Starting phenix.real_space_refine
on Thu Mar 13 18:27:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zk9_14759/03_2025/7zk9_14759.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zk9_14759/03_2025/7zk9_14759.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zk9_14759/03_2025/7zk9_14759.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zk9_14759/03_2025/7zk9_14759.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zk9_14759/03_2025/7zk9_14759.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zk9_14759/03_2025/7zk9_14759.cif"
  }
  resolution = 4.3
  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=   0.001 sd=   0.017
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: 4
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    5781      2.51       5
     N    1533      2.21       5
     O    1651      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8999
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8968
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1157, 8968
          Classifications: {'peptide': 1157}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 29, 'TRANS': 1127}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'JIZ': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.35, per 1000 atoms: 0.71
  Number of scatterers: 8999
  At special positions: 0
  Unit cell: (76.167, 112.158, 146.475, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      34     16.00
     O    1651      8.00
     N    1533      7.00
     C    5781      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: 2.49
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2122

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 6 sheets defined
      67.4% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 82
      Proline residue:  A  65  - end of helix
    Processing helix  chain 'A' and resid 87 through 90
    Processing helix  chain 'A' and resid 91 through 154
      removed outlier: 5.071A  pdb=" N   ALA A  98 " --> pdb=" O   ALA A  94 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   MET A  99 " --> pdb=" O   ASP A  95 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ILE A 127 " --> pdb=" O   ILE A 123 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLN A 145 " --> pdb=" O   HIS A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 161
      removed outlier: 3.630A  pdb=" N   PHE A 159 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 207
      removed outlier: 3.779A  pdb=" N   ASN A 168 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
      removed outlier: 5.834A  pdb=" N   ILE A 186 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
      removed outlier: 5.284A  pdb=" N   GLY A 187 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   THR A 205 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 256
      removed outlier: 3.648A  pdb=" N   VAL A 213 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      Proline residue:  A 219  - end of helix
      removed outlier: 4.206A  pdb=" N   LYS A 245 " --> pdb=" O   HIS A 241 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   ALA A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ALA A 256 " --> pdb=" O   GLU A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 264
    Processing helix  chain 'A' and resid 270 through 319
    Processing helix  chain 'A' and resid 323 through 365
      removed outlier: 3.735A  pdb=" N   VAL A 327 " --> pdb=" O   SER A 323 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   SER A 345 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      Proline residue:  A 346  - end of helix
      removed outlier: 3.786A  pdb=" N   GLY A 356 " --> pdb=" O   ALA A 352 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ALA A 357 " --> pdb=" O   ASN A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 437
      removed outlier: 3.666A  pdb=" N   GLN A 434 " --> pdb=" O   SER A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 465
    Processing helix  chain 'A' and resid 479 through 488
      removed outlier: 3.534A  pdb=" N   ASN A 483 " --> pdb=" O   THR A 479 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ARG A 488 " --> pdb=" O   ILE A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 500
    Processing helix  chain 'A' and resid 528 through 544
    Processing helix  chain 'A' and resid 564 through 576
      removed outlier: 3.763A  pdb=" N   ALA A 568 " --> pdb=" O   VAL A 564 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   GLY A 575 " --> pdb=" O   LYS A 571 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ARG A 576 " --> pdb=" O   ALA A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 591
    Processing helix  chain 'A' and resid 695 through 700
    Processing helix  chain 'A' and resid 704 through 719
      removed outlier: 3.809A  pdb=" N   VAL A 709 " --> pdb=" O   PRO A 705 " (cutoff:3.500A)
      removed outlier: 5.456A  pdb=" N   GLY A 710 " --> pdb=" O   TYR A 706 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ILE A 711 " --> pdb=" O   PHE A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 736
