Starting phenix.real_space_refine
on Thu Jul  2 08:59:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw7_54302/07_2026/9rw7_54302.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw7_54302/07_2026/9rw7_54302.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rw7_54302/07_2026/9rw7_54302.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw7_54302/07_2026/9rw7_54302.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rw7_54302/07_2026/9rw7_54302.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw7_54302/07_2026/9rw7_54302.map"
  }
  resolution = 3.4
  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=   0.054
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      98      5.49       5
     S      38      5.16       5
     C    4561      2.51       5
     N    1342      2.21       5
     O    1777      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s

  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: 7816
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 423
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 17
    Chain: "B"
      Number of atoms: 423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 423
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 17
    Chain: "C"
      Number of atoms: 1249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1249
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 4, 'TRANS': 149}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3623
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 460, 3623
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 448}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 90
          Unresolved non-hydrogen angles: 108
          Unresolved non-hydrogen dihedrals: 77
          Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 62
    Chain: "E"
      Number of atoms: 1049
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 1049
          Classifications: {'RNA': 50}
          Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 7, 'rna3p_pur': 21, 'rna3p_pyr': 21}
          Link IDs: {'rna2p': 8, 'rna3p': 41}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1049
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 1049
          Classifications: {'RNA': 50}
          Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 7, 'rna3p_pur': 21, 'rna3p_pyr': 21}
          Link IDs: {'rna2p': 8, 'rna3p': 41}
          Chain breaks: 1
  Time building chain proxies: 1.62, per 1000 atoms: 0.21
  Number of scatterers: 7816
  At special positions: 0
  Unit cell: (90.015, 97.428, 150.378, 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      38     16.00
     P      98     15.00
     O    1777      8.00
     N    1342      7.00
     C    4561      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: 0.54
  Conformation dependent library (CDL) restraints added in 215.1 milliseconds
  

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1372

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 5 sheets defined
      69.9% alpha, 7.5% beta
      42 base pairs and 46 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 695 through 747
      removed outlier: 3.605A  pdb=" N   ARG A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 747
    Processing helix  chain 'C' and resid 6 through 25
      removed outlier: 3.627A  pdb=" N   LYS C  24 " --> pdb=" O   ARG C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 35
    Processing helix  chain 'C' and resid 36 through 39
    Processing helix  chain 'C' and resid 43 through 51
      removed outlier: 3.596A  pdb=" N   GLY C  51 " --> pdb=" O   ARG C  47 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 62
    Processing helix  chain 'C' and resid 95 through 110
    Processing helix  chain 'C' and resid 119 through 125
      removed outlier: 3.679A  pdb=" N   GLY C 124 " --> pdb=" O   ARG C 120 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   HIS C 125 " --> pdb=" O   SER C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 126 through 128
      No H-bonds generated for 'chain 'C' and resid 126 through 128'
    Processing helix  chain 'C' and resid 130 through 137
    Processing helix  chain 'C' and resid 140 through 150
    Processing helix  chain 'D' and resid 5 through 25
      removed outlier: 3.831A  pdb=" N   LYS D  24 " --> pdb=" O   ARG D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 35
    Processing helix  chain 'D' and resid 36 through 39
    Processing helix  chain 'D' and resid 43 through 50
    Processing helix  chain 'D' and resid 53 through 62
    Processing helix  chain 'D' and resid 95 through 111
      removed outlier: 3.720A  pdb=" N   GLU D  99 " --> pdb=" O   ASP D  95 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   TYR D 111 " --> pdb=" O   LYS D 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 123
    Processing helix  chain 'D' and resid 124 through 128
    Processing helix  chain 'D' and resid 130 through 137
      removed outlier: 3.505A  pdb=" N   ILE D 136 " --> pdb=" O   GLN D 132 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 140 through 152
      removed outlier: 3.787A  pdb=" N   HIS D 151 " --> pdb=" O   PHE D 147 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   THR D 152 " --> pdb=" O   LEU D 148 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 521 through 529
    Processing helix  chain 'D' and resid 535 through 554
    Processing helix  chain 'D' and resid 594 through 600
      removed outlier: 4.136A  pdb=" N   THR D 598 " --> pdb=" O   PRO D 594 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 601 through 608
    Processing helix  chain 'D' and resid 617 through 630
      removed outlier: 4.380A  pdb=" N   ASP D 621 " --> pdb=" O   ASP D 617 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU D 625 " --> pdb=" O   ASP D 621 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   TYR D 626 " --> pdb=" O   ALA D 622 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 639 through 652
    Processing helix  chain 'D' and resid 662 through 670
    Processing helix  chain 'D' and resid 675 through 680
      removed outlier: 3.881A  pdb=" N   LYS D 678 " --> pdb=" O   ASN D 675 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 681 through 688
    Processing helix  chain 'D' and resid 689 through 694
      removed outlier: 4.545A  pdb=" N   TRP D 692 " --> pdb=" O   GLN D 689 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 698 through 714
      removed outlier: 4.159A  pdb=" N   ASP D 708 " --> pdb=" O   TYR D 704 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   VAL D 709 " --> pdb=" O   ALA D 705 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 717 through 725
    Processing helix  chain 'D' and resid 726 through 728
      No H-bonds generated for 'chain 'D' and resid 726 through 728'
    Processing helix  chain 'D' and resid 729 through 743
    Processing helix  chain 'D' and resid 746 through 773
      removed outlier: 3.524A  pdb=" N   SER D 764 " --> pdb=" O   SER D 760 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   THR D 773 " --> pdb=" O   LYS D 769 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 780 through 787
      removed outlier: 3.510A  pdb=" N   ARG D 785 " --> pdb=" O   ASN D 781 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU D 787 " --> pdb=" O   GLU D 783 " (cutoff:3.500A)
    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 sheet with id=AA1, first strand: chain 'C' and resid 28 through 29
      removed outlier: 3.846A  pdb=" N   TYR C  74 " --> pdb=" O   ASP C  71 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 117 through 118
    Processing sheet with id=AA3, first strand: chain 'D' and resid 28 through 29
    Processing sheet with id=AA4, first strand: chain 'D' and resid 117 through 118
    Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 533
      removed outlier: 3.524A  pdb=" N   ILE D 576 " --> pdb=" O   PHE D 588 " (cutoff:3.500A)
      removed outlier: 5.332A  pdb=" N   ILE D 573 " --> pdb=" O   ILE D 565 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   ILE D 565 " --> pdb=" O   ILE D 573 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU D 575 " --> pdb=" O   GLU D 563 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   LYS D 613 " --> pdb=" O   PHE D 637 " (cutoff:3.500A)

    362 hydrogen bonds defined for protein.
