Starting phenix.real_space_refine
on Tue Mar  3 19:13:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vg3_31964/03_2026/7vg3_31964.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vg3_31964/03_2026/7vg3_31964.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vg3_31964/03_2026/7vg3_31964.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vg3_31964/03_2026/7vg3_31964.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vg3_31964/03_2026/7vg3_31964.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vg3_31964/03_2026/7vg3_31964.cif"
  }
  resolution = 3.73
  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=   0.005
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: 7
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Zn      1      6.06       5
     P      61      5.49       5
     S      36      5.16       5
     C    4913      2.51       5
     N    1392      2.21       5
     O    1713      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  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: 8118
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 860, 6800
          Classifications: {'peptide': 860}
          Link IDs: {'PTRANS': 37, 'TRANS': 822}
          Chain breaks: 6
    Chain: "C"
      Number of atoms: 636
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 636
          Classifications: {'RNA': 30}
          Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 15, 'rna3p_pyr': 13}
          Link IDs: {'rna2p': 2, 'rna3p': 27}
    Chain: "D"
      Number of atoms: 679
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 679
          Classifications: {'RNA': 32}
          Modifications used: {'5*END': 1, 'rna3p_pur': 17, 'rna3p_pyr': 15}
          Link IDs: {'rna3p': 31}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 2, ' ZN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   3363  SG  CYS A1091      37.744  55.435  37.136  1.00 56.47           S
  ATOM   3378  SG  CYS A1093      41.924  55.592  37.534  1.00 61.85           S
  ATOM   3582  SG  CYS A1119      39.383  53.825  40.277  1.00 46.05           S

  Time building chain proxies: 2.04, per 1000 atoms: 0.25
  Number of scatterers: 8118
  At special positions: 0
  Unit cell: (115.92, 91.56, 99.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     Ca      2     19.99
     S      36     16.00
     P      61     15.00
     O    1713      8.00
     N    1392      7.00
     C    4913      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: 0.60
  Conformation dependent library (CDL) restraints added in 189.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A2003 "
        pdb="ZN    ZN A2003 " - pdb=" ND1 HIS A1123 "
        pdb="ZN    ZN A2003 " - pdb=" SG  CYS A1093 "
        pdb="ZN    ZN A2003 " - pdb=" SG  CYS A1119 "
        pdb="ZN    ZN A2003 " - pdb=" SG  CYS A1091 "
      Number of angles added : 3


  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1628

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 7 sheets defined
      39.3% alpha, 12.7% beta
      14 base pairs and 40 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 710 through 725
      removed outlier: 3.730A  pdb=" N   TYR A 719 " --> pdb=" O   VAL A 715 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   PHE A 720 " --> pdb=" O   LYS A 716 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLN A 721 " --> pdb=" O   ALA A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 778 through 795
      removed outlier: 3.609A  pdb=" N   ILE A 782 " --> pdb=" O   ASP A 778 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 888
      removed outlier: 3.730A  pdb=" N   TYR A 888 " --> pdb=" O   PHE A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 944
      No H-bonds generated for 'chain 'A' and resid 942 through 944'
    Processing helix  chain 'A' and resid 953 through 958
    Processing helix  chain 'A' and resid 961 through 972
      removed outlier: 4.449A  pdb=" N   HIS A 967 " --> pdb=" O   PRO A 963 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ARG A 968 " --> pdb=" O   SER A 964 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 972 through 983
      removed outlier: 3.547A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   ASP A 983 " --> pdb=" O   ARG A 979 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 992 through 998
      removed outlier: 3.680A  pdb=" N   ILE A 996 " --> pdb=" O   SER A 992 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   GLU A 998 " --> pdb=" O   THR A 994 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1011 through 1034
      removed outlier: 3.520A  pdb=" N   GLU A1015 " --> pdb=" O   MET A1011 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   LEU A1017 " --> pdb=" O   ARG A1013 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   SER A1020 " --> pdb=" O   LEU A1016 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1038 through 1050
      removed outlier: 3.689A  pdb=" N   GLN A1045 " --> pdb=" O   GLN A1041 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1053 through 1060
      removed outlier: 3.669A  pdb=" N   THR A1060 " --> pdb=" O   HIS A1056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1061 through 1063
      No H-bonds generated for 'chain 'A' and resid 1061 through 1063'
    Processing helix  chain 'A' and resid 1064 through 1068
      removed outlier: 3.822A  pdb=" N   ILE A1068 " --> pdb=" O   GLN A1065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1133 through 1146
      removed outlier: 3.516A  pdb=" N   ILE A1139 " --> pdb=" O   ALA A1135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1150 through 1159
      removed outlier: 3.824A  pdb=" N   MET A1154 " --> pdb=" O   ALA A1150 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   MET A1155 " --> pdb=" O   SER A1151 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY A1159 " --> pdb=" O   MET A1155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1168 through 1176
    Processing helix  chain 'A' and resid 1190 through 1196
      removed outlier: 4.243A  pdb=" N   LYS A1194 " --> pdb=" O   GLU A1190 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLN A1196 " --> pdb=" O   GLU A1192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1201 through 1208
      removed outlier: 3.725A  pdb=" N   LEU A1205 " --> pdb=" O   ALA A1201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1221 through 1243
      removed outlier: 3.786A  pdb=" N   SER A1229 " --> pdb=" O   PHE A1225 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   PHE A1240 " --> pdb=" O   THR A1236 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ASN A1241 " --> pdb=" O   ARG A1237 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   THR A1242 " --> pdb=" O   HIS A1238 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   TYR A1243 " --> pdb=" O   LEU A1239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1247 through 1259
      removed outlier: 3.847A  pdb=" N   ASP A1253 " --> pdb=" O   GLY A1249 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   CYS A1258 " --> pdb=" O   LEU A1254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1260 through 1271
      removed outlier: 3.576A  pdb=" N   VAL A1269 " --> pdb=" O   ALA A1265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1273 through 1277
      removed outlier: 3.597A  pdb=" N   HIS A1276 " --> pdb=" O   LEU A1273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1281 through 1293
      removed outlier: 3.711A  pdb=" N   GLN A1287 " --> pdb=" O   VAL A1283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1316 through 1329
      removed outlier: 3.729A  pdb=" N   ALA A1322 " --> pdb=" O   VAL A1318 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLY A1323 " --> pdb=" O   GLU A1319 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   LEU A1326 " --> pdb=" O   ALA A1322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1335 through 1344
      Proline residue:  A1342  - end of helix
    Processing helix  chain 'A' and resid 1356 through 1369
      removed outlier: 3.871A  pdb=" N   SER A1367 " --> pdb=" O   GLU A1363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1407 through 1422
      removed outlier: 3.659A  pdb=" N   GLN A1419 " --> pdb=" O   HIS A1415 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LYS A1422 " --> pdb=" O   THR A1418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1475 through 1488
    Processing helix  chain 'A' and resid 1544 through 1562
      removed outlier: 3.540A  pdb=" N   GLU A1561 " --> pdb=" O   LEU A1557 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   ARG A1562 " --> pdb=" O   TYR A1558 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 629 through 631
      removed outlier: 3.639A  pdb=" N   ARG A1124 " --> pdb=" O   HIS A 631 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 687 through 691
      removed outlier: 3.564A  pdb=" N   SER A 700 " --> pdb=" O   ASP A 658 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ASP A 658 " --> pdb=" O   SER A 700 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ALA A 650 " --> pdb=" O   LEU A 709 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 687 through 691
      removed outlier: 3.564A  pdb=" N   SER A 700 " --> pdb=" O   ASP A 658 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ASP A 658 " --> pdb=" O   SER A 700 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   SER A 670 " --> pdb=" O   VAL A 766 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 938 through 941
      removed outlier: 3.515A  pdb=" N   MET A 900 " --> pdb=" O   LEU A 941 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   LYS A 901 " --> pdb=" O   GLU A 858 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   ILE A 856 " --> pdb=" O   LYS A 903 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   VAL A 845 " --> pdb=" O   TYR A 854 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ILE A 856 " --> pdb=" O   LEU A 843 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   LEU A 843 " --> pdb=" O   ILE A 856 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   VAL A 844 " --> pdb=" O   ILE A 949 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1372 through 1377
      removed outlier: 3.628A  pdb=" N   GLN A1384 " --> pdb=" O   SER A1377 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1372 through 1377
      removed outlier: 3.628A  pdb=" N   GLN A1384 " --> pdb=" O   SER A1377 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1494 through 1498
      removed outlier: 3.950A  pdb=" N   THR A1522 " --> pdb=" O   SER A1498 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   TYR A1537 " --> pdb=" O   ILE A1525 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   VAL A1535 " --> pdb=" O   LEU A1527 " (cutoff:3.500A)

