Starting phenix.real_space_refine
on Sun Apr  5 04:50:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw0_54294/04_2026/9rw0_54294.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw0_54294/04_2026/9rw0_54294.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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rw0_54294/04_2026/9rw0_54294.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw0_54294/04_2026/9rw0_54294.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rw0_54294/04_2026/9rw0_54294.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw0_54294/04_2026/9rw0_54294.cif"
  }
  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=   0.002
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      88      5.49       5
     S      17      5.16       5
     C    4759      2.51       5
     N    1509      2.21       5
     O    1845      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8218
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 343
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 343
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 100
          Unresolved non-hydrogen angles: 125
          Unresolved non-hydrogen dihedrals: 78
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 8, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 74
    Chain: "B"
      Number of atoms: 343
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 343
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 100
          Unresolved non-hydrogen angles: 125
          Unresolved non-hydrogen dihedrals: 78
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 8, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 74
    Chain: "D"
      Number of atoms: 2928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 462, 2928
          Classifications: {'peptide': 462}
          Incomplete info: {'truncation_to_alanine': 233}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 450}
          Chain breaks: 3
          Unresolved chain link angles: 7
          Unresolved non-hydrogen bonds: 830
          Unresolved non-hydrogen angles: 1056
          Unresolved non-hydrogen dihedrals: 676
          Unresolved non-hydrogen chiralities: 82
          Planarities with less than four sites: {'GLU:plan': 16, 'ASN:plan1': 16, 'TYR:plan': 9, 'TRP:plan': 2, 'GLN:plan1': 20, 'PHE:plan': 8, 'ASP:plan': 13, 'ARG:plan': 11, 'HIS:plan': 4}
          Unresolved non-hydrogen planarities: 435
    Chain: "C"
      Number of atoms: 2754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 460, 2754
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 278}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 448}
          Chain breaks: 3
          Unresolved chain link angles: 7
          Unresolved non-hydrogen bonds: 994
          Unresolved non-hydrogen angles: 1257
          Unresolved non-hydrogen dihedrals: 812
          Unresolved non-hydrogen chiralities: 94
          Planarities with less than four sites: {'ASP:plan': 18, 'GLU:plan': 22, 'ASN:plan1': 17, 'TYR:plan': 12, 'TRP:plan': 2, 'GLN:plan1': 20, 'PHE:plan': 8, 'ARG:plan': 15, 'HIS:plan': 4}
          Unresolved non-hydrogen planarities: 518
    Chain: "E"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 925
          Classifications: {'RNA': 44}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 21, 'rna3p_pyr': 22}
          Link IDs: {'rna2p': 1, 'rna3p': 42}
    Chain: "F"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 925
          Classifications: {'RNA': 44}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 21, 'rna3p_pyr': 22}
          Link IDs: {'rna2p': 1, 'rna3p': 42}
  Time building chain proxies: 1.93, per 1000 atoms: 0.23
  Number of scatterers: 8218
  At special positions: 0
  Unit cell: (93.192, 93.192, 180.03, 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      17     16.00
     P      88     15.00
     O    1845      8.00
     N    1509      7.00
     C    4759      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: 0.51
  Conformation dependent library (CDL) restraints added in 188.8 milliseconds
  