    1038 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      96 hydrogen bonds
      176 hydrogen bond angles
      0 basepair planarities
      42 basepair parallelities
      46 stacking parallelities
  Total time for adding SS restraints: 0.89

  Time building geometry restraints manager: 0.71 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: 1105
        1.31 -     1.43: 2612
        1.43 -     1.56: 4162
        1.56 -     1.69: 196
        1.69 -     1.81: 63
  Bond restraints: 8138
  Sorted by residual:
  bond pdb=" CG  PRO D 696 "
       pdb=" CD  PRO D 696 "
    ideal  model  delta    sigma   weight residual
    1.512  1.180  0.332 2.70e-02 1.37e+03 1.52e+02
  bond pdb=" N   PRO D 696 "
       pdb=" CD  PRO D 696 "
    ideal  model  delta    sigma   weight residual
    1.474  1.562 -0.088 1.40e-02 5.10e+03 3.96e+01
  bond pdb=" N   PRO D 696 "
       pdb=" CA  PRO D 696 "
    ideal  model  delta    sigma   weight residual
    1.468  1.383  0.085 1.70e-02 3.46e+03 2.53e+01
  bond pdb=" C   HIS C  31 "
       pdb=" O   HIS C  31 "
    ideal  model  delta    sigma   weight residual
    1.237  1.186  0.051 1.17e-02 7.31e+03 1.88e+01
  bond pdb=" CB  PRO D 696 "
       pdb=" CG  PRO D 696 "
    ideal  model  delta    sigma   weight residual
    1.506  1.628 -0.122 3.90e-02 6.57e+02 9.74e+00
  ... (remaining 8133 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.55: 11388
        3.55 -     7.10: 32
        7.10 -    10.64: 6
       10.64 -    14.19: 2
       14.19 -    17.74: 2
  Bond angle restraints: 11430
  Sorted by residual:
  angle pdb=" N   PRO D 696 "
        pdb=" CD  PRO D 696 "
        pdb=" CG  PRO D 696 "
      ideal   model   delta    sigma   weight residual
     103.80   87.95   15.85 1.20e+00 6.94e-01 1.74e+02
  angle pdb=" CA  PRO D 696 "
        pdb=" N   PRO D 696 "
        pdb=" CD  PRO D 696 "
      ideal   model   delta    sigma   weight residual
     111.50   93.76   17.74 1.40e+00 5.10e-01 1.61e+02
  angle pdb=" C3'   C E  49 "
        pdb=" C2'   C E  49 "
        pdb=" O2'   C E  49 "
      ideal   model   delta    sigma   weight residual
     110.70  121.40  -10.70 1.50e+00 4.44e-01 5.09e+01
  angle pdb=" C1'   G E  18 "
        pdb=" N9    G E  18 "
        pdb=" C4    G E  18 "
      ideal   model   delta    sigma   weight residual
     126.50  135.41   -8.91 1.30e+00 5.92e-01 4.70e+01
  angle pdb=" C1'   G E  18 "
        pdb=" N9    G E  18 "
        pdb=" C8    G E  18 "
      ideal   model   delta    sigma   weight residual
     127.00  118.40    8.60 1.30e+00 5.92e-01 4.37e+01
  ... (remaining 11425 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.86: 4717
       33.86 -    67.72: 313
       67.72 -   101.58: 41
      101.58 -   135.44: 0
      135.44 -   169.30: 2
  Dihedral angle restraints: 5073
    sinusoidal: 2960
      harmonic: 2113
  Sorted by residual:
  dihedral pdb=" CA  ARG B 744 "
           pdb=" C   ARG B 744 "
           pdb=" N   GLU B 745 "
           pdb=" CA  GLU B 745 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.23   21.77     0      5.00e+00 4.00e-02 1.90e+01
  dihedral pdb=" C4'   C F  49 "
           pdb=" C3'   C F  49 "
           pdb=" O3'   C F  49 "
           pdb=" P     G F  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   50.70  169.30     1      3.50e+01 8.16e-04 1.55e+01
  dihedral pdb=" C4'   C E  49 "
           pdb=" C3'   C E  49 "
           pdb=" O3'   C E  49 "
           pdb=" P     G E  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   56.05  163.95     1      3.50e+01 8.16e-04 1.54e+01
  ... (remaining 5070 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.290: 1378
       0.290 -    0.581: 1
       0.581 -    0.871: 0
       0.871 -    1.161: 0
       1.161 -    1.452: 1
  Chirality restraints: 1380
  Sorted by residual:
  chirality pdb=" CB  VAL D 162 "
            pdb=" CA  VAL D 162 "
            pdb=" CG1 VAL D 162 "
            pdb=" CG2 VAL D 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.18   -1.45 2.00e-01 2.50e+01 5.27e+01
  chirality pdb=" C3'   C E  49 "
            pdb=" C4'   C E  49 "
            pdb=" O3'   C E  49 "
            pdb=" C2'   C E  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.14   -0.33 2.00e-01 2.50e+01 2.80e+00
  chirality pdb=" C2'   C E  49 "
            pdb=" C3'   C E  49 "
            pdb=" O2'   C E  49 "
            pdb=" C1'   C E  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.47   -0.28 2.00e-01 2.50e+01 2.03e+00
  ... (remaining 1377 not shown)

  Planarity restraints: 1105
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG D 695 "   -0.055 5.00e-02 4.00e+02   7.51e-02 9.01e+00
        pdb=" N   PRO D 696 "    0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO D 696 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO D 696 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U E  19 "   -0.028 2.00e-02 2.50e+03   1.51e-02 5.15e+00
        pdb=" N1    U E  19 "    0.034 2.00e-02 2.50e+03
        pdb=" C2    U E  19 "    0.002 2.00e-02 2.50e+03
        pdb=" O2    U E  19 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    U E  19 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    U E  19 "   -0.006 2.00e-02 2.50e+03
