Starting phenix.real_space_refine
on Tue Mar  3 15:24:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kfz_22857/03_2026/7kfz_22857.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kfz_22857/03_2026/7kfz_22857.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kfz_22857/03_2026/7kfz_22857.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kfz_22857/03_2026/7kfz_22857.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kfz_22857/03_2026/7kfz_22857.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kfz_22857/03_2026/7kfz_22857.map"
  }
  resolution = 3.47
  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: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      27      5.16       5
     C    4176      2.51       5
     N    1134      2.21       5
     O    1251      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 55 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6592
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 168, 1345
          Classifications: {'peptide': 168}
          Link IDs: {'PTRANS': 4, 'TRANS': 163}
    Chain: "B"
      Number of atoms: 3877
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 467, 3877
          Classifications: {'peptide': 467}
          Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 434}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 168, 1337
          Classifications: {'peptide': 168}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 163}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "C"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GNP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.38, per 1000 atoms: 0.21
  Number of scatterers: 6592
  At special positions: 0
  Unit cell: (73.485, 100.11, 124.605, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      27     16.00
     P       3     15.00
     Mg      1     11.99
     O    1251      8.00
     N    1134      7.00
     C    4176      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: 0.53
  Conformation dependent library (CDL) restraints added in 209.7 milliseconds
  