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1964

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 6 sheets defined
      67.9% alpha, 6.2% beta
      35 base pairs and 55 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 695 through 747
      removed outlier: 4.152A  pdb=" N   VAL A 699 " --> pdb=" O   CYS A 695 " (cutoff:3.500A)
      removed outlier: 3.509A  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 'D' and resid 3 through 25
      removed outlier: 3.773A  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 50
    Processing helix  chain 'D' and resid 53 through 63
    Processing helix  chain 'D' and resid 95 through 110
    Processing helix  chain 'D' and resid 119 through 125
      removed outlier: 3.719A  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 138
    Processing helix  chain 'D' and resid 140 through 151
    Processing helix  chain 'D' and resid 521 through 530
    Processing helix  chain 'D' and resid 535 through 554
    Processing helix  chain 'D' and resid 594 through 600
      removed outlier: 3.892A  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 628
    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 681 through 688
      removed outlier: 3.710A  pdb=" N   TYR D 685 " --> pdb=" O   LEU D 681 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 698 through 714
      removed outlier: 3.901A  pdb=" N   ASP D 708 " --> pdb=" O   TYR D 704 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   VAL D 709 " --> pdb=" O   ALA D 705 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   HIS D 714 " --> pdb=" O   LEU D 710 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 717 through 725
    Processing helix  chain 'D' and resid 729 through 743
    Processing helix  chain 'D' and resid 746 through 773
      removed outlier: 3.987A  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 802
      removed outlier: 4.183A  pdb=" N   GLY D 802 " --> pdb=" O   GLU D 798 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 803 through 816
    Processing helix  chain 'C' and resid 6 through 25
    Processing helix  chain 'C' and resid 30 through 36
    Processing helix  chain 'C' and resid 37 through 39
      No H-bonds generated for 'chain 'C' and resid 37 through 39'
    Processing helix  chain 'C' and resid 42 through 50
      removed outlier: 4.026A  pdb=" N   MET C  46 " --> pdb=" O   PHE C  42 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 62
    Processing helix  chain 'C' and resid 95 through 109
    Processing helix  chain 'C' and resid 118 through 127
      removed outlier: 3.783A  pdb=" N   LEU C 122 " --> pdb=" O   PRO C 118 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 130 through 138
    Processing helix  chain 'C' and resid 140 through 151
      removed outlier: 3.570A  pdb=" N   HIS C 151 " --> pdb=" O   PHE C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 521 through 530
      removed outlier: 3.817A  pdb=" N   GLN C 528 " --> pdb=" O   ILE C 524 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ASN C 529 " --> pdb=" O   LYS C 525 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 535 through 554
    Processing helix  chain 'C' and resid 594 through 600
      removed outlier: 4.218A  pdb=" N   THR C 598 " --> pdb=" O   PRO C 594 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 601 through 608
    Processing helix  chain 'C' and resid 617 through 628
      removed outlier: 4.622A  pdb=" N   ASP C 621 " --> pdb=" O   ASP C 617 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 639 through 652
    Processing helix  chain 'C' and resid 654 through 658
      removed outlier: 3.525A  pdb=" N   LYS C 657 " --> pdb=" O   GLN C 654 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 662 through 669
    Processing helix  chain 'C' and resid 677 through 680
    Processing helix  chain 'C' and resid 681 through 688
      removed outlier: 4.158A  pdb=" N   TYR C 685 " --> pdb=" O   LEU C 681 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 698 through 714
      removed outlier: 4.086A  pdb=" N   ASP C 708 " --> pdb=" O   TYR C 704 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   VAL C 709 " --> pdb=" O   ALA C 705 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 717 through 725
      removed outlier: 3.636A  pdb=" N   ALA C 722 " --> pdb=" O   PHE C 718 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 726 through 728
      No H-bonds generated for 'chain 'C' and resid 726 through 728'
    Processing helix  chain 'C' and resid 729 through 743
    Processing helix  chain 'C' and resid 746 through 773
      removed outlier: 4.267A  pdb=" N   THR C 773 " --> pdb=" O   LYS C 769 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 780 through 787
      removed outlier: 3.548A  pdb=" N   LEU C 787 " --> pdb=" O   GLU C 783 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 788 through 790
      No H-bonds generated for 'chain 'C' and resid 788 through 790'
    Processing helix  chain 'C' and resid 793 through 801
    Processing helix  chain 'C' and resid 803 through 816
      removed outlier: 3.707A  pdb=" N   GLU C 814 " --> pdb=" O   LEU C 810 " (cutoff:3.500A)
    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 117 through 118
    Processing sheet with id=AA3, first strand: chain 'D' and resid 531 through 533
      removed outlier: 3.668A  pdb=" N   ILE D 576 " --> pdb=" O   PHE D 588 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   ILE D 556 " --> pdb=" O   ILE D 612 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   VAL D 614 " --> pdb=" O   ILE D 556 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   VAL D 558 " --> pdb=" O   VAL D 614 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   PHE D 637 " --> pdb=" O   VAL D 611 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   LYS D 613 " --> pdb=" O   PHE D 637 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 28 through 29
    Processing sheet with id=AA5, first strand: chain 'C' and resid 155 through 158
    Processing sheet with id=AA6, first strand: chain 'C' and resid 531 through 533
      removed outlier: 6.879A  pdb=" N   VAL C 558 " --> pdb=" O   VAL C 614 " (cutoff:3.500A)

    498 hydrogen bonds defined for protein.
    1443 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      74 hydrogen bonds
      140 hydrogen bond angles
      0 basepair planarities
      35 basepair parallelities
      55 stacking parallelities
  Total time for adding SS restraints: 1.34