      removed outlier: 3.710A  pdb=" N   PHE A 735 " --> pdb=" O   VAL A 731 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 795
      removed outlier: 4.057A  pdb=" N   LYS A 775 " --> pdb=" O   PHE A 771 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LYS A 790 " --> pdb=" O   TYR A 786 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 796 through 802
      removed outlier: 3.861A  pdb=" N   PHE A 800 " --> pdb=" O   ASP A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 806 through 817
    Processing helix  chain 'A' and resid 818 through 850
      removed outlier: 3.625A  pdb=" N   GLY A 826 " --> pdb=" O   LYS A 822 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   SER A 827 " --> pdb=" O   GLY A 823 " (cutoff:3.500A)
      removed outlier: 5.310A  pdb=" N   ARG A 828 " --> pdb=" O   ALA A 824 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   LEU A 829 " --> pdb=" O   THR A 825 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 852 through 886
      Proline residue:  A 862  - end of helix
    Processing helix  chain 'A' and resid 886 through 899
    Processing helix  chain 'A' and resid 899 through 906
    Processing helix  chain 'A' and resid 909 through 962
      removed outlier: 3.686A  pdb=" N   GLU A 913 " --> pdb=" O   GLU A 909 " (cutoff:3.500A)
      Proline residue:  A 923  - end of helix
      removed outlier: 3.732A  pdb=" N   VAL A 933 " --> pdb=" O   LYS A 929 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 966 through 991
    Processing helix  chain 'A' and resid 997 through 1010
    Processing helix  chain 'A' and resid 1068 through 1080
      removed outlier: 3.607A  pdb=" N   THR A1074 " --> pdb=" O   GLY A1070 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   VAL A1075 " --> pdb=" O   GLY A1071 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL A1076 " --> pdb=" O   LYS A1072 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LEU A1079 " --> pdb=" O   VAL A1075 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   GLU A1080 " --> pdb=" O   VAL A1076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1101 through 1108
    Processing helix  chain 'A' and resid 1122 through 1128
    Processing helix  chain 'A' and resid 1129 through 1132
    Processing helix  chain 'A' and resid 1139 through 1149
      removed outlier: 4.284A  pdb=" N   ARG A1143 " --> pdb=" O   GLU A1139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1150 through 1157
    Processing helix  chain 'A' and resid 1159 through 1163
    Processing helix  chain 'A' and resid 1173 through 1188
      removed outlier: 4.621A  pdb=" N   GLN A1178 " --> pdb=" O   GLY A1174 " (cutoff:3.500A)
      removed outlier: 4.622A  pdb=" N   ARG A1179 " --> pdb=" O   GLY A1175 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   ARG A1188 " --> pdb=" O   ARG A1184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1205 through 1221
      removed outlier: 3.638A  pdb=" N   VAL A1209 " --> pdb=" O   GLU A1205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1229 through 1236
    Processing helix  chain 'A' and resid 1250 through 1255
      removed outlier: 3.700A  pdb=" N   GLN A1254 " --> pdb=" O   HIS A1250 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 391
    Processing sheet with id=AA2, first strand: chain 'A' and resid 394 through 395
    Processing sheet with id=AA3, first strand: chain 'A' and resid 466 through 467
      removed outlier: 6.200A  pdb=" N   LEU A 548 " --> pdb=" O   ILE A 579 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   ILE A 581 " --> pdb=" O   LEU A 548 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   LEU A 550 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1031 through 1032
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1061 through 1064
      removed outlier: 5.747A  pdb=" N   LEU A1062 " --> pdb=" O   VAL A1225 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   LEU A1193 " --> pdb=" O   ILE A1224 " (cutoff:3.500A)
      removed outlier: 7.800A  pdb=" N   ILE A1226 " --> pdb=" O   LEU A1193 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   LEU A1195 " --> pdb=" O   ILE A1226 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   GLY A1110 " --> pdb=" O   LEU A1194 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1091 through 1092

    577 hydrogen bonds defined for protein.
    1701 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.91

  Time building geometry restraints manager: 2.90 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1478
        1.31 -     1.44: 2369
        1.44 -     1.56: 5251
        1.56 -     1.69: 8
        1.69 -     1.82: 60
  Bond restraints: 9166
  Sorted by residual:
  bond pdb=" C03 JIZ A1301 "
       pdb=" N02 JIZ A1301 "
    ideal  model  delta    sigma   weight residual
    1.367  1.638 -0.271 2.00e-02 2.50e+03 1.83e+02
  bond pdb=" C08 JIZ A1301 "
       pdb=" N04 JIZ A1301 "
    ideal  model  delta    sigma   weight residual
    1.366  1.615 -0.249 2.00e-02 2.50e+03 1.55e+02