    240 hydrogen bonds defined for protein.
    699 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      34 hydrogen bonds
      68 hydrogen bond angles
      0 basepair planarities
      14 basepair parallelities
      40 stacking parallelities
  Total time for adding SS restraints: 1.35

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2151
        1.34 -     1.46: 2021
        1.46 -     1.58: 4059
        1.58 -     1.70: 122
        1.70 -     1.82: 54
  Bond restraints: 8407
  Sorted by residual:
  bond pdb=" P     U C   1 "
       pdb=" OP3   U C   1 "
    ideal  model  delta    sigma   weight residual
    1.480  1.606 -0.126 2.00e-02 2.50e+03 3.95e+01
  bond pdb=" N   SER A1212 "
       pdb=" CA  SER A1212 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.040 1.29e-02 6.01e+03 9.69e+00
  bond pdb=" N   ASN A1405 "
       pdb=" CA  ASN A1405 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.29e-02 6.01e+03 9.48e+00
  bond pdb=" N   HIS A1197 "
       pdb=" CA  HIS A1197 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.034 1.18e-02 7.18e+03 8.43e+00
  bond pdb=" N   LEU A 746 "
       pdb=" CA  LEU A 746 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.037 1.29e-02 6.01e+03 8.43e+00
  ... (remaining 8402 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 11006
        2.25 -     4.50: 556
        4.50 -     6.75: 58
        6.75 -     9.01: 32
        9.01 -    11.26: 6
  Bond angle restraints: 11658
  Sorted by residual:
  angle pdb=" N   ALA A 758 "
        pdb=" CA  ALA A 758 "
        pdb=" C   ALA A 758 "
      ideal   model   delta    sigma   weight residual
     114.75  107.13    7.62 1.26e+00 6.30e-01 3.65e+01
  angle pdb=" N   PRO A 757 "
        pdb=" CA  PRO A 757 "
        pdb=" C   PRO A 757 "
      ideal   model   delta    sigma   weight residual
     112.47  123.73  -11.26 2.06e+00 2.36e-01 2.99e+01
  angle pdb=" C   HIS A1211 "
        pdb=" N   SER A1212 "
        pdb=" CA  SER A1212 "
      ideal   model   delta    sigma   weight residual
     121.54  131.66  -10.12 1.91e+00 2.74e-01 2.81e+01
  angle pdb=" N   ALA A1072 "
        pdb=" CA  ALA A1072 "
        pdb=" C   ALA A1072 "
      ideal   model   delta    sigma   weight residual
     114.75  108.32    6.43 1.26e+00 6.30e-01 2.60e+01
  angle pdb=" C   THR A1404 "
        pdb=" N   ASN A1405 "
        pdb=" CA  ASN A1405 "
      ideal   model   delta    sigma   weight residual
     121.54  130.44   -8.90 1.91e+00 2.74e-01 2.17e+01
  ... (remaining 11653 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.41: 4957
       35.41 -    70.82: 171
       70.82 -   106.23: 14
      106.23 -   141.64: 0
      141.64 -   177.06: 1
  Dihedral angle restraints: 5143
    sinusoidal: 2638
      harmonic: 2505
  Sorted by residual:
  dihedral pdb=" O4'   U C   1 "
           pdb=" C1'   U C   1 "
           pdb=" N1    U C   1 "
           pdb=" C2    U C   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   49.06 -177.06     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" CA  PRO A1356 "
           pdb=" C   PRO A1356 "
           pdb=" N   PRO A1357 "
           pdb=" CA  PRO A1357 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.10  -26.90     0      5.00e+00 4.00e-02 2.89e+01
  dihedral pdb=" CA  PHE A 830 "
           pdb=" C   PHE A 830 "
           pdb=" N   ALA A 831 "
           pdb=" CA  ALA A 831 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.96   26.04     0      5.00e+00 4.00e-02 2.71e+01
  ... (remaining 5140 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1115
       0.069 -    0.138: 195
       0.138 -    0.207: 44
       0.207 -    0.276: 7
       0.276 -    0.345: 4
  Chirality restraints: 1365
  Sorted by residual:
  chirality pdb=" CA  PRO A 757 "
            pdb=" N   PRO A 757 "
            pdb=" C   PRO A 757 "
            pdb=" CB  PRO A 757 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.37    0.34 2.00e-01 2.50e+01 2.97e+00
  chirality pdb=" CA  PHE A 759 "
            pdb=" N   PHE A 759 "
            pdb=" C   PHE A 759 "
            pdb=" CB  PHE A 759 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.82e+00
  chirality pdb=" CB  VAL A 951 "
            pdb=" CA  VAL A 951 "
            pdb=" CG1 VAL A 951 "
            pdb=" CG2 VAL A 951 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.64e+00
  ... (remaining 1362 not shown)