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1538

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 4 sheets defined
      59.2% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 25
      removed outlier: 3.715A  pdb=" N   LEU A  19 " --> pdb=" O   GLY A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 39
    Processing helix  chain 'A' and resid 60 through 66
      removed outlier: 4.461A  pdb=" N   GLU A  63 " --> pdb=" O   GLY A  60 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   SER A  65 " --> pdb=" O   GLU A  62 " (cutoff:3.500A)
      removed outlier: 5.404A  pdb=" N   ALA A  66 " --> pdb=" O   GLU A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 75
      removed outlier: 3.864A  pdb=" N   THR A  74 " --> pdb=" O   GLN A  70 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   GLY A  75 " --> pdb=" O   TYR A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 92
      removed outlier: 3.708A  pdb=" N   GLU A  91 " --> pdb=" O   THR A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 105
    Processing helix  chain 'A' and resid 126 through 138
    Processing helix  chain 'A' and resid 151 through 168
    Processing helix  chain 'B' and resid 575 through 579
      removed outlier: 3.556A  pdb=" N   ALA B 578 " --> pdb=" O   TYR B 575 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 605 through 614
    Processing helix  chain 'B' and resid 620 through 631
      removed outlier: 3.740A  pdb=" N   VAL B 624 " --> pdb=" O   ASP B 620 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ARG B 625 " --> pdb=" O   PRO B 621 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   THR B 630 " --> pdb=" O   THR B 626 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 636 through 649
    Processing helix  chain 'B' and resid 656 through 666
    Processing helix  chain 'B' and resid 671 through 681
      removed outlier: 3.700A  pdb=" N   ARG B 676 " --> pdb=" O   ALA B 672 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LYS B 679 " --> pdb=" O   LYS B 675 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 681 through 699
      removed outlier: 3.550A  pdb=" N   LEU B 690 " --> pdb=" O   GLN B 686 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 701 through 707
    Processing helix  chain 'B' and resid 707 through 721
      removed outlier: 3.558A  pdb=" N   LEU B 711 " --> pdb=" O   ASP B 707 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLN B 712 " --> pdb=" O   ALA B 708 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 728 through 743
      removed outlier: 3.810A  pdb=" N   ILE B 742 " --> pdb=" O   GLN B 738 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA B 743 " --> pdb=" O   ARG B 739 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 770 through 774
      removed outlier: 3.522A  pdb=" N   PHE B 774 " --> pdb=" O   ILE B 771 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 780 through 798
    Processing helix  chain 'B' and resid 800 through 804
    Processing helix  chain 'B' and resid 807 through 811
    Processing helix  chain 'B' and resid 813 through 818
    Processing helix  chain 'B' and resid 818 through 842
      removed outlier: 3.625A  pdb=" N   THR B 842 " --> pdb=" O   CYS B 838 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 844 through 865
    Processing helix  chain 'B' and resid 867 through 879
      removed outlier: 3.735A  pdb=" N   SER B 876 " --> pdb=" O   LEU B 872 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   ALA B 877 " --> pdb=" O   GLU B 873 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 880 through 885
      removed outlier: 3.917A  pdb=" N   ARG B 885 " --> pdb=" O   SER B 881 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 886 through 892
      removed outlier: 3.502A  pdb=" N   PHE B 890 " --> pdb=" O   LEU B 886 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLU B 891 " --> pdb=" O   ASP B 887 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   GLN B 892 " --> pdb=" O   HIS B 888 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 886 through 892'
    Processing helix  chain 'B' and resid 894 through 906
    Processing helix  chain 'B' and resid 908 through 920
      removed outlier: 3.806A  pdb=" N   TYR B 912 " --> pdb=" O   SER B 908 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS B 913 " --> pdb=" O   GLU B 909 " (cutoff:3.500A)
      removed outlier: 5.440A  pdb=" N   LYS B 914 " --> pdb=" O   ASP B 910 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   TYR B 915 " --> pdb=" O   HIS B 911 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 929 through 944
      removed outlier: 4.112A  pdb=" N   TYR B 933 " --> pdb=" O   PHE B 929 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LYS B 939 " --> pdb=" O   THR B 935 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 958 through 976
      removed outlier: 3.811A  pdb=" N   GLN B 972 " --> pdb=" O   THR B 968 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLN B 973 " --> pdb=" O   GLY B 969 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   TYR B 974 " --> pdb=" O   GLU B 970 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASN B 976 " --> pdb=" O   GLN B 972 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 984 through 993
    Processing helix  chain 'B' and resid 1001 through 1017
    Processing helix  chain 'C' and resid 15 through 26
    Processing helix  chain 'C' and resid 67 through 75
      removed outlier: 3.742A  pdb=" N   TYR C  71 " --> pdb=" O   MET C  67 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ARG C  73 " --> pdb=" O   ASP C  69 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   THR C  74 " --> pdb=" O   GLN C  70 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 105
      removed outlier: 3.763A  pdb=" N   PHE C  90 " --> pdb=" O   ASN C  86 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLU C  91 " --> pdb=" O   THR C  87 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ILE C  93 " --> pdb=" O   SER C  89 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   HIS C  94 " --> pdb=" O   PHE C  90 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   HIS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 126 through 138
    Processing helix  chain 'C' and resid 151 through 168
      removed outlier: 3.581A  pdb=" N   PHE C 156 " --> pdb=" O   VAL C 152 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   TYR C 157 " --> pdb=" O   ASP C 153 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 46
      removed outlier: 6.662A  pdb=" N   TYR A   4 " --> pdb=" O   ASP A  54 " (cutoff:3.500A)
      removed outlier: 7.406A  pdb=" N   LEU A  56 " --> pdb=" O   TYR A   4 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   LEU A   6 " --> pdb=" O   LEU A  56 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   PHE A  78 " --> pdb=" O   VAL A 112 " (cutoff:3.500A)
      removed outlier: 7.310A  pdb=" N   VAL A 114 " --> pdb=" O   PHE A  78 " (cutoff:3.500A)
      removed outlier: 5.939A  pdb=" N   CYS A  80 " --> pdb=" O   VAL A 114 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   ASN A 116 " --> pdb=" O   CYS A  80 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   PHE A  82 " --> pdb=" O   ASN A 116 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 586 through 589
      removed outlier: 6.443A  pdb=" N   ILE B 587 " --> pdb=" O   LYS B 602 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   ILE B 600 " --> pdb=" O   GLU B 589 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 4
      removed outlier: 6.649A  pdb=" N   THR C   2 " --> pdb=" O   LEU C  52 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   ASP C  54 " --> pdb=" O   THR C   2 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   TYR C   4 " --> pdb=" O   ASP C  54 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   LEU C  56 " --> pdb=" O   TYR C   4 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 2 through 4
      removed outlier: 6.649A  pdb=" N   THR C   2 " --> pdb=" O   LEU C  52 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   ASP C  54 " --> pdb=" O   THR C   2 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   TYR C   4 " --> pdb=" O   ASP C  54 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   LEU C  56 " --> pdb=" O   TYR C   4 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   LEU C   6 " --> pdb=" O   LEU C  56 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   PHE C  78 " --> pdb=" O   VAL C 112 " (cutoff:3.500A)
      removed outlier: 7.627A  pdb=" N   VAL C 114 " --> pdb=" O   PHE C  78 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   CYS C  80 " --> pdb=" O   VAL C 114 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   ASN C 116 " --> pdb=" O   CYS C  80 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   PHE C  82 " --> pdb=" O   ASN C 116 " (cutoff:3.500A)

    314 hydrogen bonds defined for protein.
    903 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.68