  bond pdb=" C13 JIZ A1301 "
       pdb=" N06 JIZ A1301 "
    ideal  model  delta    sigma   weight residual
    1.366  1.613 -0.247 2.00e-02 2.50e+03 1.53e+02
  bond pdb=" C02 JIZ A1301 "
       pdb=" S01 JIZ A1301 "
    ideal  model  delta    sigma   weight residual
    1.728  1.547  0.181 2.00e-02 2.50e+03 8.16e+01
  bond pdb=" C03 JIZ A1301 "
       pdb=" C04 JIZ A1301 "
    ideal  model  delta    sigma   weight residual
    1.360  1.519 -0.159 2.00e-02 2.50e+03 6.30e+01
  ... (remaining 9161 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.54: 12234
        3.54 -     7.07: 149
        7.07 -    10.61: 6
       10.61 -    14.15: 1
       14.15 -    17.68: 3
  Bond angle restraints: 12393
  Sorted by residual:
  angle pdb=" N   SER A1206 "
        pdb=" CA  SER A1206 "
        pdb=" C   SER A1206 "
      ideal   model   delta    sigma   weight residual
     112.54  105.29    7.25 1.22e+00 6.72e-01 3.53e+01
  angle pdb=" C07 JIZ A1301 "
        pdb=" S02 JIZ A1301 "
        pdb=" C09 JIZ A1301 "
      ideal   model   delta    sigma   weight residual
      89.67  107.35  -17.68 3.00e+00 1.11e-01 3.47e+01
  angle pdb=" C12 JIZ A1301 "
        pdb=" S03 JIZ A1301 "
        pdb=" C14 JIZ A1301 "
      ideal   model   delta    sigma   weight residual
      89.68  107.08  -17.40 3.00e+00 1.11e-01 3.37e+01
  angle pdb=" N   PHE A1082 "
        pdb=" CA  PHE A1082 "
        pdb=" C   PHE A1082 "
      ideal   model   delta    sigma   weight residual
     111.28  105.53    5.75 1.09e+00 8.42e-01 2.78e+01
  angle pdb=" C02 JIZ A1301 "
        pdb=" S01 JIZ A1301 "
        pdb=" C04 JIZ A1301 "
      ideal   model   delta    sigma   weight residual
      89.57  105.17  -15.60 3.00e+00 1.11e-01 2.70e+01
  ... (remaining 12388 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.61: 4963
       17.61 -    35.22: 413
       35.22 -    52.82: 83
       52.82 -    70.43: 9
       70.43 -    88.04: 8
  Dihedral angle restraints: 5476
    sinusoidal: 2165
      harmonic: 3311
  Sorted by residual:
  dihedral pdb=" CA  PHE A 707 "
           pdb=" C   PHE A 707 "
           pdb=" N   VAL A 708 "
           pdb=" CA  VAL A 708 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.97  -21.03     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  MET A  99 "
           pdb=" C   MET A  99 "
           pdb=" N   PHE A 100 "
           pdb=" CA  PHE A 100 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.85   19.15     0      5.00e+00 4.00e-02 1.47e+01
  dihedral pdb=" CA  PRO A 740 "
           pdb=" C   PRO A 740 "
           pdb=" N   PRO A 741 "
           pdb=" CA  PRO A 741 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.90  -19.10     0      5.00e+00 4.00e-02 1.46e+01
  ... (remaining 5473 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1071
       0.058 -    0.116: 248
       0.116 -    0.174: 62
       0.174 -    0.232: 33
       0.232 -    0.290: 9
  Chirality restraints: 1423
  Sorted by residual:
  chirality pdb=" CA  VAL A1075 "
            pdb=" N   VAL A1075 "
            pdb=" C   VAL A1075 "
            pdb=" CB  VAL A1075 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.73   -0.29 2.00e-01 2.50e+01 2.10e+00
  chirality pdb=" CA  LEU A 519 "
            pdb=" N   LEU A 519 "
            pdb=" C   LEU A 519 "
            pdb=" CB  LEU A 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.07e+00
  chirality pdb=" CA  TYR A1083 "
            pdb=" N   TYR A1083 "
            pdb=" C   TYR A1083 "
            pdb=" CB  TYR A1083 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.85e+00
  ... (remaining 1420 not shown)

  Planarity restraints: 1578
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 964 "   -0.016 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   LEU A 964 "    0.058 2.00e-02 2.50e+03
        pdb=" O   LEU A 964 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   MET A 965 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 205 "   -0.015 2.00e-02 2.50e+03   2.90e-02 8.38e+00
        pdb=" C   THR A 205 "    0.050 2.00e-02 2.50e+03
        pdb=" O   THR A 205 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ARG A 206 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 507 "   -0.013 2.00e-02 2.50e+03   2.57e-02 6.63e+00
        pdb=" C   ASP A 507 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ASP A 507 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   PHE A 508 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1575 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.78: 1991
        2.78 -     3.31: 9996
        3.31 -     3.84: 15005
        3.84 -     4.37: 17015
        4.37 -     4.90: 27409
  Nonbonded interactions: 71416
  Sorted by model distance:
  nonbonded pdb=" O   ASN A1149 "
            pdb=" NH2 ARG A1179 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" O   ALA A 192 "
            pdb=" OG  SER A 340 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   ALA A 288 "
            pdb=" ND2 ASN A 292 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" O   LEU A 316 "