  Planarity restraints: 1263
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 756 "   -0.015 2.00e-02 2.50e+03   3.04e-02 9.25e+00
        pdb=" C   HIS A 756 "    0.053 2.00e-02 2.50e+03
        pdb=" O   HIS A 756 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   PRO A 757 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 851 "    0.013 2.00e-02 2.50e+03   2.66e-02 7.08e+00
        pdb=" C   GLY A 851 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   GLY A 851 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ARG A 852 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 951 "    0.042 5.00e-02 4.00e+02   6.42e-02 6.59e+00
        pdb=" N   PRO A 952 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 952 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 952 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1260 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.53: 31
        2.53 -     3.12: 5552
        3.12 -     3.71: 12743
        3.71 -     4.31: 16753
        4.31 -     4.90: 26612
  Nonbonded interactions: 61691
  Sorted by model distance:
  nonbonded pdb=" OP1   U C  25 "
            pdb="CA    CA A2002 "
     model   vdw
     1.935 2.510
  nonbonded pdb=" OE2 GLU A1224 "
            pdb="CA    CA A2002 "
     model   vdw
     2.153 2.510
  nonbonded pdb=" OP1   A D   9 "
            pdb="CA    CA A2001 "
     model   vdw
     2.221 2.510
  nonbonded pdb=" OE2 GLU A1015 "
            pdb="CA    CA A2001 "
     model   vdw
     2.248 2.510
  nonbonded pdb=" OG  SER A 855 "
            pdb=" O   LYS A 903 "
     model   vdw
     2.271 3.040
  ... (remaining 61686 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 group one per residue
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:             0.480
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.070
  Find NCS groups from input model:        0.030
  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:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
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      :  0.010   0.661   8411  Z= 0.461
  Angle     :  1.175  24.018  11661  Z= 0.657
  Chirality :  0.060   0.345   1365
  Planarity :  0.007   0.064   1263
  Dihedral  : 16.120 177.055   3515
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  : 10.76 %
    Favored  : 88.65 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  :  7.37 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.25 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.51 (0.22), residues: 846
  helix: -3.42 (0.19), residues: 331
  sheet: -0.92 (0.57), residues: 87
  loop : -3.12 (0.24), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 968 
 TYR   0.019   0.002   TYR A1370 
 PHE   0.025   0.003   PHE A 989 
 TRP   0.017   0.003   TRP A1078 
 HIS   0.010   0.002   HIS A 631 

Details of bonding type rmsd
  covalent geometry    : bond        0.00627 ( 8407)
  covalent geometry    : angle       1.14757 (11658)
  hydrogen bonds       : bond        0.24549 (  263)
  hydrogen bonds       : angle       7.98510 (  767)
  metal coordination   : bond        0.37256 (    4)
  metal coordination   : angle      15.72470 (    3)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 126
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  624 SER cc_start: 0.8856 (p) cc_final: 0.8599 (t)
REVERT: A  731 LYS cc_start: 0.8648 (ptmt) cc_final: 0.8280 (ptmm)
REVERT: A  746 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8747 (tt)
REVERT: A  914 ASP cc_start: 0.8155 (p0) cc_final: 0.7852 (p0)
REVERT: A  966 MET cc_start: 0.8072 (mtm) cc_final: 0.7848 (mtp)
REVERT: A  969 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8574 (tm)
REVERT: A 1112 THR cc_start: 0.8111 (p) cc_final: 0.7862 (t)
REVERT: A 1213 SER cc_start: 0.7024 (OUTLIER) cc_final: 0.6732 (p)
REVERT: A 1403 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.6950 (pp30)
REVERT: A 1492 MET cc_start: 0.8223 (tpp) cc_final: 0.7899 (tpt)
REVERT: A 1526 THR cc_start: 0.9043 (t) cc_final: 0.8745 (p)
  outliers start: 39
  outliers final: 16
  residues processed: 151
  average time/residue: 0.1130
  time to fit residues: 22.1254
Evaluate side-chains
  95 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue 1198 GLU
Chi-restraints excluded: chain A residue 1199 PHE
Chi-restraints excluded: chain A residue 1204 LEU
Chi-restraints excluded: chain A residue 1206 LYS
Chi-restraints excluded: chain A residue 1213 SER
Chi-restraints excluded: chain A residue 1214 LEU
Chi-restraints excluded: chain A residue 1216 GLU
Chi-restraints excluded: chain A residue 1219 SER
Chi-restraints excluded: chain A residue 1220 TYR
Chi-restraints excluded: chain A residue 1403 GLN
Chi-restraints excluded: chain A residue 1404 THR
Chi-restraints excluded: chain A residue 1405 ASN
Chi-restraints excluded: chain A residue 1407 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:   20.0000
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:    0.2980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 722 GLN
A 783 ASN
A 967 HIS
A 977 GLN
A 988 ASN
A1029 HIS
A1054 ASN
A1110 ASN
A1260 ASN
A1403 GLN
A1405 ASN
A1460 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.135415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.110271 restraints weight = 14000.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.113581 restraints weight = 7750.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.115796 restraints weight = 5399.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.117174 restraints weight = 4281.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.117993 restraints weight = 3704.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.1885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8411  Z= 0.127
  Angle     :  0.665   9.671  11661  Z= 0.341
  Chirality :  0.040   0.165   1365
  Planarity :  0.006   0.086   1263
  Dihedral  : 16.845 177.833   1895
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.87 %
    Favored  : 90.90 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 11.84 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.41 (0.25), residues: 846
  helix: -1.90 (0.24), residues: 341
  sheet: -1.11 (0.49), residues: 112
  loop : -2.95 (0.26), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1215 
 TYR   0.021   0.001   TYR A1181 
 PHE   0.016   0.001   PHE A 759 
 TRP   0.012   0.001   TRP A1078 
 HIS   0.009   0.001   HIS A 756 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8407)
  covalent geometry    : angle       0.66287 (11658)
  hydrogen bonds       : bond        0.04693 (  263)
  hydrogen bonds       : angle       4.86018 (  767)
  metal coordination   : bond        0.01417 (    4)
  metal coordination   : angle       3.30133 (    3)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 103
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
REVERT: A  624 SER cc_start: 0.8761 (p) cc_final: 0.8486 (t)
REVERT: A  731 LYS cc_start: 0.8696 (ptmt) cc_final: 0.8304 (ptmm)
REVERT: A  759 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.7055 (m-80)
REVERT: A  914 ASP cc_start: 0.8223 (p0) cc_final: 0.7910 (p0)
REVERT: A  966 MET cc_start: 0.7893 (mtm) cc_final: 0.7650 (mtp)
REVERT: A  983 ASP cc_start: 0.7415 (t70) cc_final: 0.7191 (p0)
REVERT: A 1112 THR cc_start: 0.8202 (p) cc_final: 0.7956 (t)
REVERT: A 1492 MET cc_start: 0.8170 (tpp) cc_final: 0.7835 (tpt)
REVERT: A 1526 THR cc_start: 0.8935 (t) cc_final: 0.8717 (p)
  outliers start: 38
  outliers final: 22
  residues processed: 137
  average time/residue: 0.0747
  time to fit residues: 14.8779
Evaluate side-chains
  99 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  657 PHE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  902 LEU
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  980 GLU
Chi-restraints excluded: chain A residue 1003 LEU
Chi-restraints excluded: chain A residue 1089 VAL
Chi-restraints excluded: chain A residue 1199 PHE
Chi-restraints excluded: chain A residue 1204 LEU
Chi-restraints excluded: chain A residue 1210 THR
Chi-restraints excluded: chain A residue 1220 TYR
Chi-restraints excluded: chain A residue 1404 THR
Chi-restraints excluded: chain A residue 1405 ASN
Chi-restraints excluded: chain A residue 1407 LEU
Chi-restraints excluded: chain A residue 1525 ILE
Chi-restraints excluded: chain A residue 1529 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 43 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 44 optimal weight:    6.9990
   chunk 18 optimal weight:   10.0000
   chunk 75 optimal weight:    9.9990
   chunk 58 optimal weight:    7.9990
   chunk 16 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   chunk 29 optimal weight:    0.3980
   chunk 4 optimal weight:    5.9990
   overall best weight:    5.2788