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1261
        1.30 -     1.43: 2526
        1.43 -     1.56: 4491
        1.56 -     1.68: 174
        1.68 -     1.81: 30
  Bond restraints: 8482
  Sorted by residual:
  bond pdb=" C   LYS D 101 "
       pdb=" O   LYS D 101 "
    ideal  model  delta    sigma   weight residual
    1.237  1.175  0.061 1.19e-02 7.06e+03 2.65e+01
  bond pdb=" CA  LYS D 101 "
       pdb=" C   LYS D 101 "
    ideal  model  delta    sigma   weight residual
    1.524  1.476  0.047 1.29e-02 6.01e+03 1.33e+01
  bond pdb=" CA  LYS D 809 "
       pdb=" C   LYS D 809 "
    ideal  model  delta    sigma   weight residual
    1.523  1.474  0.049 1.37e-02 5.33e+03 1.27e+01
  bond pdb=" C   LYS D 809 "
       pdb=" O   LYS D 809 "
    ideal  model  delta    sigma   weight residual
    1.236  1.198  0.038 1.29e-02 6.01e+03 8.77e+00
  bond pdb=" N   LYS D 101 "
       pdb=" CA  LYS D 101 "
    ideal  model  delta    sigma   weight residual
    1.459  1.424  0.035 1.23e-02 6.61e+03 8.31e+00
  ... (remaining 8477 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.06: 11902
        3.06 -     6.12: 59
        6.12 -     9.17: 3
        9.17 -    12.23: 1
       12.23 -    15.29: 1
  Bond angle restraints: 11966
  Sorted by residual:
  angle pdb=" C3'   C E  33 "
        pdb=" C2'   C E  33 "
        pdb=" O2'   C E  33 "
      ideal   model   delta    sigma   weight residual
     110.70  125.99  -15.29 1.50e+00 4.44e-01 1.04e+02
  angle pdb=" O3'   C E  33 "
        pdb=" C3'   C E  33 "
        pdb=" C2'   C E  33 "
      ideal   model   delta    sigma   weight residual
     113.70  125.20  -11.50 1.50e+00 4.44e-01 5.87e+01
  angle pdb=" CA  LYS D 101 "
        pdb=" C   LYS D 101 "
        pdb=" N   ASP D 102 "
      ideal   model   delta    sigma   weight residual
     117.39  122.93   -5.54 1.24e+00 6.50e-01 2.00e+01
  angle pdb=" CA  LYS D 101 "
        pdb=" C   LYS D 101 "
        pdb=" O   LYS D 101 "
      ideal   model   delta    sigma   weight residual
     120.42  116.04    4.38 1.06e+00 8.90e-01 1.71e+01
  angle pdb=" C   LYS D 775 "
        pdb=" CA  LYS D 775 "
        pdb=" CB  LYS D 775 "
      ideal   model   delta    sigma   weight residual
     109.76  102.54    7.22 1.99e+00 2.53e-01 1.32e+01
  ... (remaining 11961 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.91: 4928
       35.91 -    71.82: 184
       71.82 -   107.73: 11
      107.73 -   143.64: 2
      143.64 -   179.55: 1
  Dihedral angle restraints: 5126
    sinusoidal: 2125
      harmonic: 3001
  Sorted by residual:
  dihedral pdb=" C4'   C F  33 "
           pdb=" C3'   C F  33 "
           pdb=" O3'   C F  33 "
           pdb=" P     U F  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.55 -179.55     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CA  LYS D 659 "
           pdb=" C   LYS D 659 "
           pdb=" N   TYR D 660 "
           pdb=" CA  TYR D 660 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.71  -19.29     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" C4'   C E  33 "
           pdb=" C3'   C E  33 "
           pdb=" O3'   C E  33 "
           pdb=" P     U E  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   90.90  129.10     1      3.50e+01 8.16e-04 1.28e+01
  ... (remaining 5123 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 1449
       0.089 -    0.178: 74
       0.178 -    0.267: 1
       0.267 -    0.356: 0
       0.356 -    0.444: 2
  Chirality restraints: 1526
  Sorted by residual:
  chirality pdb=" C2'   C E  33 "
            pdb=" C3'   C E  33 "
            pdb=" O2'   C E  33 "
            pdb=" C1'   C E  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.31   -0.44 2.00e-01 2.50e+01 4.94e+00
  chirality pdb=" C3'   C E  33 "
            pdb=" C4'   C E  33 "
            pdb=" O3'   C E  33 "
            pdb=" C2'   C E  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.10   -0.38 2.00e-01 2.50e+01 3.58e+00
  chirality pdb=" CA  HIS C  31 "
            pdb=" N   HIS C  31 "
            pdb=" C   HIS C  31 "
            pdb=" CB  HIS C  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.32e+00
  ... (remaining 1523 not shown)