            pdb=" OG  SER A 319 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   ALA A 256 "
            pdb=" OG1 THR A 259 "
     model   vdw
     2.301 3.040
  ... (remaining 71411 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             1.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.980
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
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      :  0.009   0.271   9166  Z= 0.652
  Angle     :  1.002  17.683  12393  Z= 0.660
  Chirality :  0.063   0.290   1423
  Planarity :  0.004   0.039   1578
  Dihedral  : 13.586  88.038   3354
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 15.76
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.29 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  2.01 %
    Favored  : 97.25 %
  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: -0.05 (0.25), residues: 1153
  helix:  1.04 (0.19), residues: 732
  sheet: -1.02 (0.70), residues: 49
  loop : -2.09 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 704 
 HIS   0.002   0.000   HIS A1151 
 PHE   0.019   0.002   PHE A 100 
 TYR   0.022   0.001   TYR A 924 
 ARG   0.009   0.001   ARG A 589 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 273
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9265 (mt) cc_final: 0.8921 (tp)
REVERT: A   75 THR cc_start: 0.9537 (p) cc_final: 0.9333 (p)
REVERT: A   76 ASP cc_start: 0.8951 (m-30) cc_final: 0.8525 (m-30)
REVERT: A  100 PHE cc_start: 0.8316 (m-10) cc_final: 0.8052 (m-10)
REVERT: A  103 LEU cc_start: 0.9472 (tp) cc_final: 0.9147 (tp)
REVERT: A  160 ASP cc_start: 0.8800 (m-30) cc_final: 0.8469 (m-30)
REVERT: A  188 MET cc_start: 0.8620 (tpp) cc_final: 0.8256 (mmm)
REVERT: A  191 GLN cc_start: 0.9292 (tm-30) cc_final: 0.8921 (tm-30)
REVERT: A  209 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8338 (mptt)
REVERT: A  295 MET cc_start: 0.8575 (ttm) cc_final: 0.8356 (ttm)
REVERT: A  471 GLN cc_start: 0.8887 (pt0) cc_final: 0.8548 (pt0)
REVERT: A  754 LEU cc_start: 0.9044 (mt) cc_final: 0.8791 (mt)
REVERT: A  787 MET cc_start: 0.7680 (mmt) cc_final: 0.7270 (mtt)
REVERT: A  828 ARG cc_start: 0.9099 (tpt170) cc_final: 0.8713 (tpt90)
REVERT: A  872 MET cc_start: 0.7337 (mmp) cc_final: 0.7112 (mmm)
REVERT: A  928 MET cc_start: 0.9013 (mpp) cc_final: 0.8752 (mpp)
REVERT: A  953 PHE cc_start: 0.8634 (m-80) cc_final: 0.8315 (m-80)
REVERT: A  955 PHE cc_start: 0.8848 (t80) cc_final: 0.8087 (t80)
REVERT: A  960 VAL cc_start: 0.9389 (t) cc_final: 0.9158 (t)
REVERT: A 1162 ASN cc_start: 0.9106 (t0) cc_final: 0.8852 (t0)
  outliers start: 7
  outliers final: 2
  residues processed: 278
  average time/residue: 0.1690
  time to fit residues: 68.1066
Evaluate side-chains
  230 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 227
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    7.9990
   chunk 87 optimal weight:    4.9990
   chunk 48 optimal weight:   30.0000
   chunk 29 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0050
   chunk 46 optimal weight:    0.0870
   chunk 90 optimal weight:    0.8980
   chunk 34 optimal weight:    0.3980
   chunk 54 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9990
   chunk 104 optimal weight:    3.9990
   overall best weight:    0.4774

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

Flipped N/Q/H residues before XYZ refinement:
** A  60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 969 ASN
A1132 ASN
A1253 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.124305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.091916 restraints weight = 23281.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.095396 restraints weight = 14343.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.097808 restraints weight = 10168.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.1469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9166  Z= 0.173
  Angle     :  0.587   8.886  12393  Z= 0.317
  Chirality :  0.042   0.174   1423
  Planarity :  0.004   0.060   1578
  Dihedral  :  4.920  38.478   1274
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  4.86 %
    Favored  : 94.93 %
  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:  0.23 (0.25), residues: 1153
  helix:  1.22 (0.19), residues: 750
  sheet: -0.66 (0.77), residues: 43
  loop : -2.09 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 704 
 HIS   0.003   0.001   HIS A1151 
 PHE   0.023   0.002   PHE A 131 
 TYR   0.022   0.001   TYR A 924 
 ARG   0.006   0.000   ARG A 438 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 267
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9397 (mt) cc_final: 0.9162 (tp)
REVERT: A   76 ASP cc_start: 0.9080 (m-30) cc_final: 0.8553 (m-30)
REVERT: A   99 MET cc_start: 0.8543 (pmm) cc_final: 0.8297 (pmm)
REVERT: A  100 PHE cc_start: 0.8243 (m-10) cc_final: 0.7894 (m-10)
REVERT: A  103 LEU cc_start: 0.9532 (tp) cc_final: 0.9210 (tp)
REVERT: A  191 GLN cc_start: 0.9378 (tm-30) cc_final: 0.9157 (tm-30)
REVERT: A  209 LYS cc_start: 0.8987 (ptpp) cc_final: 0.8729 (mptt)
