Starting phenix.real_space_refine
on Wed Mar 12 19:52:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vg3_31964/03_2025/7vg3_31964.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vg3_31964/03_2025/7vg3_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_2025/7vg3_31964.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vg3_31964/03_2025/7vg3_31964.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vg3_31964/03_2025/7vg3_31964.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vg3_31964/03_2025/7vg3_31964.cif"
  }
  resolution = 3.73
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.18, per 1000 atoms: 0.64
  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: 2.21
  Conformation dependent library (CDL) restraints added in 779.6 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: 3.53
  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: 3.65

  Time building geometry restraints manager: 2.60 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:             0.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     27.090
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.000
-------------------------------------------------------------------------------
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      :  0.006   0.126   8407  Z= 0.405
  Angle     :  1.148  11.258  11658  Z= 0.654
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.017   0.003   TRP A1078 
 HIS   0.010   0.002   HIS A 631 
 PHE   0.025   0.003   PHE A 989 
 TYR   0.019   0.002   TYR A1370 
 ARG   0.011   0.001   ARG A 968 

*********************** 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  : 0.902 
Fit side-chains
   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: 0.8279 (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: 0.8071 (mtm) cc_final: 0.7847 (mtp)
REVERT: A  969 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8575 (tm)
REVERT: A 1112 THR cc_start: 0.8111 (p) cc_final: 0.7861 (t)
REVERT: A 1213 SER cc_start: 0.7024 (OUTLIER) cc_final: 0.6731 (p)
REVERT: A 1403 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.6952 (pp30)
REVERT: A 1492 MET cc_start: 0.8223 (tpp) cc_final: 0.7900 (tpt)
REVERT: A 1526 THR cc_start: 0.9043 (t) cc_final: 0.8747 (p)
  outliers start: 39
  outliers final: 16
  residues processed: 151
  average time/residue: 0.2516
  time to fit residues: 49.3104
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  : 0.907 
-------------------------------------------------------------------------------
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 77 optimal weight:    7.9990
   chunk 69 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 23 optimal weight:    9.9990
   chunk 47 optimal weight:    0.6980
   chunk 37 optimal weight:    6.9990
   chunk 72 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 53 optimal weight:    0.4980
   chunk 83 optimal weight:    5.9990
   overall best weight:    2.6386

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A1054 ASN
A1110 ASN
A1260 ASN
A1403 GLN
A1405 ASN
A1460 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.130737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.105070 restraints weight = 14158.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.108312 restraints weight = 8004.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.110416 restraints weight = 5604.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8407  Z= 0.274
  Angle     :  0.717   9.475  11658  Z= 0.368
  Chirality :  0.043   0.179   1365
  Planarity :  0.006   0.091   1263
  Dihedral  : 16.824 176.170   1895
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.98 %
    Favored  : 90.78 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 11.05 %
    Favored  : 82.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.46 (0.25), residues: 846
  helix: -1.80 (0.25), residues: 332
  sheet: -1.54 (0.49), residues: 112
  loop : -2.97 (0.26), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A1078 
 HIS   0.014   0.001   HIS A 756 
 PHE   0.018   0.002   PHE A 759 
 TYR   0.022   0.002   TYR A1181 
 ARG   0.009   0.001   ARG A1215 

*********************** 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
  137 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 89
  time to evaluate  : 0.849 
Fit side-chains
REVERT: A  624 SER cc_start: 0.8830 (p) cc_final: 0.8576 (t)
REVERT: A  728 MET cc_start: 0.8225 (mpp) cc_final: 0.7948 (mtm)
REVERT: A  731 LYS cc_start: 0.8757 (ptmt) cc_final: 0.8366 (ptmm)
REVERT: A  760 MET cc_start: 0.7161 (mmm) cc_final: 0.6830 (mmm)
REVERT: A  828 ILE cc_start: 0.1547 (OUTLIER) cc_final: 0.1153 (tp)
REVERT: A  914 ASP cc_start: 0.8219 (p0) cc_final: 0.7867 (p0)
REVERT: A  966 MET cc_start: 0.7938 (mtm) cc_final: 0.7583 (mtp)
  outliers start: 48
  outliers final: 27
  residues processed: 132
  average time/residue: 0.1761
  time to fit residues: 33.3802
Evaluate side-chains
  97 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 69
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
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  759 PHE
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  848 ILE
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  986 ILE
Chi-restraints excluded: chain A residue  987 ASP
Chi-restraints excluded: chain A residue 1003 LEU
Chi-restraints excluded: chain A residue 1074 GLU
Chi-restraints excluded: chain A residue 1089 VAL
Chi-restraints excluded: chain A residue 1152 LEU
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 1353 LEU
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 0 optimal weight:    7.9990
   chunk 16 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 45 optimal weight:    8.9990
   chunk 51 optimal weight:    0.0370
   chunk 71 optimal weight:    5.9990
   chunk 37 optimal weight:   10.0000
   chunk 85 optimal weight:    0.7980
   chunk 88 optimal weight:   10.0000
   chunk 76 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.3462