  Planarity restraints: 1279
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U F   9 "   -0.042 2.00e-02 2.50e+03   2.37e-02 1.26e+01
        pdb=" N1    U F   9 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    U F   9 "   -0.000 2.00e-02 2.50e+03
        pdb=" O2    U F   9 "    0.036 2.00e-02 2.50e+03
        pdb=" N3    U F   9 "   -0.017 2.00e-02 2.50e+03
        pdb=" C4    U F   9 "   -0.006 2.00e-02 2.50e+03
        pdb=" O4    U F   9 "   -0.019 2.00e-02 2.50e+03
        pdb=" C5    U F   9 "    0.022 2.00e-02 2.50e+03
        pdb=" C6    U F   9 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A F  18 "    0.041 2.00e-02 2.50e+03   1.92e-02 1.01e+01
        pdb=" N9    A F  18 "   -0.008 2.00e-02 2.50e+03
        pdb=" C8    A F  18 "   -0.016 2.00e-02 2.50e+03
        pdb=" N7    A F  18 "   -0.012 2.00e-02 2.50e+03
        pdb=" C5    A F  18 "   -0.009 2.00e-02 2.50e+03
        pdb=" C6    A F  18 "   -0.006 2.00e-02 2.50e+03
        pdb=" N6    A F  18 "    0.039 2.00e-02 2.50e+03
        pdb=" N1    A F  18 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2    A F  18 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3    A F  18 "   -0.008 2.00e-02 2.50e+03
        pdb=" C4    A F  18 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G F   8 "   -0.039 2.00e-02 2.50e+03   1.73e-02 8.96e+00
        pdb=" N9    G F   8 "    0.018 2.00e-02 2.50e+03
        pdb=" C8    G F   8 "    0.024 2.00e-02 2.50e+03
        pdb=" N7    G F   8 "    0.012 2.00e-02 2.50e+03
        pdb=" C5    G F   8 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    G F   8 "   -0.010 2.00e-02 2.50e+03
        pdb=" O6    G F   8 "   -0.017 2.00e-02 2.50e+03
        pdb=" N1    G F   8 "   -0.006 2.00e-02 2.50e+03
        pdb=" C2    G F   8 "   -0.005 2.00e-02 2.50e+03
        pdb=" N2    G F   8 "    0.024 2.00e-02 2.50e+03
        pdb=" N3    G F   8 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4    G F   8 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1276 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.56: 51
        2.56 -     3.14: 6987
        3.14 -     3.73: 13378
        3.73 -     4.31: 16870
        4.31 -     4.90: 26225
  Nonbonded interactions: 63511
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C 153 "
            pdb=" OG1 THR C 154 "
     model   vdw
     1.970 3.040
  nonbonded pdb=" O2'   C E  36 "
            pdb=" OP1   A E  38 "
     model   vdw
     2.108 3.040
  nonbonded pdb=" O   THR D 773 "
            pdb=" NH1 ARG D 799 "
     model   vdw
     2.128 3.120
  nonbonded pdb=" O   ASP C 160 "
            pdb=" OD1 ASP C 160 "
     model   vdw
     2.148 3.040
  nonbonded pdb=" NE2 GLN C 139 "
            pdb=" OP1   A F  30 "
     model   vdw
     2.223 3.120
  ... (remaining 63506 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'C' and (resid 5 through 81 or resid 92 through 816))
  selection = (chain 'D' and (resid 5 through 31 or (resid 32 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 33 through 57 or (resid 58 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 59 through 148 or (resid 149 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 150 through 158 or \ 
 (resid 159 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 
0 through 394 or (resid 520 through 563 and (name N or name CA or name C or name \ 
 O or name CB )) or (resid 564 through 801 and (name N or name CA or name C or n \ 
ame O or name CB )) or resid 802 or (resid 803 through 816 and (name N or name C \ 
A or name C or name O or name CB ))))
}
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:             0.930
  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:                     9.300
  Find NCS groups from input model:        0.140
  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:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
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   0.061   8482  Z= 0.283
  Angle     :  0.743  15.288  11966  Z= 0.434
  Chirality :  0.043   0.444   1526
  Planarity :  0.004   0.060   1279
  Dihedral  : 17.667 179.553   3162
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 21.49 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.29 (0.26), residues: 1008
  helix:  0.78 (0.21), residues: 603
  sheet: -2.57 (0.54), residues: 62
  loop : -1.40 (0.31), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG C 120 
 TYR   0.014   0.002   TYR D  64 
 PHE   0.015   0.002   PHE C  60 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.006   0.001   HIS C 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 ( 8482)
  covalent geometry    : angle       0.74286 (11966)
  hydrogen bonds       : bond        0.16836 (  572)
  hydrogen bonds       : angle       6.85728 ( 1583)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: D  809 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7723 (mmtt)
  outliers start: 1
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1243
  time to fit residues: 13.8234
Evaluate side-chains
  74 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  809 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    8.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:   40.0000
   chunk 33 optimal weight:    0.0770
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:   20.0000
   chunk 100 optimal weight:   10.0000
   chunk 106 optimal weight:    8.9990
   overall best weight:    2.5942