        pdb=" O4    U E  19 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5    U E  19 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    U E  19 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C E  38 "   -0.024 2.00e-02 2.50e+03   1.28e-02 3.68e+00
        pdb=" N1    C E  38 "    0.028 2.00e-02 2.50e+03
        pdb=" C2    C E  38 "    0.004 2.00e-02 2.50e+03
        pdb=" O2    C E  38 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    C E  38 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    C E  38 "   -0.003 2.00e-02 2.50e+03
        pdb=" N4    C E  38 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5    C E  38 "    0.005 2.00e-02 2.50e+03
        pdb=" C6    C E  38 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1102 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 69
        2.57 -     3.15: 6671
        3.15 -     3.74: 13118
        3.74 -     4.32: 17203
        4.32 -     4.90: 26741
  Nonbonded interactions: 63802
  Sorted by model distance:
  nonbonded pdb=" O2'   U E  48 "
            pdb=" OP1   G E  50 "
     model   vdw
     1.988 3.040
  nonbonded pdb=" O2'   C F  49 "
            pdb=" OP1   G F  50 "
     model   vdw
     2.010 3.040
  nonbonded pdb=" O2'   U F  19 "
            pdb=" OP2   A F  20 "
     model   vdw
     2.018 3.040
  nonbonded pdb=" O2'   U E  19 "
            pdb=" OP2   A E  20 "
     model   vdw
     2.068 3.040
  nonbonded pdb=" O   LYS C 142 "
            pdb=" OG1 THR C 145 "
     model   vdw
     2.114 3.040
  ... (remaining 63797 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' and (resid 695 through 703 or (resid 704 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 705 through 747))
  selection = (chain 'B' and (resid 695 through 702 or (resid 703 through 704 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 705 through 747))
}
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:             3.760
  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:             0.020
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     7.320
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6948
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.332   8138  Z= 0.235
  Angle     :  0.657  17.738  11430  Z= 0.493
  Chirality :  0.052   1.452   1380
  Planarity :  0.004   0.075   1105
  Dihedral  : 20.201 169.297   3701
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.11 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.39 (0.33), residues: 704
  helix:  1.48 (0.25), residues: 443
  sheet: -0.21 (0.95), residues: 31
  loop :  0.16 (0.43), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 744 
 TYR   0.010   0.001   TYR D   6 
 PHE   0.012   0.001   PHE D  17 
 TRP   0.004   0.001   TRP D 522 
 HIS   0.010   0.001   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00479 /  0.24 ( 8138)
  covalent geometry    : angle       0.65722 /  0.49 (11430)
  hydrogen bonds       : bond        0.17659 / 11.50 (  458)
  hydrogen bonds       : angle       6.48774 /  4.81 ( 1214)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  731 LEU cc_start: 0.8649 (mt) cc_final: 0.8306 (mt)
REVERT: A  735 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8279 (tm-30)
REVERT: C  106 ASN cc_start: 0.8491 (m-40) cc_final: 0.8167 (m-40)
REVERT: C  141 ILE cc_start: 0.7670 (tp) cc_final: 0.7456 (tp)
REVERT: D   19 GLU cc_start: 0.7074 (tt0) cc_final: 0.6690 (mt-10)
REVERT: D  632 LEU cc_start: 0.8062 (mt) cc_final: 0.7573 (mt)
REVERT: D  692 TRP cc_start: 0.6329 (m100) cc_final: 0.6030 (m100)
REVERT: D  735 GLU cc_start: 0.8313 (tp30) cc_final: 0.7699 (tt0)
REVERT: D  743 MET cc_start: 0.8018 (tpp) cc_final: 0.7608 (ttm)
REVERT: D  746 LYS cc_start: 0.6788 (mttt) cc_final: 0.6193 (mttt)
REVERT: D  811 GLU cc_start: 0.7974 (pt0) cc_final: 0.7550 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.0873
  time to fit residues: 14.2420
Evaluate side-chains
  102 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0770
   chunk 5 optimal weight:    0.0870
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    0.1980
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.2516

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 647 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4623 r_free = 0.4623 target = 0.234220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.188622 restraints weight = 9679.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.4196 rms_B_bonded: 3.13
r_work (final): 0.4196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6808
moved from start:          0.1351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8138  Z= 0.146
  Angle     :  0.599   7.879  11430  Z= 0.332
  Chirality :  0.039   0.214   1380
  Planarity :  0.004   0.042   1105
  Dihedral  : 20.186 179.528   2282
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 16.09 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.22 (0.32), residues: 704
  helix:  1.41 (0.24), residues: 457
  sheet: -0.79 (0.79), residues: 25
  loop : -0.11 (0.43), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 744 
 TYR   0.036   0.002   TYR D 626 
 PHE   0.013   0.002   PHE D  17 
 TRP   0.006   0.001   TRP D 522 
 HIS   0.006   0.001   HIS C 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.15 ( 8138)
  covalent geometry    : angle       0.59918 /  0.33 (11430)