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

Flipped N/Q/H residues before XYZ refinement:
A1029 HIS
A1197 HIS
A1482 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.134766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.109939 restraints weight = 14304.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.113114 restraints weight = 8179.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.115220 restraints weight = 5775.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.2460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8407  Z= 0.175
  Angle     :  0.624   9.535  11658  Z= 0.321
  Chirality :  0.040   0.156   1365
  Planarity :  0.005   0.062   1263
  Dihedral  : 16.385 177.653   1874
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.81 %
    Favored  : 90.07 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 13.55 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.27), residues: 846
  helix: -0.92 (0.28), residues: 332
  sheet: -1.56 (0.49), residues: 112
  loop : -2.68 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1078 
 HIS   0.014   0.001   HIS A 756 
 PHE   0.010   0.001   PHE A 759 
 TYR   0.014   0.001   TYR A1220 
 ARG   0.008   0.000   ARG A1215 

*********************** 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
  119 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 79
  time to evaluate  : 0.772 
Fit side-chains
REVERT: A  624 SER cc_start: 0.8810 (p) cc_final: 0.8530 (t)
REVERT: A  731 LYS cc_start: 0.8696 (ptmt) cc_final: 0.8309 (ptmm)
REVERT: A  914 ASP cc_start: 0.8177 (p0) cc_final: 0.7814 (p0)
REVERT: A  966 MET cc_start: 0.7996 (mtm) cc_final: 0.7585 (mtp)
REVERT: A 1112 THR cc_start: 0.8210 (p) cc_final: 0.7970 (t)
REVERT: A 1175 ARG cc_start: 0.6687 (OUTLIER) cc_final: 0.5916 (mmm160)
  outliers start: 40
  outliers final: 31
  residues processed: 113
  average time/residue: 0.1825
  time to fit residues: 28.9776
Evaluate side-chains
  102 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 70
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
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  754 LEU
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  846 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  986 ILE
Chi-restraints excluded: chain A residue 1001 THR
Chi-restraints excluded: chain A residue 1003 LEU
Chi-restraints excluded: chain A residue 1074 GLU
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 1213 SER
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 1403 GLN
Chi-restraints excluded: chain A residue 1405 ASN
Chi-restraints excluded: chain A residue 1417 LEU
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 1 optimal weight:    0.1980
   chunk 53 optimal weight:    0.9990
   chunk 61 optimal weight:   10.0000
   chunk 72 optimal weight:    7.9990
   chunk 0 optimal weight:    8.9990
   chunk 34 optimal weight:    0.0670
   chunk 32 optimal weight:    8.9990
   chunk 58 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 12 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    1.8322

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

Flipped N/Q/H residues before XYZ refinement:
A 722 GLN
A 896 ASN
A1196 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.133362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.108251 restraints weight = 14158.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.111349 restraints weight = 8200.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.113401 restraints weight = 5842.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.2728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8407  Z= 0.204
  Angle     :  0.611   9.796  11658  Z= 0.314
  Chirality :  0.040   0.150   1365
  Planarity :  0.005   0.054   1263
  Dihedral  : 16.216 177.269   1871
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.34 %
    Favored  : 90.54 %
  Rotamer:
    Outliers :  6.71 %
    Allowed  : 14.74 %
    Favored  : 78.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.28), residues: 846
  helix: -0.33 (0.29), residues: 331
  sheet: -1.61 (0.48), residues: 112
  loop : -2.50 (0.28), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1078 
 HIS   0.011   0.001   HIS A 756 
 PHE   0.017   0.001   PHE A 759 
 TYR   0.014   0.001   TYR A1181 
 ARG   0.009   0.001   ARG A1215 