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

Flipped N/Q/H residues before XYZ refinement:
** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 722 GLN
A 896 ASN
A 938 HIS
A1052 ASN
A1056 HIS
A1196 GLN
A1197 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.129174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.102449 restraints weight = 14296.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.105644 restraints weight = 8166.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.107723 restraints weight = 5795.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.108888 restraints weight = 4697.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.109831 restraints weight = 4151.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.065   8411  Z= 0.333
  Angle     :  0.813  10.387  11661  Z= 0.418
  Chirality :  0.047   0.186   1365
  Planarity :  0.006   0.063   1263
  Dihedral  : 16.524 174.805   1878
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 10.99 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  6.71 %
    Allowed  : 14.08 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.01 (0.26), residues: 846
  helix: -1.14 (0.27), residues: 333
  sheet: -1.72 (0.50), residues: 113
  loop : -2.85 (0.26), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1215 
 TYR   0.026   0.002   TYR A1358 
 PHE   0.022   0.003   PHE A 652 
 TRP   0.016   0.003   TRP A 643 
 HIS   0.016   0.002   HIS A 756 

Details of bonding type rmsd
  covalent geometry    : bond        0.00746 ( 8407)
  covalent geometry    : angle       0.80895 (11658)
  hydrogen bonds       : bond        0.05942 (  263)
  hydrogen bonds       : angle       4.81232 (  767)
  metal coordination   : bond        0.01146 (    4)
  metal coordination   : angle       5.05293 (    3)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 74
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A  624 SER cc_start: 0.8911 (p) cc_final: 0.8620 (t)
REVERT: A  731 LYS cc_start: 0.8788 (ptmt) cc_final: 0.8353 (ptmm)
REVERT: A  760 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6747 (mmm)
REVERT: A  828 ILE cc_start: 0.1743 (OUTLIER) cc_final: 0.1323 (tp)
REVERT: A  914 ASP cc_start: 0.8178 (p0) cc_final: 0.7769 (p0)
REVERT: A  966 MET cc_start: 0.8082 (mtm) cc_final: 0.7359 (mtm)
REVERT: A 1052 ASN cc_start: 0.9052 (OUTLIER) cc_final: 0.8811 (t0)
REVERT: A 1174 ASN cc_start: 0.6373 (m110) cc_final: 0.6140 (m110)
REVERT: A 1175 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.5904 (mtp85)
REVERT: A 1509 ILE cc_start: 0.6158 (OUTLIER) cc_final: 0.5726 (mp)
REVERT: A 1526 THR cc_start: 0.9240 (t) cc_final: 0.8843 (p)
  outliers start: 51
  outliers final: 33
  residues processed: 117
  average time/residue: 0.0815
  time to fit residues: 13.4010
Evaluate side-chains
  105 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 67
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  657 PHE
Chi-restraints excluded: chain A residue  663 ILE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  789 VAL
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  832 ASN
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  902 LEU
Chi-restraints excluded: chain A residue  911 LEU
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  980 GLU
Chi-restraints excluded: chain A residue  986 ILE
Chi-restraints excluded: chain A residue  987 ASP
Chi-restraints excluded: chain A residue 1003 LEU
Chi-restraints excluded: chain A residue 1052 ASN
Chi-restraints excluded: chain A residue 1152 LEU
Chi-restraints excluded: chain A residue 1175 ARG
Chi-restraints excluded: chain A residue 1199 PHE
Chi-restraints excluded: chain A residue 1204 LEU
Chi-restraints excluded: chain A residue 1210 THR
Chi-restraints excluded: chain A residue 1271 ASN
Chi-restraints excluded: chain A residue 1294 SER
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1379 ASP
Chi-restraints excluded: chain A residue 1397 THR
Chi-restraints excluded: chain A residue 1405 ASN
Chi-restraints excluded: chain A residue 1494 THR
Chi-restraints excluded: chain A residue 1509 ILE
Chi-restraints excluded: chain A residue 1522 THR
Chi-restraints excluded: chain A residue 1525 ILE
Chi-restraints excluded: chain A residue 1529 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 80 optimal weight:    9.9990
   chunk 68 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 43 optimal weight:    0.0010
   chunk 47 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 90 optimal weight:    6.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    1.3790