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

Flipped N/Q/H residues before XYZ refinement:
B 720 ASN
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  48 GLN
D 128 GLN
C  82 HIS
C 128 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.131112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.094776 restraints weight = 21227.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 2.59
r_work: 0.3341 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8482  Z= 0.177
  Angle     :  0.535   6.766  11966  Z= 0.289
  Chirality :  0.038   0.207   1526
  Planarity :  0.004   0.063   1279
  Dihedral  : 15.688 161.416   2335
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 18.05 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  1.43 (0.27), residues: 1008
  helix:  2.18 (0.20), residues: 627
  sheet: -1.78 (0.64), residues: 54
  loop : -1.05 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 799 
 TYR   0.009   0.001   TYR C  64 
 PHE   0.017   0.002   PHE D  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.004   0.001   HIS C 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 8482)
  covalent geometry    : angle       0.53461 (11966)
  hydrogen bonds       : bond        0.04513 (  572)
  hydrogen bonds       : angle       4.57818 ( 1583)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  739 GLU cc_start: 0.8251 (tm-30) cc_final: 0.8011 (mm-30)
REVERT: C  126 ARG cc_start: 0.8314 (tmm-80) cc_final: 0.7947 (tmm-80)
  outliers start: 14
  outliers final: 7
  residues processed: 95
  average time/residue: 0.1106
  time to fit residues: 13.8553
Evaluate side-chains
  83 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  119 VAL
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   82 HIS
Chi-restraints excluded: chain C residue  119 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 106 optimal weight:   10.0000
   chunk 28 optimal weight:   40.0000
   chunk 19 optimal weight:    2.9990
   chunk 35 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 61 optimal weight:    0.4980
   chunk 39 optimal weight:   10.0000
   chunk 57 optimal weight:    0.7980
   chunk 37 optimal weight:   40.0000
   chunk 24 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 735 GLN
C  82 HIS
C 139 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.131513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.096329 restraints weight = 20895.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 2.62
r_work: 0.3379 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8482  Z= 0.116
  Angle     :  0.463   6.346  11966  Z= 0.249
  Chirality :  0.036   0.199   1526
  Planarity :  0.003   0.050   1279
  Dihedral  : 15.591 160.416   2331
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 19.20 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  2.29 (0.27), residues: 1008
  helix:  2.78 (0.20), residues: 634
  sheet: -1.62 (0.63), residues: 60
  loop : -0.53 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 799 
 TYR   0.008   0.001   TYR D   6 
 PHE   0.015   0.002   PHE D  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.004   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 8482)
  covalent geometry    : angle       0.46275 (11966)
  hydrogen bonds       : bond        0.03628 (  572)
  hydrogen bonds       : angle       4.04350 ( 1583)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  739 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7948 (mm-30)
REVERT: B  735 GLN cc_start: 0.8318 (mm-40) cc_final: 0.8091 (mm-40)
REVERT: B  739 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7979 (tp30)
REVERT: D  158 THR cc_start: 0.8293 (m) cc_final: 0.7775 (p)
REVERT: C  126 ARG cc_start: 0.8286 (tmm-80) cc_final: 0.7726 (tmm-80)
  outliers start: 9
  outliers final: 5
  residues processed: 88
  average time/residue: 0.1112
  time to fit residues: 12.8958
Evaluate side-chains
  79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  737 LEU
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  123 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 45 optimal weight:    8.9990
   chunk 56 optimal weight:    0.8980
   chunk 64 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9990
   chunk 29 optimal weight:   50.0000
   chunk 34 optimal weight:   10.0000
   chunk 85 optimal weight:   10.0000
   chunk 46 optimal weight:   30.0000
   chunk 26 optimal weight:   30.0000
   chunk 103 optimal weight:   10.0000
   chunk 10 optimal weight:    0.5980
   overall best weight:    3.6986

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

Flipped N/Q/H residues before XYZ refinement:
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.128902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.095670 restraints weight = 21159.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 3.15
r_work: 0.3278 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.2658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8482  Z= 0.228
  Angle     :  0.564   6.646  11966  Z= 0.304
  Chirality :  0.040   0.197   1526
  Planarity :  0.004   0.054   1279
  Dihedral  : 16.063 160.769   2331
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.07 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 19.77 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  1.89 (0.27), residues: 1008
  helix:  2.35 (0.20), residues: 638
  sheet: -1.71 (0.62), residues: 59
  loop : -0.47 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 120 
 TYR   0.013   0.002   TYR C  80 
 PHE   0.018   0.003   PHE C  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.003   0.001   HIS C 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 8482)
  covalent geometry    : angle       0.56357 (11966)
  hydrogen bonds       : bond        0.04721 (  572)
  hydrogen bonds       : angle       4.46749 ( 1583)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  735 GLN cc_start: 0.8352 (mm-40) cc_final: 0.8140 (mm-40)
REVERT: B  739 GLU cc_start: 0.8516 (tm-30) cc_final: 0.7989 (tp30)
REVERT: C   12 MET cc_start: 0.8924 (mmm) cc_final: 0.8440 (tpt)
REVERT: C  126 ARG cc_start: 0.8590 (tmm-80) cc_final: 0.7885 (tmm-80)
  outliers start: 16
  outliers final: 13
  residues processed: 87
  average time/residue: 0.0998
  time to fit residues: 11.7997
Evaluate side-chains
  85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain D residue  106 ASN
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  119 VAL
Chi-restraints excluded: chain D residue  149 MET
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  159 ASP
Chi-restraints excluded: chain D residue  780 SER
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   64 TYR
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  125 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 109 optimal weight:    9.9990
   chunk 26 optimal weight:   30.0000
   chunk 72 optimal weight:    0.9990
   chunk 39 optimal weight:    8.9990
   chunk 31 optimal weight:    0.0050
   chunk 6 optimal weight:   20.0000
   chunk 56 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.7998