  hydrogen bonds       : bond        0.06308 /  4.13 (  458)
  hydrogen bonds       : angle       4.98569 /  3.68 ( 1214)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  742 MET cc_start: 0.6054 (tmm) cc_final: 0.5778 (tmm)
REVERT: D   48 GLN cc_start: 0.8462 (tm-30) cc_final: 0.7976 (tm-30)
REVERT: D  743 MET cc_start: 0.7856 (tpp) cc_final: 0.7463 (ttm)
  outliers start: 14
  outliers final: 10
  residues processed: 118
  average time/residue: 0.0834
  time to fit residues: 13.4551
Evaluate side-chains
  103 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  738 GLU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  162 VAL
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  602 LEU
Chi-restraints excluded: chain D residue  616 HIS
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  764 SER
Chi-restraints excluded: chain D residue  815 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 28 optimal weight:    0.1980
   chunk 45 optimal weight:    4.9990
   chunk 76 optimal weight:    7.9990
   chunk 13 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 80 optimal weight:    6.9990
   chunk 25 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 56 optimal weight:    4.9990
   overall best weight:    0.6580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.231208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.175913 restraints weight = 9604.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.4087 rms_B_bonded: 1.59
r_work: 0.3638 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8138  Z= 0.168
  Angle     :  0.568   5.937  11430  Z= 0.313
  Chirality :  0.038   0.252   1380
  Planarity :  0.004   0.061   1105
  Dihedral  : 20.127 175.898   2282
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 16.58 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.09 (0.31), residues: 704
  helix:  1.31 (0.24), residues: 459
  sheet: -1.04 (0.82), residues: 25
  loop : -0.14 (0.43), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 120 
 TYR   0.028   0.002   TYR D 626 
 PHE   0.014   0.002   PHE D  17 
 TRP   0.012   0.002   TRP D 692 
 HIS   0.004   0.001   HIS C 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.17 ( 8138)
  covalent geometry    : angle       0.56765 /  0.31 (11430)
  hydrogen bonds       : bond        0.06073 /  4.00 (  458)
  hydrogen bonds       : angle       4.68067 /  3.45 ( 1214)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   80 TYR cc_start: 0.8441 (m-80) cc_final: 0.7725 (m-80)
REVERT: C  143 GLU cc_start: 0.6684 (mp0) cc_final: 0.6460 (mp0)
REVERT: C  163 MET cc_start: 0.7579 (ttp) cc_final: 0.7251 (tpt)
REVERT: D   48 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8269 (tm-30)
REVERT: D  692 TRP cc_start: 0.6406 (m100) cc_final: 0.5826 (m100)
REVERT: D  702 MET cc_start: 0.4608 (mtm) cc_final: 0.4009 (mpp)
REVERT: D  741 ILE cc_start: 0.7977 (mt) cc_final: 0.7660 (tp)
REVERT: D  743 MET cc_start: 0.7829 (tpp) cc_final: 0.7390 (ttm)
  outliers start: 23
  outliers final: 17
  residues processed: 114
  average time/residue: 0.0709
  time to fit residues: 11.2250
Evaluate side-chains
  109 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  738 GLU
Chi-restraints excluded: chain C residue  159 ASP
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  146 ASP
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  557 VAL
Chi-restraints excluded: chain D residue  606 LEU
Chi-restraints excluded: chain D residue  616 HIS
Chi-restraints excluded: chain D residue  639 THR
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  746 LYS
Chi-restraints excluded: chain D residue  750 VAL
Chi-restraints excluded: chain D residue  764 SER
Chi-restraints excluded: chain D residue  815 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 35 optimal weight:    0.0970
   chunk 51 optimal weight:    0.9980
   chunk 68 optimal weight:    0.3980
   chunk 26 optimal weight:    0.4980
   chunk 54 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 61 optimal weight:    0.3980
   chunk 71 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.4578

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 721 GLN
** C 135 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 = 0.4607 r_free = 0.4607 target = 0.232694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.178594 restraints weight = 9805.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.4108 rms_B_bonded: 1.77
r_work: 0.3618 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8138  Z= 0.140
  Angle     :  0.531   6.391  11430  Z= 0.294
  Chirality :  0.037   0.246   1380
  Planarity :  0.004   0.047   1105
  Dihedral  : 20.071 175.832   2282
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.70 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 19.05 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.09 (0.32), residues: 704
  helix:  1.36 (0.24), residues: 459
  sheet: -1.16 (0.79), residues: 25
  loop : -0.29 (0.43), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 757 
 TYR   0.012   0.001   TYR D 626 
 PHE   0.015   0.002   PHE D  17 
 TRP   0.005   0.001   TRP D 692 
 HIS   0.004   0.001   HIS C 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.14 ( 8138)
  covalent geometry    : angle       0.53075 /  0.29 (11430)
  hydrogen bonds       : bond        0.05647 /  3.70 (  458)