  Time building geometry restraints manager: 0.63 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1862
        1.33 -     1.45: 1020
        1.45 -     1.57: 3799
        1.57 -     1.68: 3
        1.68 -     1.80: 44
  Bond restraints: 6728
  Sorted by residual:
  bond pdb=" N3B GNP C 201 "
       pdb=" PG  GNP C 201 "
    ideal  model  delta    sigma   weight residual
    1.801  1.689  0.112 2.00e-02 2.50e+03 3.12e+01
  bond pdb=" O5' GNP C 201 "
       pdb=" PA  GNP C 201 "
    ideal  model  delta    sigma   weight residual
    1.660  1.548  0.112 2.00e-02 2.50e+03 3.12e+01
  bond pdb=" N3B GNP C 201 "
       pdb=" PB  GNP C 201 "
    ideal  model  delta    sigma   weight residual
    1.681  1.621  0.060 2.00e-02 2.50e+03 9.10e+00
  bond pdb=" O3A GNP C 201 "
       pdb=" PB  GNP C 201 "
    ideal  model  delta    sigma   weight residual
    1.687  1.631  0.056 2.00e-02 2.50e+03 7.72e+00
  bond pdb=" N   ILE C 163 "
       pdb=" CA  ILE C 163 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.19e-02 7.06e+03 7.65e+00
  ... (remaining 6723 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.15: 8869
        2.15 -     4.30: 202
        4.30 -     6.46: 22
        6.46 -     8.61: 3
        8.61 -    10.76: 5
  Bond angle restraints: 9101
  Sorted by residual:
  angle pdb=" N3B GNP C 201 "
        pdb=" PB  GNP C 201 "
        pdb=" O3A GNP C 201 "
      ideal   model   delta    sigma   weight residual
     100.48  111.12  -10.64 3.00e+00 1.11e-01 1.26e+01
  angle pdb=" PB  GNP C 201 "
        pdb=" N3B GNP C 201 "
        pdb=" PG  GNP C 201 "
      ideal   model   delta    sigma   weight residual
     123.35  113.90    9.45 3.00e+00 1.11e-01 9.92e+00
  angle pdb=" O1B GNP C 201 "
        pdb=" PB  GNP C 201 "
        pdb=" O2B GNP C 201 "
      ideal   model   delta    sigma   weight residual
     119.66  110.34    9.32 3.00e+00 1.11e-01 9.66e+00
  angle pdb=" CA  LEU A  23 "
        pdb=" CB  LEU A  23 "
        pdb=" CG  LEU A  23 "
      ideal   model   delta    sigma   weight residual
     116.30  105.54   10.76 3.50e+00 8.16e-02 9.45e+00
  angle pdb=" N   PRO B 925 "
        pdb=" CA  PRO B 925 "
        pdb=" C   PRO B 925 "
      ideal   model   delta    sigma   weight residual
     112.47  106.25    6.22 2.06e+00 2.36e-01 9.12e+00
  ... (remaining 9096 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.90: 3674
       15.90 -    31.80: 362
       31.80 -    47.69: 76
       47.69 -    63.59: 18
       63.59 -    79.49: 9
  Dihedral angle restraints: 4139
    sinusoidal: 1770
      harmonic: 2369
  Sorted by residual:
  dihedral pdb=" CA  PRO B 924 "
           pdb=" C   PRO B 924 "
           pdb=" N   PRO B 925 "
           pdb=" CA  PRO B 925 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  113.20   66.80     0      5.00e+00 4.00e-02 1.78e+02
  dihedral pdb=" CA  CYS B 926 "
           pdb=" C   CYS B 926 "
           pdb=" N   VAL B 927 "
           pdb=" CA  VAL B 927 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.92   18.08     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CA  ASN B 923 "
           pdb=" C   ASN B 923 "
           pdb=" N   PRO B 924 "
           pdb=" CA  PRO B 924 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.04  -17.96     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 4136 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 490
       0.039 -    0.077: 376
       0.077 -    0.116: 116
       0.116 -    0.154: 18
       0.154 -    0.193: 4
  Chirality restraints: 1004
  Sorted by residual:
  chirality pdb=" C2' GNP C 201 "
            pdb=" C1' GNP C 201 "
            pdb=" C3' GNP C 201 "
            pdb=" O2' GNP C 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.74    0.19 2.00e-01 2.50e+01 9.31e-01
  chirality pdb=" CA  ILE C 163 "
            pdb=" N   ILE C 163 "
            pdb=" C   ILE C 163 "
            pdb=" CB  ILE C 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.46e-01
  chirality pdb=" CB  VAL B 840 "
            pdb=" CA  VAL B 840 "
            pdb=" CG1 VAL B 840 "
            pdb=" CG2 VAL B 840 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 6.96e-01
  ... (remaining 1001 not shown)