REVERT: A  228 TRP cc_start: 0.8828 (m100) cc_final: 0.8515 (m100)
REVERT: A  239 GLU cc_start: 0.9060 (pp20) cc_final: 0.8860 (pp20)
REVERT: A  720 LEU cc_start: 0.9411 (mm) cc_final: 0.8934 (mm)
REVERT: A  754 LEU cc_start: 0.9010 (mt) cc_final: 0.8718 (mt)
REVERT: A  787 MET cc_start: 0.7734 (mmt) cc_final: 0.7523 (mtt)
REVERT: A  828 ARG cc_start: 0.9002 (tpt170) cc_final: 0.8539 (tpt90)
REVERT: A  872 MET cc_start: 0.7384 (mmp) cc_final: 0.7143 (mmm)
REVERT: A  902 THR cc_start: 0.9550 (p) cc_final: 0.9346 (t)
REVERT: A  928 MET cc_start: 0.9014 (mpp) cc_final: 0.8777 (mpp)
REVERT: A  930 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8012 (pttp)
REVERT: A  938 PHE cc_start: 0.9442 (t80) cc_final: 0.9194 (t80)
REVERT: A  953 PHE cc_start: 0.8676 (m-80) cc_final: 0.8468 (m-80)
REVERT: A  955 PHE cc_start: 0.8792 (t80) cc_final: 0.8027 (t80)
REVERT: A  960 VAL cc_start: 0.9478 (t) cc_final: 0.9237 (t)
REVERT: A 1080 GLU cc_start: 0.7963 (pm20) cc_final: 0.7500 (pm20)
REVERT: A 1205 GLU cc_start: 0.9020 (tt0) cc_final: 0.8743 (tp30)
  outliers start: 2
  outliers final: 1
  residues processed: 268
  average time/residue: 0.1751
  time to fit residues: 67.4328
Evaluate side-chains
  233 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 232
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 18 optimal weight:    8.9990
   chunk 1 optimal weight:    6.9990
   chunk 96 optimal weight:   30.0000
   chunk 21 optimal weight:    7.9990
   chunk 65 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 104 optimal weight:    9.9990
   chunk 47 optimal weight:    9.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A  60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  83 GLN
** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 795 GLN
A 899 ASN
A 926 ASN
A1191 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.121401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.089193 restraints weight = 24120.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.092674 restraints weight = 14601.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.095115 restraints weight = 10205.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9166  Z= 0.212
  Angle     :  0.572   9.338  12393  Z= 0.314
  Chirality :  0.041   0.144   1423
  Planarity :  0.004   0.039   1578
  Dihedral  :  4.877  40.978   1274
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  3.48 %
    Favored  : 96.20 %
  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:  0.23 (0.25), residues: 1153
  helix:  1.19 (0.19), residues: 753
  sheet: -0.70 (0.79), residues: 43
  loop : -2.04 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 704 
 HIS   0.005   0.001   HIS A  60 
 PHE   0.057   0.002   PHE A 934 
 TYR   0.022   0.002   TYR A 924 
 ARG   0.003   0.000   ARG A 589 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 264
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9470 (mt) cc_final: 0.9248 (tp)
REVERT: A   73 ASP cc_start: 0.8651 (t70) cc_final: 0.8342 (t0)
REVERT: A   74 MET cc_start: 0.9280 (tpp) cc_final: 0.8978 (tpt)
REVERT: A   76 ASP cc_start: 0.9034 (m-30) cc_final: 0.8542 (m-30)
REVERT: A   99 MET cc_start: 0.8483 (pmm) cc_final: 0.8210 (pmm)
REVERT: A  100 PHE cc_start: 0.8196 (m-10) cc_final: 0.7959 (m-10)
REVERT: A  103 LEU cc_start: 0.9559 (tp) cc_final: 0.9145 (tp)
REVERT: A  228 TRP cc_start: 0.8864 (m100) cc_final: 0.8518 (m100)
REVERT: A  359 TYR cc_start: 0.8817 (t80) cc_final: 0.8001 (t80)
REVERT: A  720 LEU cc_start: 0.9459 (mm) cc_final: 0.8889 (mm)
REVERT: A  749 ASN cc_start: 0.8754 (m-40) cc_final: 0.8448 (m-40)
REVERT: A  754 LEU cc_start: 0.9081 (mt) cc_final: 0.8819 (mt)
REVERT: A  787 MET cc_start: 0.8005 (mmt) cc_final: 0.7679 (mtt)
REVERT: A  872 MET cc_start: 0.7453 (mmp) cc_final: 0.7118 (mmm)
REVERT: A  938 PHE cc_start: 0.9412 (t80) cc_final: 0.9203 (t80)
REVERT: A  953 PHE cc_start: 0.8740 (m-80) cc_final: 0.8471 (m-80)
REVERT: A  955 PHE cc_start: 0.8800 (t80) cc_final: 0.8029 (t80)
REVERT: A 1080 GLU cc_start: 0.7734 (pm20) cc_final: 0.7365 (pm20)
REVERT: A 1104 TRP cc_start: 0.8997 (t60) cc_final: 0.8780 (t60)
REVERT: A 1105 LEU cc_start: 0.9699 (tp) cc_final: 0.9426 (tp)
REVERT: A 1109 LEU cc_start: 0.9336 (mt) cc_final: 0.9018 (mt)
REVERT: A 1196 ASP cc_start: 0.9088 (t0) cc_final: 0.8373 (t0)
  outliers start: 3
  outliers final: 1
  residues processed: 265
  average time/residue: 0.1837
  time to fit residues: 71.6345
Evaluate side-chains
  223 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 222
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 88 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 69 optimal weight:    0.4980
   chunk 103 optimal weight:    9.9990
   chunk 32 optimal weight:    8.9990
   chunk 56 optimal weight:    9.9990
   chunk 58 optimal weight:    8.9990
   chunk 70 optimal weight:    8.9990
   chunk 108 optimal weight:    0.0970