  hydrogen bonds       : angle       4.55100 /  3.33 ( 1214)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  742 MET cc_start: 0.5721 (tmm) cc_final: 0.5454 (tmm)
REVERT: C   80 TYR cc_start: 0.8489 (m-80) cc_final: 0.7936 (m-80)
REVERT: C   99 GLU cc_start: 0.7080 (pt0) cc_final: 0.6804 (pt0)
REVERT: D   48 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8266 (tm-30)
REVERT: D  538 GLN cc_start: 0.7080 (tp40) cc_final: 0.6682 (tp40)
REVERT: D  741 ILE cc_start: 0.7977 (mt) cc_final: 0.7663 (tp)
REVERT: D  743 MET cc_start: 0.7689 (tpp) cc_final: 0.7261 (ttm)
  outliers start: 23
  outliers final: 16
  residues processed: 110
  average time/residue: 0.0799
  time to fit residues: 11.9747
Evaluate side-chains
  108 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 GLN
Chi-restraints excluded: chain B residue  738 GLU
Chi-restraints excluded: chain B residue  744 ARG
Chi-restraints excluded: chain C residue  159 ASP
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  146 ASP
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  557 VAL
Chi-restraints excluded: chain D residue  616 HIS
Chi-restraints excluded: chain D residue  639 THR
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  750 VAL
Chi-restraints excluded: chain D residue  764 SER
Chi-restraints excluded: chain D residue  815 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 15 optimal weight:    0.2980
   chunk 57 optimal weight:    5.9990
   chunk 4 optimal weight:    0.6980
   chunk 80 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9980
   chunk 47 optimal weight:    9.9990
   chunk 23 optimal weight:    0.8980
   chunk 32 optimal weight:    0.3980
   overall best weight:    0.5380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.232253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.176977 restraints weight = 9631.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.4092 rms_B_bonded: 1.65
r_work: 0.3622 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.2273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8138  Z= 0.147
  Angle     :  0.536   6.434  11430  Z= 0.297
  Chirality :  0.037   0.252   1380
  Planarity :  0.004   0.050   1105
  Dihedral  : 20.012 174.656   2282
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.13 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 19.54 %
    Favored  : 76.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.04 (0.31), residues: 704
  helix:  1.30 (0.24), residues: 461
  sheet: -1.25 (0.77), residues: 25
  loop : -0.25 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 757 
 TYR   0.018   0.001   TYR D 626 
 PHE   0.015   0.002   PHE D  17 
 TRP   0.016   0.002   TRP D 692 
 HIS   0.009   0.001   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.15 ( 8138)
  covalent geometry    : angle       0.53627 /  0.30 (11430)
  hydrogen bonds       : bond        0.05585 /  3.67 (  458)
  hydrogen bonds       : angle       4.46657 /  3.28 ( 1214)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   80 TYR cc_start: 0.8473 (m-80) cc_final: 0.7954 (m-80)
REVERT: D    4 MET cc_start: 0.4757 (ppp) cc_final: 0.4541 (ppp)
REVERT: D   48 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8279 (tm-30)
REVERT: D  596 MET cc_start: 0.3183 (ptp) cc_final: 0.2864 (ptp)
REVERT: D  741 ILE cc_start: 0.7997 (mt) cc_final: 0.7678 (tp)
REVERT: D  743 MET cc_start: 0.7662 (tpp) cc_final: 0.7256 (ttm)
  outliers start: 24
  outliers final: 21
  residues processed: 112
  average time/residue: 0.0822
  time to fit residues: 12.6184
Evaluate side-chains
  114 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 GLN
Chi-restraints excluded: chain B residue  705 LEU
Chi-restraints excluded: chain B residue  738 GLU
Chi-restraints excluded: chain B residue  744 ARG
Chi-restraints excluded: chain C residue   81 GLN
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  159 ASP
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  146 ASP
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  557 VAL
Chi-restraints excluded: chain D residue  616 HIS
Chi-restraints excluded: chain D residue  639 THR
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  749 GLU
Chi-restraints excluded: chain D residue  750 VAL
Chi-restraints excluded: chain D residue  764 SER
Chi-restraints excluded: chain D residue  815 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 3 optimal weight:    0.0870
   chunk 12 optimal weight:    0.0980
   chunk 21 optimal weight:    0.3980
   chunk 26 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 11 optimal weight:    0.2980
   overall best weight:    0.2958

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4692 r_free = 0.4692 target = 0.240718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.196556 restraints weight = 9728.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.4292 rms_B_bonded: 3.02
r_work (final): 0.4292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6806
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8138  Z= 0.118
  Angle     :  0.508   7.219  11430  Z= 0.283
  Chirality :  0.036   0.253   1380
  Planarity :  0.004   0.037   1105
  Dihedral  : 19.960 174.478   2282
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.85 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 20.20 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.18 (0.32), residues: 704