  Planarity restraints: 1176
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 924 "   -0.062 5.00e-02 4.00e+02   9.23e-02 1.36e+01
        pdb=" N   PRO B 925 "    0.160 5.00e-02 4.00e+02
        pdb=" CA  PRO B 925 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO B 925 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 930 "   -0.019 2.00e-02 2.50e+03   1.50e-02 3.95e+00
        pdb=" CG  PHE B 930 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 930 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 930 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 930 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 930 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 930 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 923 "   -0.028 5.00e-02 4.00e+02   4.25e-02 2.88e+00
        pdb=" N   PRO B 924 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B 924 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 924 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1173 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 27
        2.50 -     3.10: 4830
        3.10 -     3.70: 9801
        3.70 -     4.30: 14713
        4.30 -     4.90: 24663
  Nonbonded interactions: 54034
  Sorted by model distance:
  nonbonded pdb=" OG  SER C  17 "
            pdb="MG    MG C 202 "
     model   vdw
     1.897 2.170
  nonbonded pdb=" OG1 THR C  35 "
            pdb="MG    MG C 202 "
     model   vdw
     1.994 2.170
  nonbonded pdb=" O1G GNP C 201 "
            pdb="MG    MG C 202 "
     model   vdw
     2.123 2.170
  nonbonded pdb=" OE2 GLU B 783 "
            pdb=" NE2 GLN B 787 "
     model   vdw
     2.188 3.120
  nonbonded pdb=" O   VAL C   8 "
            pdb=" OG1 THR C  58 "
     model   vdw
     2.223 3.040
  ... (remaining 54029 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 1 through 30 or (resid 31 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 32 through 167 or (resid 168 and (name N or na \ 
me CA or name C or name O or name CB ))))
  selection = (chain 'C' and resid 1 through 168)
}

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:             0.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     6.440
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
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      :  0.012   0.112   6728  Z= 0.490
  Angle     :  0.805  10.759   9101  Z= 0.430
  Chirality :  0.053   0.193   1004
  Planarity :  0.005   0.092   1176
  Dihedral  : 13.579  79.491   2601
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    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: -1.10 (0.28), residues: 793
  helix: -1.10 (0.25), residues: 390
  sheet: -0.69 (0.52), residues: 85
  loop :  0.10 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 135 
 TYR   0.014   0.002   TYR B 615 
 PHE   0.034   0.002   PHE B 930 
 TRP   0.014   0.002   TRP B 729 
 HIS   0.005   0.001   HIS B 888 

Details of bonding type rmsd
  covalent geometry    : bond        0.01177 ( 6728)
  covalent geometry    : angle       0.80473 ( 9101)
  hydrogen bonds       : bond        0.26240 (  314)
  hydrogen bonds       : angle       8.78090 (  903)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.6418 (ttm) cc_final: 0.5883 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.0887
  time to fit residues: 6.2467
Evaluate side-chains
  24 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0020
   chunk 61 optimal weight:    0.0970
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.6390

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

Flipped N/Q/H residues before XYZ refinement:
B 566 GLN
** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 869 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.034417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2417 r_free = 0.2417 target = 0.026104 restraints weight = 37473.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.2421 rms_B_bonded: 4.60
r_work (final): 0.2421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.1968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6728  Z= 0.129
  Angle     :  0.537   7.608   9101  Z= 0.284
  Chirality :  0.041   0.203   1004
  Planarity :  0.004   0.075   1176
  Dihedral  :  5.417  59.535    915
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  5.33 %
    Favored  : 93.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    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:  0.31 (0.29), residues: 793
  helix:  0.50 (0.26), residues: 403
  sheet: -0.72 (0.50), residues: 88
  loop :  0.37 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  97 
 TYR   0.025   0.001   TYR A 157 
 PHE   0.012   0.001   PHE B 588 
 TRP   0.006   0.001   TRP B 729 
 HIS   0.002   0.001   HIS A  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6728)
  covalent geometry    : angle       0.53741 ( 9101)
  hydrogen bonds       : bond        0.04601 (  314)
  hydrogen bonds       : angle       4.75132 (  903)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.9117 (ttm) cc_final: 0.8777 (ttp)
REVERT: C   41 ARG cc_start: 0.8749 (ttm-80) cc_final: 0.8534 (ttm-80)
REVERT: C   72 MET cc_start: 0.9211 (mtt) cc_final: 0.8940 (mtt)
REVERT: C   93 ILE cc_start: 0.9823 (mm) cc_final: 0.9621 (mm)
  outliers start: 5
  outliers final: 1
  residues processed: 38
  average time/residue: 0.0662
  time to fit residues: 3.8342
Evaluate side-chains
  25 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   71 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 53 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9990
   chunk 73 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 12 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  27 HIS
C 131 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.034051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2420 r_free = 0.2420 target = 0.025446 restraints weight = 38738.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.2395 rms_B_bonded: 4.56
r_work (final): 0.2395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.2505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6728  Z= 0.134
  Angle     :  0.484   6.988   9101  Z= 0.251
  Chirality :  0.040   0.136   1004
  Planarity :  0.004   0.076   1176
  Dihedral  :  4.944  59.466    915
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  6.01 %
    Favored  : 93.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    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:  1.12 (0.30), residues: 793
  helix:  1.24 (0.26), residues: 402
  sheet: -0.29 (0.50), residues: 88
  loop :  0.61 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 149 
 TYR   0.014   0.001   TYR A 157 
 PHE   0.008   0.001   PHE C  78 
 TRP   0.008   0.001   TRP B 729 
 HIS   0.002   0.001   HIS B 911 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6728)
  covalent geometry    : angle       0.48353 ( 9101)
  hydrogen bonds       : bond        0.03619 (  314)
  hydrogen bonds       : angle       4.21075 (  903)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.9206 (ttm) cc_final: 0.8831 (ttp)
REVERT: C   67 MET cc_start: 0.8477 (mtm) cc_final: 0.8017 (mpp)
  outliers start: 3
  outliers final: 1
  residues processed: 29
  average time/residue: 0.0591
  time to fit residues: 2.8426
Evaluate side-chains
  25 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   71 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0870
   chunk 19 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    1.5564