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

Flipped N/Q/H residues before XYZ refinement:
A 662 ASN
** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1196 GLN
A1482 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.132544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.107342 restraints weight = 14356.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.110493 restraints weight = 8183.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.112571 restraints weight = 5785.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.113696 restraints weight = 4661.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.114637 restraints weight = 4111.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8411  Z= 0.134
  Angle     :  0.637   9.318  11661  Z= 0.326
  Chirality :  0.040   0.170   1365
  Planarity :  0.005   0.056   1263
  Dihedral  : 16.312 177.337   1869
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.46 %
    Favored  : 90.43 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 16.18 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.49 (0.27), residues: 846
  helix: -0.58 (0.29), residues: 337
  sheet: -1.70 (0.49), residues: 111
  loop : -2.62 (0.28), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A1215 
 TYR   0.014   0.001   TYR A1218 
 PHE   0.014   0.001   PHE A 759 
 TRP   0.016   0.001   TRP A1078 
 HIS   0.010   0.001   HIS A 756 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8407)
  covalent geometry    : angle       0.63534 (11658)
  hydrogen bonds       : bond        0.04051 (  263)
  hydrogen bonds       : angle       4.16317 (  767)
  metal coordination   : bond        0.00538 (    4)
  metal coordination   : angle       3.00128 (    3)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 77
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A  624 SER cc_start: 0.8844 (p) cc_final: 0.8572 (t)
REVERT: A  630 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8551 (mt)
REVERT: A  828 ILE cc_start: 0.1688 (OUTLIER) cc_final: 0.1329 (tp)
REVERT: A  914 ASP cc_start: 0.8126 (p0) cc_final: 0.7730 (p0)
REVERT: A  966 MET cc_start: 0.7949 (mtm) cc_final: 0.7441 (mtp)
REVERT: A 1112 THR cc_start: 0.8178 (p) cc_final: 0.7922 (t)
REVERT: A 1174 ASN cc_start: 0.6435 (m110) cc_final: 0.6185 (m110)
REVERT: A 1379 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.6854 (p0)
REVERT: A 1526 THR cc_start: 0.9161 (t) cc_final: 0.8821 (p)
  outliers start: 44
  outliers final: 28
  residues processed: 113
  average time/residue: 0.0774
  time to fit residues: 12.5933
Evaluate side-chains
  107 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 76
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  657 PHE
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  762 LEU
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  853 ILE
Chi-restraints excluded: chain A residue  857 VAL
Chi-restraints excluded: chain A residue  911 LEU
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  980 GLU
Chi-restraints excluded: chain A residue  986 ILE
Chi-restraints excluded: chain A residue  987 ASP
Chi-restraints excluded: chain A residue 1003 LEU
Chi-restraints excluded: chain A residue 1089 VAL
Chi-restraints excluded: chain A residue 1189 ILE
Chi-restraints excluded: chain A residue 1199 PHE
Chi-restraints excluded: chain A residue 1204 LEU
Chi-restraints excluded: chain A residue 1210 THR
Chi-restraints excluded: chain A residue 1271 ASN
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1379 ASP
Chi-restraints excluded: chain A residue 1405 ASN
Chi-restraints excluded: chain A residue 1417 LEU
Chi-restraints excluded: chain A residue 1494 THR
Chi-restraints excluded: chain A residue 1522 THR
Chi-restraints excluded: chain A residue 1525 ILE
Chi-restraints excluded: chain A residue 1529 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 25 optimal weight:    0.7980
   chunk 32 optimal weight:    0.1980
   chunk 38 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 2 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   chunk 48 optimal weight:    6.9990
   chunk 63 optimal weight:    0.7980
   chunk 20 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1196 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.135502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.110715 restraints weight = 14359.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.113774 restraints weight = 8290.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.115803 restraints weight = 5906.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.117081 restraints weight = 4777.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.117841 restraints weight = 4183.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.3111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050   8411  Z= 0.109
  Angle     :  0.596   9.422  11661  Z= 0.304
  Chirality :  0.038   0.188   1365
  Planarity :  0.004   0.044   1263
  Dihedral  : 16.109 178.292   1863
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.34 %
    Favored  : 90.54 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 17.37 %
    Favored  : 77.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.99 (0.28), residues: 846
  helix: -0.03 (0.29), residues: 334
  sheet: -1.58 (0.48), residues: 109
  loop : -2.41 (0.28), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1215 
 TYR   0.011   0.001   TYR A1181 
 PHE   0.011   0.001   PHE A 989 
 TRP   0.013   0.001   TRP A1078 
 HIS   0.009   0.001   HIS A 756 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 8407)
  covalent geometry    : angle       0.59511 (11658)
  hydrogen bonds       : bond        0.03387 (  263)
  hydrogen bonds       : angle       3.84134 (  767)
  metal coordination   : bond        0.00382 (    4)
  metal coordination   : angle       2.49555 (    3)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 85
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  624 SER cc_start: 0.8810 (p) cc_final: 0.8493 (t)
REVERT: A  914 ASP cc_start: 0.8103 (p0) cc_final: 0.7685 (p0)
REVERT: A  966 MET cc_start: 0.7904 (mtm) cc_final: 0.7277 (mtm)
REVERT: A 1112 THR cc_start: 0.8116 (p) cc_final: 0.7886 (t)
REVERT: A 1174 ASN cc_start: 0.6380 (m110) cc_final: 0.6174 (m110)
REVERT: A 1175 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.5934 (mtp85)
REVERT: A 1190 GLU cc_start: 0.7753 (pm20) cc_final: 0.7531 (mp0)
REVERT: A 1193 ARG cc_start: 0.7967 (mtm180) cc_final: 0.7734 (mtm180)
REVERT: A 1379 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.6921 (p0)
REVERT: A 1509 ILE cc_start: 0.6215 (OUTLIER) cc_final: 0.6010 (mp)
REVERT: A 1542 ARG cc_start: 0.6766 (OUTLIER) cc_final: 0.5719 (ptp-170)
  outliers start: 41
  outliers final: 26
  residues processed: 114
  average time/residue: 0.0792
  time to fit residues: 12.7868
Evaluate side-chains
  110 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 80
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  762 LEU
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  853 ILE
Chi-restraints excluded: chain A residue  911 LEU
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  980 GLU
Chi-restraints excluded: chain A residue 1003 LEU
Chi-restraints excluded: chain A residue 1089 VAL
Chi-restraints excluded: chain A residue 1175 ARG
Chi-restraints excluded: chain A residue 1189 ILE
Chi-restraints excluded: chain A residue 1199 PHE
Chi-restraints excluded: chain A residue 1204 LEU
Chi-restraints excluded: chain A residue 1210 THR
Chi-restraints excluded: chain A residue 1221 GLU
Chi-restraints excluded: chain A residue 1271 ASN
Chi-restraints excluded: chain A residue 1325 LEU
Chi-restraints excluded: chain A residue 1333 LEU
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1379 ASP
Chi-restraints excluded: chain A residue 1405 ASN
Chi-restraints excluded: chain A residue 1417 LEU
Chi-restraints excluded: chain A residue 1494 THR
Chi-restraints excluded: chain A residue 1509 ILE
Chi-restraints excluded: chain A residue 1522 THR
Chi-restraints excluded: chain A residue 1525 ILE
Chi-restraints excluded: chain A residue 1529 ILE
Chi-restraints excluded: chain A residue 1542 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 34 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 82 optimal weight:    4.9990
   chunk 18 optimal weight:   10.0000
   chunk 91 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 70 optimal weight:    9.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1196 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.128735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.103281 restraints weight = 14349.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.106201 restraints weight = 8542.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.107996 restraints weight = 6198.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.109258 restraints weight = 5134.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.109931 restraints weight = 4532.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   8411  Z= 0.254
  Angle     :  0.723  10.544  11661  Z= 0.366
  Chirality :  0.043   0.166   1365
  Planarity :  0.005   0.039   1263
  Dihedral  : 16.196 175.418   1863
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 11.35 %
    Favored  : 88.53 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 18.29 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.11 (0.28), residues: 846
  helix:  0.03 (0.29), residues: 332
  sheet: -1.88 (0.47), residues: 113
  loop : -2.56 (0.28), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1215 
 TYR   0.018   0.002   TYR A1358 
 PHE   0.025   0.002   PHE A 759 
 TRP   0.013   0.002   TRP A 643 
 HIS   0.012   0.002   HIS A 756 