   overall best weight:    2.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 168 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.119437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.086894 restraints weight = 24294.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.090261 restraints weight = 14740.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.092579 restraints weight = 10364.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9166  Z= 0.244
  Angle     :  0.586  10.219  12393  Z= 0.327
  Chirality :  0.041   0.160   1423
  Planarity :  0.004   0.052   1578
  Dihedral  :  4.958  35.043   1274
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 15.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.06 %
    Favored  : 96.73 %
  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:  0.17 (0.25), residues: 1153
  helix:  1.14 (0.19), residues: 754
  sheet: -0.93 (0.77), residues: 49
  loop : -2.03 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 694 
 HIS   0.006   0.001   HIS A  60 
 PHE   0.032   0.002   PHE A 204 
 TYR   0.032   0.002   TYR A 306 
 ARG   0.006   0.000   ARG A 573 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 254
  time to evaluate  : 1.020 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.9033 (pmm) cc_final: 0.8734 (pmm)
REVERT: A   58 ILE cc_start: 0.9477 (mt) cc_final: 0.9238 (tp)
REVERT: A   99 MET cc_start: 0.8521 (pmm) cc_final: 0.8287 (pmm)
REVERT: A  100 PHE cc_start: 0.8562 (m-10) cc_final: 0.8170 (m-80)
REVERT: A  103 LEU cc_start: 0.9595 (tp) cc_final: 0.9116 (tp)
REVERT: A  107 MET cc_start: 0.9508 (mmp) cc_final: 0.9073 (mmp)
REVERT: A  152 MET cc_start: 0.8980 (tmm) cc_final: 0.8719 (tmm)
REVERT: A  228 TRP cc_start: 0.8861 (m100) cc_final: 0.8522 (m100)
REVERT: A  293 ILE cc_start: 0.9168 (tp) cc_final: 0.8866 (tp)
REVERT: A  359 TYR cc_start: 0.8838 (t80) cc_final: 0.7997 (t80)
REVERT: A  438 ARG cc_start: 0.8719 (mtt180) cc_final: 0.8406 (mtt180)
REVERT: A  720 LEU cc_start: 0.9486 (mm) cc_final: 0.8884 (mm)
REVERT: A  749 ASN cc_start: 0.8816 (m-40) cc_final: 0.8505 (m-40)
REVERT: A  754 LEU cc_start: 0.9121 (mt) cc_final: 0.8856 (mt)
REVERT: A  787 MET cc_start: 0.7899 (mmt) cc_final: 0.7541 (mtt)
REVERT: A  872 MET cc_start: 0.7423 (mmp) cc_final: 0.7044 (mmm)
REVERT: A  928 MET cc_start: 0.9072 (mpp) cc_final: 0.8755 (mpp)
REVERT: A  930 LYS cc_start: 0.8738 (ttpt) cc_final: 0.8359 (pttp)
REVERT: A  938 PHE cc_start: 0.9427 (t80) cc_final: 0.9220 (t80)
REVERT: A  953 PHE cc_start: 0.8698 (m-80) cc_final: 0.8397 (m-80)
REVERT: A  955 PHE cc_start: 0.8799 (t80) cc_final: 0.8005 (t80)
REVERT: A 1080 GLU cc_start: 0.7877 (pm20) cc_final: 0.7515 (pm20)
REVERT: A 1109 LEU cc_start: 0.9361 (mt) cc_final: 0.9011 (mt)
REVERT: A 1196 ASP cc_start: 0.9103 (t0) cc_final: 0.8440 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 255
  average time/residue: 0.1672
  time to fit residues: 62.7828
Evaluate side-chains
  226 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 56 optimal weight:   40.0000
   chunk 17 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0370
   chunk 37 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0870
   chunk 67 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 112 optimal weight:   10.0000
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
A 168 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.122752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.090240 restraints weight = 23538.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.093715 restraints weight = 14299.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.096132 restraints weight = 10005.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.2541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9166  Z= 0.167
  Angle     :  0.556   9.368  12393  Z= 0.299
  Chirality :  0.041   0.157   1423
  Planarity :  0.004   0.038   1578
  Dihedral  :  4.696  33.634   1274
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.43 %
    Favored  : 97.47 %
  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:  0.35 (0.25), residues: 1153
  helix:  1.28 (0.19), residues: 754
  sheet: -0.89 (0.78), residues: 49
  loop : -1.95 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 694 
 HIS   0.004   0.000   HIS A  60 
 PHE   0.026   0.002   PHE A 934 
 TYR   0.023   0.001   TYR A 924 
 ARG   0.004   0.000   ARG A 573 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 259
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.8991 (pmm) cc_final: 0.8725 (pmm)
REVERT: A   58 ILE cc_start: 0.9444 (mt) cc_final: 0.9212 (tp)
REVERT: A   74 MET cc_start: 0.9520 (ttt) cc_final: 0.9264 (ttp)
REVERT: A   99 MET cc_start: 0.8507 (pmm) cc_final: 0.8276 (pmm)
REVERT: A  100 PHE cc_start: 0.8557 (m-10) cc_final: 0.8140 (m-80)
REVERT: A  103 LEU cc_start: 0.9581 (tp) cc_final: 0.9083 (tp)
REVERT: A  107 MET cc_start: 0.9500 (mmp) cc_final: 0.9011 (mmp)
REVERT: A  228 TRP cc_start: 0.8779 (m100) cc_final: 0.8387 (m100)
REVERT: A  239 GLU cc_start: 0.9116 (pp20) cc_final: 0.8913 (pp20)
REVERT: A  306 TYR cc_start: 0.8548 (m-80) cc_final: 0.8345 (m-80)
REVERT: A  359 TYR cc_start: 0.8737 (t80) cc_final: 0.7914 (t80)