*********************** 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
  130 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 79
  time to evaluate  : 0.809 
Fit side-chains
REVERT: A  624 SER cc_start: 0.8870 (p) cc_final: 0.8573 (t)
REVERT: A  731 LYS cc_start: 0.8672 (ptmt) cc_final: 0.8288 (ptmm)
REVERT: A  828 ILE cc_start: 0.1612 (OUTLIER) cc_final: 0.1297 (tp)
REVERT: A  902 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9041 (pp)
REVERT: A  914 ASP cc_start: 0.8128 (p0) cc_final: 0.7735 (p0)
REVERT: A  966 MET cc_start: 0.8005 (mtm) cc_final: 0.7546 (mtp)
REVERT: A 1112 THR cc_start: 0.8059 (p) cc_final: 0.7827 (t)
REVERT: A 1154 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8370 (tpp)
REVERT: A 1174 ASN cc_start: 0.6112 (m110) cc_final: 0.5907 (m110)
REVERT: A 1175 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.5814 (mtp85)
REVERT: A 1472 MET cc_start: 0.8513 (mmt) cc_final: 0.8241 (mmp)
REVERT: A 1509 ILE cc_start: 0.6079 (OUTLIER) cc_final: 0.5653 (mp)
  outliers start: 51
  outliers final: 30
  residues processed: 124
  average time/residue: 0.1831
  time to fit residues: 31.8531
Evaluate side-chains
  107 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 72
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
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  709 LEU
Chi-restraints excluded: chain A residue  754 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  848 ILE
Chi-restraints excluded: chain A residue  857 VAL
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 1003 LEU
Chi-restraints excluded: chain A residue 1028 CYS
Chi-restraints excluded: chain A residue 1074 GLU
Chi-restraints excluded: chain A residue 1089 VAL
Chi-restraints excluded: chain A residue 1154 MET
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 1213 SER
Chi-restraints excluded: chain A residue 1219 SER
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 1403 GLN
Chi-restraints excluded: chain A residue 1405 ASN
Chi-restraints excluded: chain A residue 1417 LEU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 20 optimal weight:    7.9990
   chunk 11 optimal weight:    8.9990
   chunk 56 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 51 optimal weight:    0.3980
   chunk 57 optimal weight:    5.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    2.6788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.131354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.105911 restraints weight = 14240.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.109015 restraints weight = 8313.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.111067 restraints weight = 5931.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8407  Z= 0.264
  Angle     :  0.647   9.837  11658  Z= 0.329
  Chirality :  0.041   0.156   1365
  Planarity :  0.005   0.045   1263
  Dihedral  : 16.167 176.532   1865
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 10.64 %
    Favored  : 89.24 %
  Rotamer:
    Outliers :  6.58 %
    Allowed  : 15.92 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.28), residues: 846
  helix: -0.08 (0.29), residues: 331
  sheet: -1.76 (0.48), residues: 112
  loop : -2.46 (0.28), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A1078 
 HIS   0.012   0.001   HIS A 756 
 PHE   0.020   0.002   PHE A 759 
 TYR   0.014   0.001   TYR A1358 
 ARG   0.010   0.001   ARG A1215 

*********************** 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
  123 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 73
  time to evaluate  : 0.996 
Fit side-chains
REVERT: A  630 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8562 (mt)
REVERT: A  762 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8309 (mm)
REVERT: A  788 ILE cc_start: 0.9187 (tp) cc_final: 0.8981 (tp)
REVERT: A  828 ILE cc_start: 0.1713 (OUTLIER) cc_final: 0.1394 (tp)
REVERT: A  914 ASP cc_start: 0.8154 (p0) cc_final: 0.7736 (p0)
REVERT: A  966 MET cc_start: 0.7966 (mtm) cc_final: 0.7281 (mtm)
REVERT: A 1112 THR cc_start: 0.8106 (p) cc_final: 0.7858 (t)
REVERT: A 1154 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8432 (tpp)
REVERT: A 1175 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.5906 (mtp85)
REVERT: A 1509 ILE cc_start: 0.6153 (OUTLIER) cc_final: 0.5738 (mp)
REVERT: A 1542 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6268 (ptp-170)
  outliers start: 50
  outliers final: 31
  residues processed: 113
  average time/residue: 0.2048
  time to fit residues: 32.1514
Evaluate side-chains
  106 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 68
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
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  673 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  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  857 VAL
Chi-restraints excluded: chain A residue  890 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 1003 LEU
Chi-restraints excluded: chain A residue 1074 GLU
Chi-restraints excluded: chain A residue 1089 VAL
Chi-restraints excluded: chain A residue 1154 MET
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 1219 SER
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 1397 THR
Chi-restraints excluded: chain A residue 1405 ASN
Chi-restraints excluded: chain A residue 1417 LEU
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 15 optimal weight:   10.0000
   chunk 30 optimal weight:    0.0870
   chunk 31 optimal weight:    5.9990
   chunk 85 optimal weight:   10.0000
   chunk 55 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 12 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 51 optimal weight:    8.9990
   chunk 91 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   overall best weight:    5.2166