Details of bonding type rmsd
  covalent geometry    : bond        0.00574 ( 8407)
  covalent geometry    : angle       0.72067 (11658)
  hydrogen bonds       : bond        0.04977 (  263)
  hydrogen bonds       : angle       4.27846 (  767)
  metal coordination   : bond        0.00753 (    4)
  metal coordination   : angle       3.81408 (    3)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 74
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A  630 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8566 (mt)
REVERT: A  762 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8338 (mm)
REVERT: A  843 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9061 (tp)
REVERT: A  914 ASP cc_start: 0.8090 (p0) cc_final: 0.7787 (p0)
REVERT: A  966 MET cc_start: 0.8032 (mtm) cc_final: 0.7335 (mtm)
REVERT: A 1112 THR cc_start: 0.8162 (p) cc_final: 0.7899 (t)
REVERT: A 1175 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6127 (mtp85)
REVERT: A 1509 ILE cc_start: 0.6178 (OUTLIER) cc_final: 0.5753 (mp)
REVERT: A 1542 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.5971 (ptp-170)
  outliers start: 41
  outliers final: 27
  residues processed: 105
  average time/residue: 0.0885
  time to fit residues: 12.7938
Evaluate side-chains
  105 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 72
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  762 LEU
Chi-restraints excluded: chain A residue  789 VAL
Chi-restraints excluded: chain A residue  832 ASN
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  857 VAL
Chi-restraints excluded: chain A residue  911 LEU
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  980 GLU
Chi-restraints excluded: chain A residue  987 ASP
Chi-restraints excluded: chain A residue 1003 LEU
Chi-restraints excluded: chain A residue 1089 VAL
Chi-restraints excluded: chain A residue 1175 ARG
Chi-restraints excluded: chain A residue 1199 PHE
Chi-restraints excluded: chain A residue 1204 LEU
Chi-restraints excluded: chain A residue 1210 THR
Chi-restraints excluded: chain A residue 1221 GLU
Chi-restraints excluded: chain A residue 1271 ASN
Chi-restraints excluded: chain A residue 1325 LEU
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1405 ASN
Chi-restraints excluded: chain A residue 1494 THR
Chi-restraints excluded: chain A residue 1509 ILE
Chi-restraints excluded: chain A residue 1522 THR
Chi-restraints excluded: chain A residue 1525 ILE
Chi-restraints excluded: chain A residue 1526 THR
Chi-restraints excluded: chain A residue 1529 ILE
Chi-restraints excluded: chain A residue 1542 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 73 optimal weight:    8.9990
   chunk 43 optimal weight:   20.0000
   chunk 62 optimal weight:   10.0000
   chunk 49 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 8 optimal weight:    8.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1196 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.133793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.108547 restraints weight = 14425.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.111697 restraints weight = 8276.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.113794 restraints weight = 5880.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.115081 restraints weight = 4734.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.115722 restraints weight = 4146.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8411  Z= 0.126
  Angle     :  0.624  10.442  11661  Z= 0.315
  Chirality :  0.039   0.178   1365
  Planarity :  0.005   0.049   1263
  Dihedral  : 16.101 177.531   1863
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.63 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 18.95 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.90 (0.29), residues: 846
  helix:  0.21 (0.30), residues: 337
  sheet: -1.67 (0.48), residues: 110
  loop : -2.50 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A1532 
 TYR   0.010   0.001   TYR A1181 
 PHE   0.016   0.001   PHE A 759 
 TRP   0.015   0.001   TRP A1078 
 HIS   0.010   0.001   HIS A 756 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 8407)
  covalent geometry    : angle       0.62346 (11658)
  hydrogen bonds       : bond        0.03750 (  263)
  hydrogen bonds       : angle       3.89575 (  767)
  metal coordination   : bond        0.00369 (    4)
  metal coordination   : angle       2.32008 (    3)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 76
  time to evaluate  : 0.408 
Fit side-chains
REVERT: A  630 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8478 (mt)
REVERT: A  914 ASP cc_start: 0.8080 (p0) cc_final: 0.7801 (p0)
REVERT: A  966 MET cc_start: 0.7901 (mtm) cc_final: 0.7303 (mtm)
REVERT: A 1112 THR cc_start: 0.8071 (p) cc_final: 0.7826 (t)
REVERT: A 1175 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6150 (mtp85)
REVERT: A 1379 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.6868 (p0)
REVERT: A 1509 ILE cc_start: 0.6141 (OUTLIER) cc_final: 0.5743 (mp)
REVERT: A 1542 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.6196 (ptp-170)
  outliers start: 39
  outliers final: 25
  residues processed: 103
  average time/residue: 0.0762
  time to fit residues: 11.2295
Evaluate side-chains
  101 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 71
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  762 LEU
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  857 VAL
Chi-restraints excluded: chain A residue  911 LEU
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  980 GLU