REVERT: A  438 ARG cc_start: 0.8729 (mtt180) cc_final: 0.8481 (mtt180)
REVERT: A  720 LEU cc_start: 0.9425 (mm) cc_final: 0.8777 (mm)
REVERT: A  749 ASN cc_start: 0.8723 (m-40) cc_final: 0.8406 (m-40)
REVERT: A  754 LEU cc_start: 0.9091 (mt) cc_final: 0.8820 (mt)
REVERT: A  787 MET cc_start: 0.7765 (mmt) cc_final: 0.7503 (mtt)
REVERT: A  872 MET cc_start: 0.7448 (mmp) cc_final: 0.7101 (mmm)
REVERT: A  928 MET cc_start: 0.8992 (mpp) cc_final: 0.8774 (mpp)
REVERT: A  938 PHE cc_start: 0.9414 (t80) cc_final: 0.9210 (t80)
REVERT: A  953 PHE cc_start: 0.8672 (m-80) cc_final: 0.8428 (m-80)
REVERT: A  955 PHE cc_start: 0.8770 (t80) cc_final: 0.7942 (t80)
REVERT: A  965 MET cc_start: 0.8300 (tmm) cc_final: 0.8062 (tmm)
REVERT: A 1080 GLU cc_start: 0.7760 (pm20) cc_final: 0.7547 (pm20)
REVERT: A 1104 TRP cc_start: 0.9109 (t60) cc_final: 0.8807 (t60)
REVERT: A 1105 LEU cc_start: 0.9734 (tp) cc_final: 0.9367 (tp)
REVERT: A 1109 LEU cc_start: 0.9339 (mt) cc_final: 0.8975 (mt)
REVERT: A 1196 ASP cc_start: 0.9089 (t0) cc_final: 0.8419 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 260
  average time/residue: 0.1686
  time to fit residues: 65.2707
Evaluate side-chains
  222 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 56 optimal weight:   40.0000
   chunk 80 optimal weight:    3.9990
   chunk 101 optimal weight:    5.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.120193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.087729 restraints weight = 23871.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.091133 restraints weight = 14472.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.093526 restraints weight = 10161.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9166  Z= 0.215
  Angle     :  0.570  12.270  12393  Z= 0.312
  Chirality :  0.041   0.173   1423
  Planarity :  0.004   0.048   1578
  Dihedral  :  4.819  35.088   1274
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 14.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  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:  0.35 (0.25), residues: 1153
  helix:  1.26 (0.19), residues: 757
  sheet: -0.97 (0.75), residues: 49
  loop : -1.91 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 694 
 HIS   0.005   0.001   HIS A  60 
 PHE   0.023   0.002   PHE A 204 
 TYR   0.023   0.002   TYR A 924 
 ARG   0.004   0.000   ARG A 573 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.9054 (pmm) cc_final: 0.8809 (pmm)
REVERT: A   49 TYR cc_start: 0.8783 (m-10) cc_final: 0.8476 (m-80)
REVERT: A   58 ILE cc_start: 0.9463 (mt) cc_final: 0.9244 (tp)
REVERT: A   74 MET cc_start: 0.9553 (ttt) cc_final: 0.9252 (ttp)
REVERT: A   83 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7511 (pp30)
REVERT: A   99 MET cc_start: 0.8462 (pmm) cc_final: 0.8234 (pmm)
REVERT: A  100 PHE cc_start: 0.8604 (m-10) cc_final: 0.8176 (m-80)
REVERT: A  103 LEU cc_start: 0.9581 (tp) cc_final: 0.9093 (tp)
REVERT: A  107 MET cc_start: 0.9499 (mmp) cc_final: 0.9138 (mmm)
REVERT: A  228 TRP cc_start: 0.8852 (m100) cc_final: 0.8633 (m100)
REVERT: A  359 TYR cc_start: 0.8769 (t80) cc_final: 0.7918 (t80)
REVERT: A  438 ARG cc_start: 0.8777 (mtt180) cc_final: 0.8522 (mtt180)
REVERT: A  720 LEU cc_start: 0.9458 (mm) cc_final: 0.8812 (mm)
REVERT: A  749 ASN cc_start: 0.8816 (m-40) cc_final: 0.8516 (m-40)
REVERT: A  754 LEU cc_start: 0.9096 (mt) cc_final: 0.8833 (mt)
REVERT: A  787 MET cc_start: 0.7829 (mmt) cc_final: 0.7517 (mtt)
REVERT: A  872 MET cc_start: 0.7474 (mmp) cc_final: 0.7115 (mmm)
REVERT: A  928 MET cc_start: 0.9011 (mpp) cc_final: 0.8794 (mpp)
REVERT: A  953 PHE cc_start: 0.8642 (m-80) cc_final: 0.8372 (m-80)
REVERT: A  955 PHE cc_start: 0.8780 (t80) cc_final: 0.7950 (t80)
REVERT: A 1104 TRP cc_start: 0.9165 (t60) cc_final: 0.8839 (t60)
REVERT: A 1105 LEU cc_start: 0.9715 (tp) cc_final: 0.9339 (tp)
REVERT: A 1109 LEU cc_start: 0.9331 (mt) cc_final: 0.8988 (mt)
REVERT: A 1196 ASP cc_start: 0.9065 (t0) cc_final: 0.8423 (t0)
REVERT: A 1205 GLU cc_start: 0.8967 (tt0) cc_final: 0.8731 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 248
  average time/residue: 0.1984
  time to fit residues: 74.1718
Evaluate side-chains
  218 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 70 optimal weight:    0.8980
   chunk 54 optimal weight:   10.0000
   chunk 36 optimal weight:   20.0000
   chunk 57 optimal weight:   20.0000
   chunk 51 optimal weight:    8.9990
   chunk 98 optimal weight:    9.9990
   chunk 102 optimal weight:    9.9990
   chunk 79 optimal weight:    7.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    2.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 483 ASN
A1132 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.118481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.085618 restraints weight = 24773.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.088939 restraints weight = 14945.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.091287 restraints weight = 10509.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.2893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9166  Z= 0.253