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

Flipped N/Q/H residues before XYZ refinement:
B 755 GLN
** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  26 ASN ** 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 = 0.2698 r_free = 0.2698 target = 0.032775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2384 r_free = 0.2384 target = 0.024772 restraints weight = 38794.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.2387 rms_B_bonded: 4.57
r_work (final): 0.2387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8707
moved from start:          0.2827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6728  Z= 0.123
  Angle     :  0.465   7.779   9101  Z= 0.237
  Chirality :  0.039   0.136   1004
  Planarity :  0.004   0.075   1176
  Dihedral  :  4.698  58.044    915
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  5.60 %
    Favored  : 93.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    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:  1.52 (0.29), residues: 793
  helix:  1.63 (0.25), residues: 405
  sheet: -0.07 (0.51), residues: 88
  loop :  0.68 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 632 
 TYR   0.010   0.001   TYR A 157 
 PHE   0.008   0.001   PHE A 156 
 TRP   0.007   0.001   TRP B 729 
 HIS   0.002   0.001   HIS B 911 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6728)
  covalent geometry    : angle       0.46534 ( 9101)
  hydrogen bonds       : bond        0.03166 (  314)
  hydrogen bonds       : angle       3.97645 (  903)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 23
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  111 MET cc_start: 0.9240 (ttm) cc_final: 0.8948 (ttp)
REVERT: B  836 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8810 (mm-30)
REVERT: B  930 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8428 (m-80)
REVERT: B  997 MET cc_start: 0.9464 (mtp) cc_final: 0.8885 (mmm)
REVERT: C   67 MET cc_start: 0.8525 (mtm) cc_final: 0.8180 (mpp)
REVERT: C  131 GLN cc_start: 0.9458 (mt0) cc_final: 0.9251 (mt0)
  outliers start: 9
  outliers final: 3
  residues processed: 31
  average time/residue: 0.0592
  time to fit residues: 3.0388
Evaluate side-chains
  26 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  606 VAL
Chi-restraints excluded: chain B residue  836 GLU
Chi-restraints excluded: chain B residue  930 PHE
Chi-restraints excluded: chain C residue   71 TYR
Chi-restraints excluded: chain C residue  152 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 71 optimal weight:    7.9990
   chunk 25 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9980
   chunk 52 optimal weight:    0.4980
   chunk 24 optimal weight:    7.9990
   chunk 47 optimal weight:    0.6980
   chunk 40 optimal weight:    5.9990
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  26 ASN ** 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 = 0.2700 r_free = 0.2700 target = 0.032901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2360 r_free = 0.2360 target = 0.024391 restraints weight = 39698.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.2369 rms_B_bonded: 4.84
r_work (final): 0.2369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8713
moved from start:          0.3059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6728  Z= 0.106
  Angle     :  0.463   8.125   9101  Z= 0.231
  Chirality :  0.039   0.135   1004
  Planarity :  0.004   0.074   1176
  Dihedral  :  4.584  57.242    915
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  6.83 %
    Favored  : 92.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    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:  1.81 (0.30), residues: 793
  helix:  1.94 (0.25), residues: 407
  sheet: -0.05 (0.50), residues: 88
  loop :  0.73 (0.37), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 568 
 TYR   0.007   0.001   TYR A 157 
 PHE   0.008   0.001   PHE A 156 
 TRP   0.006   0.001   TRP B 809 
 HIS   0.002   0.000   HIS B 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 6728)
  covalent geometry    : angle       0.46273 ( 9101)
  hydrogen bonds       : bond        0.02912 (  314)
  hydrogen bonds       : angle       3.81924 (  903)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 23
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A  111 MET cc_start: 0.9185 (ttm) cc_final: 0.8932 (ttp)
REVERT: B  606 VAL cc_start: 0.9548 (OUTLIER) cc_final: 0.9329 (p)
REVERT: B  836 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8798 (mm-30)
REVERT: B  997 MET cc_start: 0.9472 (mtp) cc_final: 0.8870 (mmm)
REVERT: C   67 MET cc_start: 0.8653 (mtm) cc_final: 0.8305 (mpp)
REVERT: C  131 GLN cc_start: 0.9460 (mt0) cc_final: 0.9129 (mt0)
  outliers start: 5
  outliers final: 2
  residues processed: 27
  average time/residue: 0.0827
  time to fit residues: 3.1665
Evaluate side-chains
  25 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  606 VAL
Chi-restraints excluded: chain B residue  836 GLU
Chi-restraints excluded: chain C residue   71 TYR
Chi-restraints excluded: chain C residue  152 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 72 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   chunk 21 optimal weight:    6.9990
   chunk 60 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    2.1384