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

Flipped N/Q/H residues before XYZ refinement:
A 938 HIS
A1052 ASN
A1174 ASN
A1278 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.126175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.100605 restraints weight = 14450.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.103583 restraints weight = 8496.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.105529 restraints weight = 6119.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068   8407  Z= 0.465
  Angle     :  0.793  10.957  11658  Z= 0.400
  Chirality :  0.046   0.177   1365
  Planarity :  0.005   0.045   1263
  Dihedral  : 16.334 174.750   1865
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 12.06 %
    Favored  : 87.83 %
  Rotamer:
    Outliers :  6.58 %
    Allowed  : 18.03 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.28), residues: 846
  helix: -0.23 (0.29), residues: 329
  sheet: -2.02 (0.47), residues: 113
  loop : -2.60 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP A1078 
 HIS   0.014   0.002   HIS A 756 
 PHE   0.024   0.003   PHE A 759 
 TYR   0.023   0.002   TYR A1358 
 ARG   0.006   0.001   ARG A1215 

*********************** 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
  117 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 67
  time to evaluate  : 0.823 
Fit side-chains
REVERT: A  630 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8574 (mt)
REVERT: A  788 ILE cc_start: 0.9196 (tp) cc_final: 0.8986 (tp)
REVERT: A  828 ILE cc_start: 0.1727 (OUTLIER) cc_final: 0.1415 (tp)
REVERT: A  914 ASP cc_start: 0.8084 (p0) cc_final: 0.7632 (p0)
REVERT: A  966 MET cc_start: 0.8119 (mtm) cc_final: 0.7556 (mtp)
REVERT: A 1052 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8798 (t0)
REVERT: A 1154 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8544 (tpp)
REVERT: A 1175 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6139 (mtp85)
REVERT: A 1509 ILE cc_start: 0.6091 (OUTLIER) cc_final: 0.5661 (mp)
REVERT: A 1542 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6150 (ptp-170)
  outliers start: 50
  outliers final: 33
  residues processed: 110
  average time/residue: 0.1998
  time to fit residues: 30.4051
Evaluate side-chains
  103 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 63
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
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  657 PHE
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  709 LEU
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  857 VAL
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 1003 LEU
Chi-restraints excluded: chain A residue 1052 ASN
Chi-restraints excluded: chain A residue 1074 GLU
Chi-restraints excluded: chain A residue 1089 VAL
Chi-restraints excluded: chain A residue 1154 MET
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 1379 ASP
Chi-restraints excluded: chain A residue 1397 THR
Chi-restraints excluded: chain A residue 1405 ASN
Chi-restraints excluded: chain A residue 1417 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 81 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   chunk 17 optimal weight:   10.0000
   chunk 43 optimal weight:    0.0170
   chunk 77 optimal weight:    5.9990
   overall best weight:    1.1824

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

Flipped N/Q/H residues before XYZ refinement:
A 662 ASN

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 = 0.132918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.107805 restraints weight = 14226.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.110942 restraints weight = 8192.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.113031 restraints weight = 5820.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.3258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8407  Z= 0.171
  Angle     :  0.639  10.863  11658  Z= 0.321
  Chirality :  0.039   0.160   1365
  Planarity :  0.004   0.045   1263
  Dihedral  : 16.172 177.707   1865
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.75 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 19.08 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.29), residues: 846
  helix:  0.17 (0.30), residues: 335
  sheet: -1.92 (0.47), residues: 111
  loop : -2.38 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A1078 
 HIS   0.010   0.001   HIS A 756 
 PHE   0.015   0.001   PHE A 759 
 TYR   0.009   0.001   TYR A1181 
 ARG   0.010   0.000   ARG A1215 