Chi-restraints excluded: chain A residue 1003 LEU
Chi-restraints excluded: chain A residue 1089 VAL
Chi-restraints excluded: chain A residue 1175 ARG
Chi-restraints excluded: chain A residue 1199 PHE
Chi-restraints excluded: chain A residue 1210 THR
Chi-restraints excluded: chain A residue 1221 GLU
Chi-restraints excluded: chain A residue 1271 ASN
Chi-restraints excluded: chain A residue 1325 LEU
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1379 ASP
Chi-restraints excluded: chain A residue 1405 ASN
Chi-restraints excluded: chain A residue 1417 LEU
Chi-restraints excluded: chain A residue 1494 THR
Chi-restraints excluded: chain A residue 1509 ILE
Chi-restraints excluded: chain A residue 1522 THR
Chi-restraints excluded: chain A residue 1525 ILE
Chi-restraints excluded: chain A residue 1526 THR
Chi-restraints excluded: chain A residue 1529 ILE
Chi-restraints excluded: chain A residue 1542 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 90 optimal weight:    7.9990
   chunk 80 optimal weight:   20.0000
   chunk 9 optimal weight:   10.0000
   chunk 36 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 69 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1196 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.129430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.104023 restraints weight = 14355.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.106982 restraints weight = 8510.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.108908 restraints weight = 6160.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.110213 restraints weight = 5034.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.110761 restraints weight = 4423.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   8411  Z= 0.225
  Angle     :  0.697   9.912  11661  Z= 0.352
  Chirality :  0.042   0.176   1365
  Planarity :  0.005   0.047   1263
  Dihedral  : 16.070 176.039   1861
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.11 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 19.61 %
    Favored  : 75.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.88 (0.29), residues: 846
  helix:  0.22 (0.30), residues: 338
  sheet: -1.84 (0.47), residues: 113
  loop : -2.42 (0.29), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A1215 
 TYR   0.015   0.001   TYR A1358 
 PHE   0.019   0.002   PHE A 759 
 TRP   0.011   0.002   TRP A1078 
 HIS   0.012   0.001   HIS A 756 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 8407)
  covalent geometry    : angle       0.69502 (11658)
  hydrogen bonds       : bond        0.04633 (  263)
  hydrogen bonds       : angle       4.14984 (  767)
  metal coordination   : bond        0.00546 (    4)
  metal coordination   : angle       3.23930 (    3)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 70
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  630 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8556 (mt)
REVERT: A  843 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9041 (tp)
REVERT: A  914 ASP cc_start: 0.8086 (p0) cc_final: 0.7778 (p0)
REVERT: A  966 MET cc_start: 0.8015 (mtm) cc_final: 0.7365 (mtm)
REVERT: A 1112 THR cc_start: 0.8135 (p) cc_final: 0.7876 (t)
REVERT: A 1175 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6189 (mtp85)
REVERT: A 1193 ARG cc_start: 0.7904 (ttp-110) cc_final: 0.7690 (mtm180)
REVERT: A 1213 SER cc_start: 0.7913 (OUTLIER) cc_final: 0.7689 (p)
REVERT: A 1379 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.6940 (p0)
REVERT: A 1509 ILE cc_start: 0.6181 (OUTLIER) cc_final: 0.5758 (mp)
REVERT: A 1542 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6022 (ptp-170)
  outliers start: 40
  outliers final: 27
  residues processed: 99
  average time/residue: 0.0685
  time to fit residues: 9.7258
Evaluate side-chains
  102 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 68
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain A residue  762 LEU
Chi-restraints excluded: chain A residue  832 ASN
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  857 VAL
Chi-restraints excluded: chain A residue  911 LEU
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  980 GLU
Chi-restraints excluded: chain A residue 1003 LEU
Chi-restraints excluded: chain A residue 1089 VAL
Chi-restraints excluded: chain A residue 1175 ARG
Chi-restraints excluded: chain A residue 1199 PHE
Chi-restraints excluded: chain A residue 1210 THR
Chi-restraints excluded: chain A residue 1213 SER
Chi-restraints excluded: chain A residue 1221 GLU
Chi-restraints excluded: chain A residue 1271 ASN
Chi-restraints excluded: chain A residue 1318 VAL
Chi-restraints excluded: chain A residue 1325 LEU
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1379 ASP
Chi-restraints excluded: chain A residue 1405 ASN
Chi-restraints excluded: chain A residue 1417 LEU
Chi-restraints excluded: chain A residue 1494 THR
Chi-restraints excluded: chain A residue 1509 ILE
Chi-restraints excluded: chain A residue 1522 THR
Chi-restraints excluded: chain A residue 1525 ILE
Chi-restraints excluded: chain A residue 1526 THR
Chi-restraints excluded: chain A residue 1529 ILE
Chi-restraints excluded: chain A residue 1542 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9990
   chunk 15 optimal weight:    9.9990
   chunk 29 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 12 optimal weight:    6.9990
   chunk 23 optimal weight:   20.0000
   chunk 84 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0270
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.7442