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

Flipped N/Q/H residues before XYZ refinement:
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.132244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.098770 restraints weight = 21289.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 3.00
r_work: 0.3362 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.3069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8482  Z= 0.096
  Angle     :  0.441   8.551  11966  Z= 0.234
  Chirality :  0.035   0.173   1526
  Planarity :  0.002   0.034   1279
  Dihedral  : 15.737 161.987   2331
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 22.64 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  2.59 (0.27), residues: 1008
  helix:  2.88 (0.20), residues: 641
  sheet: -1.56 (0.64), residues: 61
  loop : -0.11 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 120 
 TYR   0.006   0.001   TYR C  64 
 PHE   0.012   0.001   PHE D  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.001   0.000   HIS D 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00193 ( 8482)
  covalent geometry    : angle       0.44145 (11966)
  hydrogen bonds       : bond        0.03241 (  572)
  hydrogen bonds       : angle       3.74881 ( 1583)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
REVERT: B  739 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7962 (tp30)
REVERT: D  109 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8041 (mm)
REVERT: C  106 ASN cc_start: 0.7998 (t0) cc_final: 0.7738 (t0)
REVERT: C  126 ARG cc_start: 0.8389 (tmm-80) cc_final: 0.7616 (ttt-90)
  outliers start: 6
  outliers final: 3
  residues processed: 84
  average time/residue: 0.1003
  time to fit residues: 11.5214
Evaluate side-chains
  80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  123 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 109 optimal weight:   10.0000
   chunk 83 optimal weight:    8.9990
   chunk 102 optimal weight:   10.0000
   chunk 77 optimal weight:   50.0000
   chunk 100 optimal weight:    8.9990
   chunk 38 optimal weight:   30.0000
   chunk 39 optimal weight:   20.0000
   chunk 99 optimal weight:    0.2980
   chunk 79 optimal weight:   40.0000
   chunk 17 optimal weight:    5.9990
   chunk 74 optimal weight:   50.0000
   overall best weight:    6.8590