*********************** 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
  120 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 78
  time to evaluate  : 0.937 
Fit side-chains
REVERT: A  624 SER cc_start: 0.8871 (p) cc_final: 0.8620 (t)
REVERT: A  630 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8492 (mt)
REVERT: A  762 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8214 (mm)
REVERT: A  828 ILE cc_start: 0.1669 (OUTLIER) cc_final: 0.1389 (tp)
REVERT: A  914 ASP cc_start: 0.8115 (p0) cc_final: 0.7692 (p0)
REVERT: A  966 MET cc_start: 0.7859 (mtm) cc_final: 0.7244 (mtm)
REVERT: A 1154 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8364 (tpp)
REVERT: A 1175 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6152 (mtp85)
REVERT: A 1379 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.6907 (p0)
REVERT: A 1509 ILE cc_start: 0.6137 (OUTLIER) cc_final: 0.5716 (mp)
  outliers start: 42
  outliers final: 27
  residues processed: 107
  average time/residue: 0.2007
  time to fit residues: 30.1736
Evaluate side-chains
  107 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 73
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
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  733 PHE
Chi-restraints excluded: chain A residue  762 LEU
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  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 1154 MET
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 1271 ASN
Chi-restraints excluded: chain A residue 1325 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 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 91 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 49 optimal weight:    7.9990
   chunk 3 optimal weight:    6.9990
   chunk 15 optimal weight:   10.0000
   chunk 75 optimal weight:    0.1980
   chunk 66 optimal weight:    0.0050
   chunk 45 optimal weight:    7.9990
   overall best weight:    0.9796

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

Flipped N/Q/H residues before XYZ refinement:
A 662 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.134575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.109508 restraints weight = 14351.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.112626 restraints weight = 8283.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.114658 restraints weight = 5878.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.3397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8407  Z= 0.161
  Angle     :  0.617  10.120  11658  Z= 0.309
  Chirality :  0.038   0.145   1365
  Planarity :  0.004   0.049   1263
  Dihedral  : 16.049 177.694   1865
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.28 %
    Favored  : 89.72 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 20.92 %
    Favored  : 74.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.29), residues: 846
  helix:  0.47 (0.30), residues: 334
  sheet: -1.74 (0.48), residues: 110
  loop : -2.25 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1078 
 HIS   0.009   0.001   HIS A 756 
 PHE   0.016   0.001   PHE A 759 
 TYR   0.016   0.001   TYR A1034 
 ARG   0.011   0.000   ARG A1215 

*********************** 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
  115 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 79
  time to evaluate  : 0.796 
Fit side-chains
REVERT: A  624 SER cc_start: 0.8877 (p) cc_final: 0.8600 (t)
REVERT: A  630 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8478 (mt)
REVERT: A  762 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8191 (mm)
REVERT: A  914 ASP cc_start: 0.8077 (p0) cc_final: 0.7792 (p0)
REVERT: A  966 MET cc_start: 0.7912 (mtm) cc_final: 0.7317 (mtm)
REVERT: A 1175 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6193 (mtp85)
REVERT: A 1379 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.6960 (p0)
REVERT: A 1509 ILE cc_start: 0.6183 (OUTLIER) cc_final: 0.5786 (mp)
REVERT: A 1542 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.5904 (ptp-170)
  outliers start: 36
  outliers final: 20
  residues processed: 105
  average time/residue: 0.1931
  time to fit residues: 28.3122
Evaluate side-chains
  98 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 72
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
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  836 ASP
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 1001 THR
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 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 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
Chi-restraints excluded: chain A residue 1547 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    7.9990
   chunk 8 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   chunk 45 optimal weight:    6.9990
   chunk 11 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 17 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0870
   overall best weight:    0.9962

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.135608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.110838 restraints weight = 14456.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.113871 restraints weight = 8492.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.115876 restraints weight = 6090.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.3509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   8407  Z= 0.160
  Angle     :  0.611  10.303  11658  Z= 0.306
  Chirality :  0.038   0.147   1365
  Planarity :  0.004   0.053   1263
  Dihedral  : 15.904 177.372   1861
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.87 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 20.66 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.29), residues: 846
  helix:  0.58 (0.30), residues: 334
  sheet: -1.63 (0.48), residues: 112
  loop : -2.18 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1078 
 HIS   0.010   0.001   HIS A 756 
 PHE   0.021   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A1034 
 ARG   0.012   0.000   ARG A1215 