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

Flipped N/Q/H residues before XYZ refinement:
** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 977 GLN
A1196 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.134932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.110123 restraints weight = 14242.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.113201 restraints weight = 8338.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.115171 restraints weight = 5956.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.116234 restraints weight = 4848.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.117076 restraints weight = 4311.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.3487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   8411  Z= 0.114
  Angle     :  0.619   9.973  11661  Z= 0.312
  Chirality :  0.038   0.169   1365
  Planarity :  0.004   0.050   1263
  Dihedral  : 15.955 177.837   1861
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.87 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 19.47 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.70 (0.29), residues: 846
  helix:  0.41 (0.30), residues: 338
  sheet: -1.63 (0.48), residues: 110
  loop : -2.41 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A1215 
 TYR   0.009   0.001   TYR A1181 
 PHE   0.012   0.001   PHE A 759 
 TRP   0.016   0.001   TRP A1078 
 HIS   0.009   0.001   HIS A 756 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 8407)
  covalent geometry    : angle       0.61838 (11658)
  hydrogen bonds       : bond        0.03551 (  263)
  hydrogen bonds       : angle       3.83573 (  767)
  metal coordination   : bond        0.00311 (    4)
  metal coordination   : angle       1.95504 (    3)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 73
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  630 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8456 (mt)
REVERT: A  843 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8836 (tp)
REVERT: A  914 ASP cc_start: 0.8068 (p0) cc_final: 0.7770 (p0)
REVERT: A 1112 THR cc_start: 0.8077 (p) cc_final: 0.7841 (t)
REVERT: A 1175 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6183 (mtp85)
REVERT: A 1190 GLU cc_start: 0.7936 (pm20) cc_final: 0.7574 (mp0)
REVERT: A 1193 ARG cc_start: 0.7875 (ttp-110) cc_final: 0.7560 (mtm180)
REVERT: A 1379 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.6987 (p0)
REVERT: A 1509 ILE cc_start: 0.6211 (OUTLIER) cc_final: 0.5819 (mp)
REVERT: A 1542 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6008 (ptp-170)
  outliers start: 40
  outliers final: 27
  residues processed: 102
  average time/residue: 0.0773
  time to fit residues: 11.2715
Evaluate side-chains
  105 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 72
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain A residue  762 LEU
Chi-restraints excluded: chain A residue  832 ASN
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  853 ILE
Chi-restraints excluded: chain A residue  857 VAL
Chi-restraints excluded: chain A residue  911 LEU
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  980 GLU
Chi-restraints excluded: chain A residue 1003 LEU
Chi-restraints excluded: chain A residue 1089 VAL
Chi-restraints excluded: chain A residue 1175 ARG
Chi-restraints excluded: chain A residue 1199 PHE
Chi-restraints excluded: chain A residue 1210 THR
Chi-restraints excluded: chain A residue 1271 ASN
Chi-restraints excluded: chain A residue 1318 VAL
Chi-restraints excluded: chain A residue 1325 LEU
Chi-restraints excluded: chain A residue 1333 LEU
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1379 ASP
Chi-restraints excluded: chain A residue 1405 ASN
Chi-restraints excluded: chain A residue 1494 THR
Chi-restraints excluded: chain A residue 1509 ILE
Chi-restraints excluded: chain A residue 1522 THR
Chi-restraints excluded: chain A residue 1525 ILE
Chi-restraints excluded: chain A residue 1526 THR
Chi-restraints excluded: chain A residue 1529 ILE
Chi-restraints excluded: chain A residue 1542 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 91 optimal weight:   10.0000
   chunk 9 optimal weight:    6.9990
   chunk 55 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0170
   chunk 67 optimal weight:    0.0980
   chunk 40 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0170
   chunk 46 optimal weight:    0.2980
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1196 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.137873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.113215 restraints weight = 14351.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.116360 restraints weight = 8324.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.118417 restraints weight = 5917.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.119721 restraints weight = 4795.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.120438 restraints weight = 4187.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.3719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   8411  Z= 0.108
  Angle     :  0.608   9.641  11661  Z= 0.305
  Chirality :  0.038   0.183   1365
  Planarity :  0.005   0.053   1263
  Dihedral  : 15.859 177.933   1861
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.10 %
    Favored  : 90.90 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 20.00 %
    Favored  : 75.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.36 (0.29), residues: 846
  helix:  0.78 (0.30), residues: 330
  sheet: -1.44 (0.49), residues: 109
  loop : -2.24 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A1215 
 TYR   0.013   0.001   TYR A1291 
 PHE   0.018   0.001   PHE A 759 
 TRP   0.008   0.001   TRP A1078 
 HIS   0.009   0.001   HIS A 756 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 8407)
  covalent geometry    : angle       0.60760 (11658)
  hydrogen bonds       : bond        0.03167 (  263)
  hydrogen bonds       : angle       3.73208 (  767)
  metal coordination   : bond        0.00264 (    4)
  metal coordination   : angle       1.60892 (    3)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 81
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A  624 SER cc_start: 0.8863 (p) cc_final: 0.8585 (t)
REVERT: A  843 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8713 (tp)
REVERT: A  914 ASP cc_start: 0.8063 (p0) cc_final: 0.7793 (p0)
REVERT: A 1112 THR cc_start: 0.8127 (p) cc_final: 0.7870 (t)
REVERT: A 1175 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6235 (mtp85)
REVERT: A 1190 GLU cc_start: 0.7923 (pm20) cc_final: 0.7574 (mp0)
REVERT: A 1193 ARG cc_start: 0.7864 (ttp-110) cc_final: 0.7576 (mtm180)
REVERT: A 1326 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8725 (tt)
REVERT: A 1379 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7025 (p0)
REVERT: A 1509 ILE cc_start: 0.6043 (OUTLIER) cc_final: 0.5655 (mp)
REVERT: A 1542 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6022 (ptp-170)
  outliers start: 35
  outliers final: 24
  residues processed: 103
  average time/residue: 0.0758
  time to fit residues: 11.1873
Evaluate side-chains
  103 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 73
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain A residue  762 LEU
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  857 VAL
Chi-restraints excluded: chain A residue  911 LEU
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  980 GLU
Chi-restraints excluded: chain A residue 1003 LEU
Chi-restraints excluded: chain A residue 1089 VAL
Chi-restraints excluded: chain A residue 1175 ARG
Chi-restraints excluded: chain A residue 1210 THR
Chi-restraints excluded: chain A residue 1271 ASN
Chi-restraints excluded: chain A residue 1318 VAL
Chi-restraints excluded: chain A residue 1325 LEU
Chi-restraints excluded: chain A residue 1326 LEU
Chi-restraints excluded: chain A residue 1333 LEU
Chi-restraints excluded: chain A residue 1353 LEU
Chi-restraints excluded: chain A residue 1379 ASP
Chi-restraints excluded: chain A residue 1405 ASN
Chi-restraints excluded: chain A residue 1494 THR
Chi-restraints excluded: chain A residue 1509 ILE
Chi-restraints excluded: chain A residue 1522 THR
Chi-restraints excluded: chain A residue 1525 ILE
Chi-restraints excluded: chain A residue 1526 THR
Chi-restraints excluded: chain A residue 1529 ILE
Chi-restraints excluded: chain A residue 1542 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 64 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 36 optimal weight:    4.9990
   chunk 57 optimal weight:    0.0010
   chunk 14 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   overall best weight:    2.1992

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

Flipped N/Q/H residues before XYZ refinement:
** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1196 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.133005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.107912 restraints weight = 14454.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.110928 restraints weight = 8463.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.112861 restraints weight = 6075.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.114138 restraints weight = 4953.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.114844 restraints weight = 4352.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.3657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8411  Z= 0.161
  Angle     :  0.649  10.132  11661  Z= 0.326
  Chirality :  0.040   0.177   1365
  Planarity :  0.005   0.050   1263
  Dihedral  : 15.840 176.246   1859
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.93 %
    Favored  : 90.07 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 21.32 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.30), residues: 846
  helix:  0.83 (0.31), residues: 333
  sheet: -1.67 (0.47), residues: 112
  loop : -2.26 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A1215 
 TYR   0.009   0.001   TYR A1181 
 PHE   0.018   0.001   PHE A 759 
 TRP   0.009   0.002   TRP A1078 
 HIS   0.010   0.001   HIS A 756 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 8407)
  covalent geometry    : angle       0.64744 (11658)
  hydrogen bonds       : bond        0.04003 (  263)
  hydrogen bonds       : angle       3.89892 (  767)
  metal coordination   : bond        0.00379 (    4)
  metal coordination   : angle       2.50254 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1272.63 seconds
wall clock time: 22 minutes 39.33 seconds (1359.33 seconds total)