  helix:  1.40 (0.24), residues: 463
  sheet: -1.23 (0.81), residues: 25
  loop : -0.19 (0.43), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 757 
 TYR   0.014   0.001   TYR D 626 
 PHE   0.014   0.001   PHE D  17 
 TRP   0.006   0.001   TRP D 692 
 HIS   0.005   0.001   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.12 ( 8138)
  covalent geometry    : angle       0.50769 /  0.28 (11430)
  hydrogen bonds       : bond        0.05212 /  3.41 (  458)
  hydrogen bonds       : angle       4.33034 /  3.18 ( 1214)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  740 MET cc_start: 0.5985 (ttp) cc_final: 0.5469 (ttp)
REVERT: C   80 TYR cc_start: 0.8327 (m-80) cc_final: 0.7837 (m-80)
REVERT: C  143 GLU cc_start: 0.6271 (mp0) cc_final: 0.5854 (mp0)
REVERT: D   48 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8015 (tm-30)
REVERT: D  596 MET cc_start: 0.1599 (ptp) cc_final: 0.1253 (ptp)
REVERT: D  692 TRP cc_start: 0.4858 (m100) cc_final: 0.4419 (m100)
  outliers start: 22
  outliers final: 20
  residues processed: 111
  average time/residue: 0.0724
  time to fit residues: 11.1378
Evaluate side-chains
  109 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  705 LEU
Chi-restraints excluded: chain B residue  738 GLU
Chi-restraints excluded: chain B residue  740 MET
Chi-restraints excluded: chain B residue  744 ARG
Chi-restraints excluded: chain C residue   81 GLN
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  159 ASP
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  146 ASP
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  557 VAL
Chi-restraints excluded: chain D residue  616 HIS
Chi-restraints excluded: chain D residue  639 THR
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  749 GLU
Chi-restraints excluded: chain D residue  750 VAL
Chi-restraints excluded: chain D residue  764 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 71 optimal weight:    6.9990
   chunk 74 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    1.4384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4697 r_free = 0.4697 target = 0.239730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.199309 restraints weight = 9707.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.4326 rms_B_bonded: 2.77
r_work (final): 0.4326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6885
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068   8138  Z= 0.282
  Angle     :  0.656   7.745  11430  Z= 0.353
  Chirality :  0.042   0.284   1380
  Planarity :  0.005   0.050   1105
  Dihedral  : 19.974 171.678   2282
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.41 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 20.03 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.31), residues: 704
  helix:  0.84 (0.23), residues: 463
  sheet: -1.58 (0.73), residues: 25
  loop : -0.50 (0.43), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 619 
 TYR   0.020   0.002   TYR D  64 
 PHE   0.021   0.003   PHE C  60 
 TRP   0.007   0.002   TRP D 692 
 HIS   0.008   0.002   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00666 /  0.28 ( 8138)
  covalent geometry    : angle       0.65624 /  0.35 (11430)
  hydrogen bonds       : bond        0.06683 /  4.41 (  458)
  hydrogen bonds       : angle       4.61734 /  3.38 ( 1214)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 89
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   63 GLN cc_start: 0.8030 (mt0) cc_final: 0.7808 (mt0)
REVERT: C  128 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7092 (mm-40)
REVERT: D   48 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8143 (tm-30)
REVERT: D  692 TRP cc_start: 0.4851 (m100) cc_final: 0.4454 (m100)
REVERT: D  743 MET cc_start: 0.7916 (tpp) cc_final: 0.7505 (ttm)
  outliers start: 31
  outliers final: 23
  residues processed: 111
  average time/residue: 0.0723
  time to fit residues: 11.0669
Evaluate side-chains
  104 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 80
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 GLN
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  705 LEU
Chi-restraints excluded: chain B residue  738 GLU
Chi-restraints excluded: chain B residue  744 ARG
Chi-restraints excluded: chain C residue   81 GLN
Chi-restraints excluded: chain C residue  128 GLN
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  159 ASP
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  146 ASP
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  557 VAL
Chi-restraints excluded: chain D residue  606 LEU
Chi-restraints excluded: chain D residue  616 HIS
Chi-restraints excluded: chain D residue  639 THR
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  749 GLU
Chi-restraints excluded: chain D residue  750 VAL
Chi-restraints excluded: chain D residue  764 SER
Chi-restraints excluded: chain D residue  815 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 73 optimal weight:    4.9990
   chunk 36 optimal weight:    0.5980
   chunk 69 optimal weight:    0.3980
   chunk 6 optimal weight:    0.7980
   chunk 56 optimal weight:   10.0000
   chunk 45 optimal weight:    6.9990
   chunk 16 optimal weight:    0.5980