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

Flipped N/Q/H residues before XYZ refinement:
B 721 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.127790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.093950 restraints weight = 21233.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 3.43
r_work: 0.3253 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.3333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.074   8482  Z= 0.391
  Angle     :  0.718  10.088  11966  Z= 0.381
  Chirality :  0.045   0.201   1526
  Planarity :  0.005   0.069   1279
  Dihedral  : 16.386 162.849   2331
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.46 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 20.92 %
    Favored  : 74.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  1.37 (0.27), residues: 1008
  helix:  1.87 (0.20), residues: 639
  sheet: -1.63 (0.67), residues: 53
  loop : -0.59 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  10 
 TYR   0.018   0.003   TYR C 103 
 PHE   0.036   0.004   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.006   0.001   HIS C 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00856 ( 8482)
  covalent geometry    : angle       0.71829 (11966)
  hydrogen bonds       : bond        0.05726 (  572)
  hydrogen bonds       : angle       4.88772 ( 1583)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A  738 GLU cc_start: 0.7840 (pp20) cc_final: 0.7502 (pp20)
REVERT: B  739 GLU cc_start: 0.8526 (tm-30) cc_final: 0.7969 (tp30)
REVERT: D  109 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8204 (mm)
REVERT: C  143 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8034 (mt-10)
  outliers start: 16
  outliers final: 12
  residues processed: 82
  average time/residue: 0.0924
  time to fit residues: 10.6225
Evaluate side-chains
  78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue  106 ASN
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  119 VAL
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  159 ASP
Chi-restraints excluded: chain D residue  793 THR
Chi-restraints excluded: chain C residue   64 TYR
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  143 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 49 optimal weight:    0.7980
   chunk 55 optimal weight:    6.9990
   chunk 81 optimal weight:   20.0000
   chunk 66 optimal weight:    0.9980
   chunk 87 optimal weight:    0.4980
   chunk 73 optimal weight:    0.2980
   chunk 74 optimal weight:   20.0000
   chunk 36 optimal weight:   20.0000
   chunk 63 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.7182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.133172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.101293 restraints weight = 20976.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 3.20
r_work: 0.3369 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.3542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8482  Z= 0.100
  Angle     :  0.477  10.641  11966  Z= 0.249
  Chirality :  0.035   0.171   1526
  Planarity :  0.003   0.038   1279
  Dihedral  : 15.857 163.985   2331
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.78 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 22.64 %
    Favored  : 74.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  2.41 (0.27), residues: 1008
  helix:  2.68 (0.20), residues: 643
  sheet: -1.44 (0.65), residues: 56
  loop : -0.13 (0.37), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D  47 
 TYR   0.007   0.001   TYR D   6 
 PHE   0.023   0.002   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.005   0.001   HIS C 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 8482)
  covalent geometry    : angle       0.47717 (11966)
  hydrogen bonds       : bond        0.03356 (  572)
  hydrogen bonds       : angle       3.81650 ( 1583)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.260 
Fit side-chains
REVERT: B  739 GLU cc_start: 0.8504 (tm-30) cc_final: 0.7988 (tp30)
REVERT: D  109 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8087 (mm)
REVERT: C   73 ASP cc_start: 0.8022 (t70) cc_final: 0.7796 (t70)
REVERT: C  106 ASN cc_start: 0.7927 (t0) cc_final: 0.7685 (t0)
REVERT: C  126 ARG cc_start: 0.8468 (tmm-80) cc_final: 0.7721 (ptm-80)
  outliers start: 10
  outliers final: 6
  residues processed: 79
  average time/residue: 0.0932
  time to fit residues: 10.2085
Evaluate side-chains
  78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  119 VAL
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain C residue  119 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 103 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 50 optimal weight:   20.0000
   chunk 107 optimal weight:   10.0000
   chunk 94 optimal weight:   50.0000
   chunk 84 optimal weight:    1.9990
   chunk 83 optimal weight:   20.0000
   chunk 36 optimal weight:    0.3980
   chunk 67 optimal weight:    1.9990
   chunk 58 optimal weight:    0.3980
   overall best weight:    1.1584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.132449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.100870 restraints weight = 21245.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 3.11
r_work: 0.3364 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.3717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.062   8482  Z= 0.111
  Angle     :  0.477  10.133  11966  Z= 0.250
  Chirality :  0.035   0.163   1526
  Planarity :  0.003   0.038   1279
  Dihedral  : 15.662 165.747   2331
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.17 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 22.64 %
    Favored  : 74.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  2.71 (0.27), residues: 1008
  helix:  2.89 (0.20), residues: 644
  sheet: -1.21 (0.65), residues: 56
  loop : -0.02 (0.38), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 120 
 TYR   0.007   0.001   TYR C  64 
 PHE   0.017   0.002   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.003   0.001   HIS C 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 8482)
  covalent geometry    : angle       0.47735 (11966)
  hydrogen bonds       : bond        0.03137 (  572)
  hydrogen bonds       : angle       3.66851 ( 1583)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.368 
Fit side-chains
REVERT: B  739 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7909 (tp30)
REVERT: D  109 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8066 (mm)
REVERT: C   95 ASP cc_start: 0.7958 (t70) cc_final: 0.7725 (t0)
REVERT: C  106 ASN cc_start: 0.7988 (t0) cc_final: 0.7765 (t0)
REVERT: C  126 ARG cc_start: 0.8511 (tmm-80) cc_final: 0.7643 (ttt-90)
  outliers start: 10
  outliers final: 7
  residues processed: 85
  average time/residue: 0.0969
  time to fit residues: 11.3136
Evaluate side-chains
  83 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  119 VAL
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  123 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 89 optimal weight:   40.0000
   chunk 36 optimal weight:    9.9990
   chunk 56 optimal weight:    1.9990
   chunk 38 optimal weight:   30.0000
   chunk 43 optimal weight:    7.9990
   chunk 8 optimal weight:    0.8980
   chunk 96 optimal weight:   20.0000
   chunk 62 optimal weight:    0.7980
   chunk 84 optimal weight:   10.0000
   chunk 12 optimal weight:    0.0030
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.9394