*********************** 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
  108 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 76
  time to evaluate  : 0.866 
Fit side-chains
REVERT: A  624 SER cc_start: 0.8873 (p) cc_final: 0.8600 (t)
REVERT: A  630 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8466 (mt)
REVERT: A  762 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8195 (mm)
REVERT: A  828 ILE cc_start: 0.1524 (OUTLIER) cc_final: 0.1092 (tp)
REVERT: A  914 ASP cc_start: 0.8090 (p0) cc_final: 0.7808 (p0)
REVERT: A  966 MET cc_start: 0.7931 (mtm) cc_final: 0.7344 (mtm)
REVERT: A 1112 THR cc_start: 0.8177 (p) cc_final: 0.7942 (t)
REVERT: A 1175 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6213 (mtp85)
REVERT: A 1191 LEU cc_start: 0.8767 (tt) cc_final: 0.8563 (tt)
REVERT: A 1379 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7012 (p0)
REVERT: A 1509 ILE cc_start: 0.6178 (OUTLIER) cc_final: 0.5757 (mp)
REVERT: A 1542 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6133 (ptp-170)
  outliers start: 32
  outliers final: 20
  residues processed: 100
  average time/residue: 0.2424
  time to fit residues: 33.7046
Evaluate side-chains
  98 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 71
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
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  734 VAL
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  846 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 1001 THR
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 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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 81 optimal weight:   10.0000
   chunk 58 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 36 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 48 optimal weight:    8.9990
   chunk 82 optimal weight:    1.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    3.3988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.129524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.104204 restraints weight = 14393.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.107152 restraints weight = 8497.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.109080 restraints weight = 6159.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.3494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   8407  Z= 0.316
  Angle     :  0.701  10.005  11658  Z= 0.354
  Chirality :  0.042   0.155   1365
  Planarity :  0.005   0.051   1263
  Dihedral  : 15.981 175.717   1861
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.11 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 21.97 %
    Favored  : 74.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.29), residues: 846
  helix:  0.46 (0.30), residues: 339
  sheet: -1.86 (0.47), residues: 112
  loop : -2.29 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 643 
 HIS   0.012   0.001   HIS A 756 
 PHE   0.024   0.002   PHE A 759 
 TYR   0.010   0.001   TYR A1181 
 ARG   0.013   0.001   ARG A1215 

********************** 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
  95 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 67
  time to evaluate  : 0.980 
Fit side-chains
REVERT: A  762 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8329 (mm)
REVERT: A  828 ILE cc_start: 0.1406 (OUTLIER) cc_final: 0.1100 (tp)
REVERT: A  914 ASP cc_start: 0.8088 (p0) cc_final: 0.7772 (p0)
REVERT: A  966 MET cc_start: 0.8005 (mtm) cc_final: 0.7309 (mtm)
REVERT: A 1175 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6235 (mtp85)
REVERT: A 1379 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7020 (p0)
REVERT: A 1509 ILE cc_start: 0.6173 (OUTLIER) cc_final: 0.5736 (mp)
REVERT: A 1542 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6486 (ptp-170)
  outliers start: 28
  outliers final: 18
  residues processed: 89
  average time/residue: 0.2050
  time to fit residues: 25.4926
Evaluate side-chains
  91 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 67
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  639 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  828 ILE
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  846 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 1210 THR
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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 33 optimal weight:    0.7980
   chunk 32 optimal weight:    9.9990
   chunk 11 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9980
   chunk 20 optimal weight:    7.9990
   chunk 4 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 67 optimal weight:    8.9990
   chunk 31 optimal weight:    0.4980
   overall best weight:    1.8584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.132233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.107126 restraints weight = 14378.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.110186 restraints weight = 8439.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.112141 restraints weight = 6053.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8407  Z= 0.209
  Angle     :  0.659   9.795  11658  Z= 0.331
  Chirality :  0.040   0.187   1365
  Planarity :  0.004   0.053   1263
  Dihedral  : 15.897 176.869   1859
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 21.84 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.29), residues: 846
  helix:  0.55 (0.30), residues: 337
  sheet: -1.77 (0.48), residues: 112
  loop : -2.26 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1078 
 HIS   0.011   0.001   HIS A 756 
 PHE   0.021   0.001   PHE A 759 
 TYR   0.008   0.001   TYR A1181 
 ARG   0.013   0.001   ARG A1215 
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 2442.00 seconds
wall clock time: 43 minutes 58.74 seconds (2638.74 seconds total)