   chunk 72 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.6180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4714 r_free = 0.4714 target = 0.242245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.201512 restraints weight = 9749.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.4345 rms_B_bonded: 2.77
r_work (final): 0.4345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6839
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8138  Z= 0.159
  Angle     :  0.560   8.248  11430  Z= 0.305
  Chirality :  0.038   0.252   1380
  Planarity :  0.004   0.064   1105
  Dihedral  : 20.019 173.481   2282
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.13 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 20.20 %
    Favored  : 75.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.31), residues: 704
  helix:  0.92 (0.24), residues: 465
  sheet: -1.52 (0.75), residues: 25
  loop : -0.38 (0.44), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 744 
 TYR   0.023   0.002   TYR D 549 
 PHE   0.016   0.002   PHE D  17 
 TRP   0.006   0.001   TRP D 692 
 HIS   0.005   0.001   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00363 /  0.16 ( 8138)
  covalent geometry    : angle       0.55996 /  0.30 (11430)
  hydrogen bonds       : bond        0.05783 /  3.77 (  458)
  hydrogen bonds       : angle       4.41735 /  3.23 ( 1214)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 82
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  740 MET cc_start: 0.6200 (ttp) cc_final: 0.5363 (ttp)
REVERT: C  128 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7059 (mm-40)
REVERT: D   48 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8095 (tm-30)
REVERT: D  692 TRP cc_start: 0.4827 (m100) cc_final: 0.4409 (m100)
  outliers start: 27
  outliers final: 22
  residues processed: 102
  average time/residue: 0.0869
  time to fit residues: 11.9994
Evaluate side-chains
  104 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 GLN
Chi-restraints excluded: chain B residue  705 LEU
Chi-restraints excluded: chain B residue  738 GLU
Chi-restraints excluded: chain B residue  744 ARG
Chi-restraints excluded: chain C residue   81 GLN
Chi-restraints excluded: chain C residue  128 GLN
Chi-restraints excluded: chain C residue  159 ASP
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  146 ASP
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  557 VAL
Chi-restraints excluded: chain D residue  580 THR
Chi-restraints excluded: chain D residue  606 LEU
Chi-restraints excluded: chain D residue  616 HIS
Chi-restraints excluded: chain D residue  639 THR
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  749 GLU
Chi-restraints excluded: chain D residue  750 VAL
Chi-restraints excluded: chain D residue  764 SER
Chi-restraints excluded: chain D residue  815 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 7 optimal weight:    0.0970
   chunk 1 optimal weight:    0.7980
   chunk 80 optimal weight:    7.9990
   chunk 65 optimal weight:    1.9990
   chunk 53 optimal weight:    0.2980
   chunk 47 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 79 optimal weight:    8.9990
   overall best weight:    0.5378

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.235652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.185299 restraints weight = 9770.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.4186 rms_B_bonded: 1.61
r_work: 0.3728 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8138  Z= 0.153
  Angle     :  0.577   8.141  11430  Z= 0.311
  Chirality :  0.038   0.252   1380
  Planarity :  0.004   0.053   1105
  Dihedral  : 19.980 173.185   2282
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.56 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 21.02 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.31), residues: 704
  helix:  0.95 (0.24), residues: 465
  sheet: -1.44 (0.78), residues: 25
  loop : -0.32 (0.44), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 757 
 TYR   0.024   0.002   TYR D 626 
 PHE   0.016   0.001   PHE D  17 
 TRP   0.006   0.001   TRP D 692 
 HIS   0.004   0.001   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.15 ( 8138)
  covalent geometry    : angle       0.57656 /  0.31 (11430)
  hydrogen bonds       : bond        0.05591 /  3.63 (  458)
  hydrogen bonds       : angle       4.36568 /  3.19 ( 1214)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  128 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7564 (mm-40)
REVERT: C  143 GLU cc_start: 0.6654 (mp0) cc_final: 0.6096 (mp0)
REVERT: C  163 MET cc_start: 0.7615 (ttp) cc_final: 0.7334 (tpp)
REVERT: D    4 MET cc_start: 0.5184 (ppp) cc_final: 0.4828 (ppp)
REVERT: D   48 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8288 (tm-30)
REVERT: D  692 TRP cc_start: 0.5817 (m100) cc_final: 0.5254 (m100)
REVERT: D  743 MET cc_start: 0.8131 (tpp) cc_final: 0.7731 (ttm)
  outliers start: 23
  outliers final: 21
  residues processed: 99
  average time/residue: 0.0900
  time to fit residues: 11.9968
Evaluate side-chains
  100 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  705 LEU
Chi-restraints excluded: chain B residue  738 GLU
Chi-restraints excluded: chain B residue  744 ARG
Chi-restraints excluded: chain C residue   81 GLN
Chi-restraints excluded: chain C residue  128 GLN
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  159 ASP