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.133859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.103444 restraints weight = 21445.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 3.10
r_work: 0.3395 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.3941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.056   8482  Z= 0.104
  Angle     :  0.472  10.777  11966  Z= 0.247
  Chirality :  0.035   0.161   1526
  Planarity :  0.003   0.037   1279
  Dihedral  : 15.576 165.464   2331
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 24.07 %
    Favored  : 73.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  2.89 (0.27), residues: 1008
  helix:  3.02 (0.20), residues: 643
  sheet: -0.93 (0.68), residues: 56
  loop :  0.05 (0.38), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 736 
 TYR   0.007   0.001   TYR D   6 
 PHE   0.015   0.001   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.002   0.000   HIS C 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 8482)
  covalent geometry    : angle       0.47203 (11966)
  hydrogen bonds       : bond        0.02925 (  572)
  hydrogen bonds       : angle       3.52203 ( 1583)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.277 
Fit side-chains
REVERT: B  739 GLU cc_start: 0.8428 (tm-30) cc_final: 0.7913 (tp30)
REVERT: D  109 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8055 (mm)
REVERT: D  149 MET cc_start: 0.7341 (mmt) cc_final: 0.7078 (mmt)
REVERT: D  158 THR cc_start: 0.8363 (m) cc_final: 0.7988 (p)
REVERT: C  106 ASN cc_start: 0.7947 (t0) cc_final: 0.7738 (t0)
REVERT: C  126 ARG cc_start: 0.8468 (tmm-80) cc_final: 0.7570 (ttt-90)
  outliers start: 8
  outliers final: 6
  residues processed: 86
  average time/residue: 0.0917
  time to fit residues: 10.9351
Evaluate side-chains
  84 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  123 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 3 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   chunk 73 optimal weight:   50.0000
   chunk 45 optimal weight:   30.0000
   chunk 92 optimal weight:   10.0000
   chunk 30 optimal weight:   20.0000
   chunk 70 optimal weight:    0.6980
   chunk 33 optimal weight:   40.0000
   chunk 11 optimal weight:    0.5980
   chunk 98 optimal weight:   20.0000
   overall best weight:    3.2584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.130649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.098186 restraints weight = 21271.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 3.31
r_work: 0.3310 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.3859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8482  Z= 0.198
  Angle     :  0.553  10.453  11966  Z= 0.291
  Chirality :  0.038   0.178   1526
  Planarity :  0.004   0.066   1279
  Dihedral  : 15.748 163.387   2331
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.47 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 24.64 %
    Favored  : 73.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.50 (0.27), residues: 1008
  helix:  2.71 (0.20), residues: 644
  sheet: -0.93 (0.69), residues: 56
  loop : -0.14 (0.38), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 120 
 TYR   0.010   0.001   TYR C  80 
 PHE   0.024   0.003   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.004   0.001   HIS C 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 8482)
  covalent geometry    : angle       0.55266 (11966)
  hydrogen bonds       : bond        0.03962 (  572)
  hydrogen bonds       : angle       3.93004 ( 1583)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.258 
Fit side-chains
REVERT: B  739 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7904 (tp30)
REVERT: D  109 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8119 (mm)
REVERT: C  106 ASN cc_start: 0.7926 (t0) cc_final: 0.7670 (t0)
REVERT: C  126 ARG cc_start: 0.8642 (tmm-80) cc_final: 0.7831 (tmm-80)
  outliers start: 8
  outliers final: 7
  residues processed: 78
  average time/residue: 0.0923
  time to fit residues: 10.0123
Evaluate side-chains
  78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  119 VAL
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  123 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 88 optimal weight:    9.9990
   chunk 76 optimal weight:   10.0000
   chunk 38 optimal weight:   30.0000
   chunk 52 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 90 optimal weight:    0.0040
   chunk 79 optimal weight:   20.0000
   chunk 3 optimal weight:   10.0000
   chunk 36 optimal weight:   40.0000
   chunk 78 optimal weight:    9.9990
   chunk 47 optimal weight:   40.0000
   overall best weight:    5.0000

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.128047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.095388 restraints weight = 21348.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 3.27
r_work: 0.3259 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.4042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065   8482  Z= 0.291
  Angle     :  0.650   8.688  11966  Z= 0.348
  Chirality :  0.041   0.191   1526
  Planarity :  0.004   0.047   1279
  Dihedral  : 16.239 161.127   2331
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.97 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 23.78 %
    Favored  : 73.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  1.69 (0.27), residues: 1008
  helix:  2.06 (0.20), residues: 644
  sheet: -1.21 (0.68), residues: 56
  loop : -0.40 (0.37), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 120 
 TYR   0.017   0.002   TYR C 103 
 PHE   0.027   0.004   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.006   0.002   HIS C 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00643 ( 8482)
  covalent geometry    : angle       0.65027 (11966)
  hydrogen bonds       : bond        0.05009 (  572)
  hydrogen bonds       : angle       4.47598 ( 1583)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2286.93 seconds
wall clock time: 39 minutes 45.68 seconds (2385.68 seconds total)