT: C   80 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.8535 (m-80)
  outliers start: 21
  outliers final: 17
  residues processed: 118
  average time/residue: 0.0997
  time to fit residues: 15.6215
Evaluate side-chains
  123 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain B residue  735 GLN
Chi-restraints excluded: chain D residue  110 GLN
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  666 LEU
Chi-restraints excluded: chain D residue  702 MET
Chi-restraints excluded: chain D residue  720 ASN
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   45 GLU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 72 optimal weight:   10.0000
   chunk 60 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 0 optimal weight:   20.0000
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 708 GLN
** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 125 HIS ** 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 = 0.4217 r_free = 0.4217 target = 0.153669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.115291 restraints weight = 13068.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 2.31
r_work: 0.3340 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.2324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7783  Z= 0.131
  Angle     :  0.538  14.135  10883  Z= 0.280
  Chirality :  0.035   0.232   1301
  Planarity :  0.004   0.057   1088
  Dihedral  : 18.612 108.800   2092
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 19.87 %
    Favored  : 76.29 %
  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:  2.03 (0.33), residues: 703
  helix:  2.16 (0.24), residues: 473
  sheet: -1.99 (1.00), residues: 26
  loop : -0.08 (0.45), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 120 
 TYR   0.028   0.002   TYR D 704 
 PHE   0.020   0.002   PHE D 588 
 TRP   0.003   0.001   TRP D 522 
 HIS   0.005   0.001   HIS D 643 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 ( 7783)
  covalent geometry    : angle       0.53832 /  0.28 (10883)
  hydrogen bonds       : bond        0.04227 /  3.05 (  458)
  hydrogen bonds       : angle       4.09837 /  3.11 ( 1245)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2000.82 seconds
wall clock time: 35 minutes 10.22 seconds (2110.22 seconds total)