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  146 ASP
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  557 VAL
Chi-restraints excluded: chain D residue  580 THR
Chi-restraints excluded: chain D residue  606 LEU
Chi-restraints excluded: chain D residue  616 HIS
Chi-restraints excluded: chain D residue  639 THR
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  750 VAL
Chi-restraints excluded: chain D residue  764 SER
Chi-restraints excluded: chain D residue  815 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 7 optimal weight:    0.0970
   chunk 72 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0870
   chunk 11 optimal weight:    0.1980
   chunk 48 optimal weight:    0.0270
   chunk 22 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 79 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.2414

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4664 r_free = 0.4664 target = 0.238210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.192278 restraints weight = 9813.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.4254 rms_B_bonded: 1.63
r_work: 0.3752 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.2972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8138  Z= 0.120
  Angle     :  0.549   9.629  11430  Z= 0.296
  Chirality :  0.036   0.247   1380
  Planarity :  0.004   0.036   1105
  Dihedral  : 19.951 173.076   2282
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.85 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 21.67 %
    Favored  : 75.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.32), residues: 704
  helix:  1.12 (0.24), residues: 466
  sheet: -1.37 (0.81), residues: 25
  loop : -0.20 (0.44), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 744 
 TYR   0.024   0.001   TYR D 626 
 PHE   0.015   0.001   PHE D  17 
 TRP   0.005   0.001   TRP D 692 
 HIS   0.004   0.001   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.12 ( 8138)
  covalent geometry    : angle       0.54865 /  0.30 (11430)
  hydrogen bonds       : bond        0.05007 /  3.22 (  458)
  hydrogen bonds       : angle       4.28409 /  3.14 ( 1214)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  740 MET cc_start: 0.6596 (ttp) cc_final: 0.6197 (ttp)
REVERT: C   80 TYR cc_start: 0.8523 (m-80) cc_final: 0.8004 (m-80)
REVERT: C  143 GLU cc_start: 0.6740 (mp0) cc_final: 0.6192 (mp0)
REVERT: C  163 MET cc_start: 0.7667 (ttp) cc_final: 0.7276 (tpp)
REVERT: D    4 MET cc_start: 0.5286 (ppp) cc_final: 0.4999 (ppp)
REVERT: D   48 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8251 (tm-30)
REVERT: D  626 TYR cc_start: 0.6592 (m-80) cc_final: 0.6378 (m-80)
REVERT: D  692 TRP cc_start: 0.5835 (m100) cc_final: 0.5269 (m100)
REVERT: D  743 MET cc_start: 0.8121 (tpp) cc_final: 0.7624 (ttm)
  outliers start: 17
  outliers final: 17
  residues processed: 103
  average time/residue: 0.0762
  time to fit residues: 10.5757
Evaluate side-chains
  97 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  705 LEU
Chi-restraints excluded: chain B residue  738 GLU
Chi-restraints excluded: chain B residue  744 ARG
Chi-restraints excluded: chain C residue   81 GLN
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  159 ASP
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   76 GLN
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  557 VAL
Chi-restraints excluded: chain D residue  580 THR
Chi-restraints excluded: chain D residue  616 HIS
Chi-restraints excluded: chain D residue  639 THR
Chi-restraints excluded: chain D residue  708 ASP
Chi-restraints excluded: chain D residue  749 GLU
Chi-restraints excluded: chain D residue  815 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 66 optimal weight:    6.9990
   chunk 11 optimal weight:    0.5980
   chunk 74 optimal weight:    6.9990
   chunk 39 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0980
   chunk 77 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.5780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.236793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.186183 restraints weight = 9811.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.4195 rms_B_bonded: 1.59
r_work: 0.3739 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8138  Z= 0.154
  Angle     :  0.577   9.700  11430  Z= 0.310
  Chirality :  0.038   0.251   1380
  Planarity :  0.004   0.048   1105
  Dihedral  : 19.917 171.544   2282
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.99 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.67 %
    Favored  : 75.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.32), residues: 704
  helix:  1.06 (0.24), residues: 466
  sheet: -1.45 (0.80), residues: 25
  loop : -0.18 (0.45), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 744 
 TYR   0.044   0.002   TYR D 549 
 PHE   0.015   0.002   PHE D  17 
 TRP   0.005   0.001   TRP D 692 
 HIS   0.003   0.001   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.15 ( 8138)
  covalent geometry    : angle       0.57736 /  0.31 (11430)
  hydrogen bonds       : bond        0.05263 /  3.39 (  458)
  hydrogen bonds       : angle       4.32742 /  3.17 ( 1214)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1551.45 seconds
wall clock time: 27 minutes 26.40 seconds (1646.40 seconds total)