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

Flipped N/Q/H residues before XYZ refinement:
** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  26 ASN ** 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 = 0.2676 r_free = 0.2676 target = 0.032156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2334 r_free = 0.2334 target = 0.023717 restraints weight = 40134.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.2345 rms_B_bonded: 4.83
r_work (final): 0.2345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8761
moved from start:          0.3136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6728  Z= 0.152
  Angle     :  0.479   9.656   9101  Z= 0.240
  Chirality :  0.039   0.128   1004
  Planarity :  0.004   0.075   1176
  Dihedral  :  4.602  58.469    915
  Min Nonbonded Distance : 1.880

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  7.79 %
    Favored  : 91.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    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:  2.02 (0.30), residues: 793
  helix:  2.12 (0.25), residues: 407
  sheet: -0.09 (0.49), residues: 90
  loop :  0.87 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 135 
 TYR   0.006   0.001   TYR B 681 
 PHE   0.009   0.001   PHE A 156 
 TRP   0.007   0.001   TRP B 729 
 HIS   0.002   0.001   HIS B 699 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6728)
  covalent geometry    : angle       0.47897 ( 9101)
  hydrogen bonds       : bond        0.03044 (  314)
  hydrogen bonds       : angle       3.86236 (  903)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A  111 MET cc_start: 0.9201 (ttm) cc_final: 0.8825 (ttp)
REVERT: B  930 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8449 (m-80)
REVERT: B  997 MET cc_start: 0.9492 (mtp) cc_final: 0.8973 (mmm)
REVERT: B 1001 MET cc_start: 0.9229 (mmm) cc_final: 0.8982 (mmp)
REVERT: C   67 MET cc_start: 0.8605 (mtm) cc_final: 0.8318 (mpp)
REVERT: C  131 GLN cc_start: 0.9479 (mt0) cc_final: 0.9125 (mt0)
REVERT: C  135 ARG cc_start: 0.9442 (ttm110) cc_final: 0.9219 (ttm110)
  outliers start: 6
  outliers final: 3
  residues processed: 28
  average time/residue: 0.0830
  time to fit residues: 3.2881
Evaluate side-chains
  25 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  610 ILE
Chi-restraints excluded: chain B residue  930 PHE
Chi-restraints excluded: chain C residue   71 TYR
Chi-restraints excluded: chain C residue  152 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 54 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  26 ASN ** 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 = 0.2686 r_free = 0.2686 target = 0.032395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2346 r_free = 0.2346 target = 0.023973 restraints weight = 39398.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.2353 rms_B_bonded: 4.80
r_work (final): 0.2353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8757
moved from start:          0.3291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6728  Z= 0.128
  Angle     :  0.465   9.601   9101  Z= 0.231
  Chirality :  0.039   0.129   1004
  Planarity :  0.004   0.074   1176
  Dihedral  :  4.567  57.683    915
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  8.33 %
    Favored  : 91.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    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:  2.11 (0.30), residues: 793
  helix:  2.17 (0.25), residues: 408
  sheet:  0.10 (0.51), residues: 87
  loop :  0.88 (0.38), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 632 
 TYR   0.004   0.001   TYR A 157 
 PHE   0.009   0.001   PHE A 156 
 TRP   0.006   0.001   TRP B 729 
 HIS   0.005   0.001   HIS B 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6728)
  covalent geometry    : angle       0.46522 ( 9101)
  hydrogen bonds       : bond        0.02863 (  314)
  hydrogen bonds       : angle       3.76448 (  903)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.202 
Fit side-chains
REVERT: B  930 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8399 (m-80)
REVERT: B  997 MET cc_start: 0.9450 (mtp) cc_final: 0.9060 (mmm)
REVERT: C   67 MET cc_start: 0.8690 (mtm) cc_final: 0.8443 (mpp)
REVERT: C  131 GLN cc_start: 0.9453 (mt0) cc_final: 0.9086 (mp10)
  outliers start: 4
  outliers final: 3
  residues processed: 25
  average time/residue: 0.0565
  time to fit residues: 2.3490
Evaluate side-chains
  24 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 20
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  831 LEU
Chi-restraints excluded: chain B residue  930 PHE
Chi-restraints excluded: chain C residue   71 TYR
Chi-restraints excluded: chain C residue  152 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 61 optimal weight:    9.9990
   chunk 34 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0670
   chunk 26 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    1.2126

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

Flipped N/Q/H residues before XYZ refinement:
** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  26 ASN ** 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 = 0.2698 r_free = 0.2698 target = 0.032689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2356 r_free = 0.2356 target = 0.024200 restraints weight = 39608.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.2366 rms_B_bonded: 4.86
r_work (final): 0.2366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8751
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6728  Z= 0.102
  Angle     :  0.460  11.315   9101  Z= 0.229
  Chirality :  0.039   0.130   1004
  Planarity :  0.004   0.073   1176
  Dihedral  :  4.534  56.928    915
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  8.33 %
    Favored  : 90.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.19 (0.30), residues: 793
  helix:  2.25 (0.25), residues: 408
  sheet:  0.20 (0.51), residues: 87
  loop :  0.89 (0.38), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 694 
 TYR   0.004   0.001   TYR C  96 
 PHE   0.009   0.001   PHE A 156 
 TRP   0.005   0.001   TRP B 809 
 HIS   0.005   0.001   HIS B 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 6728)
  covalent geometry    : angle       0.46020 ( 9101)
  hydrogen bonds       : bond        0.02735 (  314)
  hydrogen bonds       : angle       3.70112 (  903)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A  111 MET cc_start: 0.9034 (ttp) cc_final: 0.8691 (ttp)
REVERT: B  930 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8395 (m-80)
REVERT: B  997 MET cc_start: 0.9490 (mtp) cc_final: 0.9146 (mmm)
REVERT: C   72 MET cc_start: 0.8756 (mtt) cc_final: 0.8425 (mmm)
REVERT: C  131 GLN cc_start: 0.9436 (mt0) cc_final: 0.9081 (mp10)
  outliers start: 6
  outliers final: 4
  residues processed: 27
  average time/residue: 0.0594
  time to fit residues: 2.7108
Evaluate side-chains
  25 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 20
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  610 ILE
Chi-restraints excluded: chain B residue  831 LEU
Chi-restraints excluded: chain B residue  930 PHE
Chi-restraints excluded: chain C residue   71 TYR
Chi-restraints excluded: chain C residue  152 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 50 optimal weight:    0.0370
   chunk 26 optimal weight:    0.4980
   chunk 38 optimal weight:    0.1980
   chunk 56 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.5260

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

Flipped N/Q/H residues before XYZ refinement:
** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  26 ASN ** 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 = 0.2746 r_free = 0.2746 target = 0.033673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2426 r_free = 0.2426 target = 0.025451 restraints weight = 39316.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.2413 rms_B_bonded: 4.77
r_work (final): 0.2413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8726
moved from start:          0.3651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6728  Z= 0.077
  Angle     :  0.450  10.895   9101  Z= 0.221
  Chirality :  0.039   0.135   1004
  Planarity :  0.003   0.071   1176
  Dihedral  :  4.410  54.128    915
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  8.88 %
    Favored  : 90.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.35 (0.30), residues: 793
  helix:  2.37 (0.25), residues: 409
  sheet:  0.37 (0.52), residues: 87
  loop :  0.92 (0.38), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 694 
 TYR   0.006   0.001   TYR B 615 
 PHE   0.009   0.001   PHE A 156 
 TRP   0.007   0.001   TRP B 809 
 HIS   0.009   0.001   HIS B 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00179 ( 6728)
  covalent geometry    : angle       0.44952 ( 9101)
  hydrogen bonds       : bond        0.02434 (  314)
  hydrogen bonds       : angle       3.56931 (  903)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A  111 MET cc_start: 0.8998 (ttp) cc_final: 0.8671 (ttp)
REVERT: B  930 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8313 (m-80)
REVERT: B  997 MET cc_start: 0.9440 (mtp) cc_final: 0.9239 (mmm)
REVERT: C  131 GLN cc_start: 0.9409 (mt0) cc_final: 0.8984 (mp10)
REVERT: C  135 ARG cc_start: 0.9429 (ttm110) cc_final: 0.9224 (ttm110)
  outliers start: 5
  outliers final: 3
  residues processed: 26
  average time/residue: 0.0743
  time to fit residues: 2.9602
Evaluate side-chains
  25 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  831 LEU
Chi-restraints excluded: chain B residue  930 PHE
Chi-restraints excluded: chain C residue   71 TYR
Chi-restraints excluded: chain C residue  152 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 13 optimal weight:    9.9990
   chunk 67 optimal weight:    0.3980
   chunk 74 optimal weight:    7.9990
   chunk 73 optimal weight:    8.9990
   chunk 68 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   chunk 47 optimal weight:    0.0170
   chunk 24 optimal weight:    7.9990
   overall best weight:    1.0824

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

Flipped N/Q/H residues before XYZ refinement:
** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  26 ASN ** 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 = 0.2722 r_free = 0.2722 target = 0.033296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2386 r_free = 0.2386 target = 0.024791 restraints weight = 39511.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.2384 rms_B_bonded: 4.88
r_work (final): 0.2384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8746
moved from start:          0.3666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6728  Z= 0.095
  Angle     :  0.466  11.350   9101  Z= 0.226
  Chirality :  0.039   0.130   1004
  Planarity :  0.003   0.068   1176
  Dihedral  :  4.376  54.837    915
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  9.02 %
    Favored  : 90.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    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 (0.30), residues: 793
  helix:  2.40 (0.25), residues: 410
  sheet:  0.46 (0.51), residues: 87
  loop :  0.95 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 135 
 TYR   0.004   0.001   TYR B 796 
 PHE   0.009   0.001   PHE A 156 
 TRP   0.005   0.001   TRP B 809 
 HIS   0.006   0.001   HIS B 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 6728)
  covalent geometry    : angle       0.46625 ( 9101)
  hydrogen bonds       : bond        0.02528 (  314)
  hydrogen bonds       : angle       3.60467 (  903)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A  111 MET cc_start: 0.9026 (ttp) cc_final: 0.8658 (ttp)
REVERT: B  617 MET cc_start: 0.9412 (mmm) cc_final: 0.9127 (mpp)
REVERT: B  930 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8363 (m-80)
REVERT: B  997 MET cc_start: 0.9469 (mtp) cc_final: 0.9246 (mmm)
REVERT: C   72 MET cc_start: 0.9230 (mmm) cc_final: 0.8678 (mmm)
REVERT: C  131 GLN cc_start: 0.9404 (mt0) cc_final: 0.8998 (mt0)
REVERT: C  135 ARG cc_start: 0.9447 (ttm110) cc_final: 0.9246 (ttm110)
  outliers start: 5
  outliers final: 4
  residues processed: 25
  average time/residue: 0.0775
  time to fit residues: 2.8787
Evaluate side-chains
  25 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 20
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  831 LEU
Chi-restraints excluded: chain B residue  930 PHE
Chi-restraints excluded: chain C residue   67 MET
Chi-restraints excluded: chain C residue   71 TYR
Chi-restraints excluded: chain C residue  152 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0670
   chunk 61 optimal weight:    8.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.9522

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

Flipped N/Q/H residues before XYZ refinement:
** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  26 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.033487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2396 r_free = 0.2396 target = 0.024990 restraints weight = 39067.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.2394 rms_B_bonded: 4.88
r_work (final): 0.2394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8744
moved from start:          0.3772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6728  Z= 0.087
  Angle     :  0.461  11.350   9101  Z= 0.223
  Chirality :  0.039   0.129   1004
  Planarity :  0.003   0.068   1176
  Dihedral  :  4.330  54.316    915
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  9.29 %
    Favored  : 90.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    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:  2.51 (0.30), residues: 793
  helix:  2.56 (0.25), residues: 402
  sheet:  0.48 (0.51), residues: 87
  loop :  0.93 (0.37), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 694 
 TYR   0.004   0.001   TYR B 796 
 PHE   0.008   0.001   PHE A 156 
 TRP   0.005   0.001   TRP B 809 
 HIS   0.005   0.000   HIS B 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 6728)
  covalent geometry    : angle       0.46052 ( 9101)
  hydrogen bonds       : bond        0.02443 (  314)
  hydrogen bonds       : angle       3.55613 (  903)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1022.14 seconds
wall clock time: 18 minutes 23.85 seconds (1103.85 seconds total)