  Angle     :  0.604  10.512  12393  Z= 0.335
  Chirality :  0.042   0.179   1423
  Planarity :  0.004   0.043   1578
  Dihedral  :  4.957  35.679   1274
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 15.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.43 %
    Favored  : 97.47 %
  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:  0.20 (0.25), residues: 1153
  helix:  1.13 (0.19), residues: 755
  sheet: -0.89 (0.77), residues: 49
  loop : -1.93 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 694 
 HIS   0.006   0.001   HIS A  60 
 PHE   0.021   0.002   PHE A 204 
 TYR   0.024   0.002   TYR A 924 
 ARG   0.003   0.000   ARG A 573 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 244
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.9069 (pmm) cc_final: 0.8820 (pmm)
REVERT: A   58 ILE cc_start: 0.9520 (mt) cc_final: 0.9295 (tp)
REVERT: A   74 MET cc_start: 0.9460 (ttt) cc_final: 0.9179 (ttp)
REVERT: A  100 PHE cc_start: 0.8648 (m-10) cc_final: 0.8268 (m-80)
REVERT: A  103 LEU cc_start: 0.9597 (tp) cc_final: 0.9115 (tp)
REVERT: A  107 MET cc_start: 0.9512 (mmp) cc_final: 0.9103 (mmm)
REVERT: A  228 TRP cc_start: 0.8868 (m100) cc_final: 0.8624 (m100)
REVERT: A  237 ASP cc_start: 0.8711 (m-30) cc_final: 0.8248 (p0)
REVERT: A  359 TYR cc_start: 0.8772 (t80) cc_final: 0.7845 (t80)
REVERT: A  438 ARG cc_start: 0.8807 (mtt180) cc_final: 0.8561 (ttt180)
REVERT: A  720 LEU cc_start: 0.9479 (mm) cc_final: 0.8817 (mm)
REVERT: A  749 ASN cc_start: 0.8920 (m-40) cc_final: 0.8605 (m-40)
REVERT: A  754 LEU cc_start: 0.9144 (mt) cc_final: 0.8887 (mt)
REVERT: A  787 MET cc_start: 0.8009 (mmt) cc_final: 0.7661 (mtt)
REVERT: A  915 MET cc_start: 0.9422 (mtm) cc_final: 0.9066 (mtm)
REVERT: A  928 MET cc_start: 0.9041 (mpp) cc_final: 0.8819 (mpp)
REVERT: A  953 PHE cc_start: 0.8679 (m-80) cc_final: 0.8348 (m-80)
REVERT: A  955 PHE cc_start: 0.8813 (t80) cc_final: 0.7976 (t80)
REVERT: A 1080 GLU cc_start: 0.8287 (pm20) cc_final: 0.7487 (pm20)
REVERT: A 1104 TRP cc_start: 0.9224 (t60) cc_final: 0.8874 (t60)
REVERT: A 1105 LEU cc_start: 0.9709 (tp) cc_final: 0.9362 (tp)
REVERT: A 1109 LEU cc_start: 0.9381 (mt) cc_final: 0.9083 (mt)
REVERT: A 1196 ASP cc_start: 0.9076 (t0) cc_final: 0.8607 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 244
  average time/residue: 0.1772
  time to fit residues: 64.8251
Evaluate side-chains
  214 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 105 optimal weight:    0.9980
   chunk 102 optimal weight:    8.9990
   chunk 50 optimal weight:    6.9990
   chunk 27 optimal weight:    0.8980
   chunk 95 optimal weight:    0.0050
   chunk 51 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 98 optimal weight:    0.0980
   chunk 112 optimal weight:    0.9990
   chunk 91 optimal weight:    0.1980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.4394

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.122763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.089857 restraints weight = 23938.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.093466 restraints weight = 14406.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.095935 restraints weight = 10052.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.2999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9166  Z= 0.177
  Angle     :  0.595  13.302  12393  Z= 0.315
  Chirality :  0.042   0.199   1423
  Planarity :  0.004   0.044   1578
  Dihedral  :  4.757  33.741   1274
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  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:  0.40 (0.25), residues: 1153
  helix:  1.27 (0.19), residues: 756
  sheet: -0.96 (0.76), residues: 49
  loop : -1.82 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP A 694 
 HIS   0.004   0.001   HIS A  60 
 PHE   0.025   0.002   PHE A 196 
 TYR   0.045   0.002   TYR A  49 
 ARG   0.003   0.000   ARG A 828 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 265
  time to evaluate  : 1.074 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.9031 (pmm) cc_final: 0.8767 (pmm)
REVERT: A   58 ILE cc_start: 0.9451 (mt) cc_final: 0.9245 (tp)
REVERT: A   73 ASP cc_start: 0.8772 (t70) cc_final: 0.8464 (t0)
REVERT: A   99 MET cc_start: 0.8546 (pmm) cc_final: 0.8330 (pmm)
REVERT: A  100 PHE cc_start: 0.8598 (m-10) cc_final: 0.8198 (m-80)
REVERT: A  103 LEU cc_start: 0.9596 (tp) cc_final: 0.9130 (tp)
REVERT: A  107 MET cc_start: 0.9537 (mmp) cc_final: 0.9172 (mmm)
REVERT: A  110 TYR cc_start: 0.9212 (m-10) cc_final: 0.8968 (m-80)
REVERT: A  228 TRP cc_start: 0.8847 (m100) cc_final: 0.8593 (m100)
REVERT: A  237 ASP cc_start: 0.8678 (m-30) cc_final: 0.8177 (p0)
REVERT: A  306 TYR cc_start: 0.8512 (m-80) cc_final: 0.8169 (m-80)
REVERT: A  359 TYR cc_start: 0.8674 (t80) cc_final: 0.7839 (t80)
REVERT: A  438 ARG cc_start: 0.8788 (mtt180) cc_final: 0.8399 (ttt180)
REVERT: A  720 LEU cc_start: 0.9410 (mm) cc_final: 0.8760 (mm)
REVERT: A  749 ASN cc_start: 0.8792 (m-40) cc_final: 0.8487 (m-40)
REVERT: A  754 LEU cc_start: 0.9097 (mt) cc_final: 0.8826 (mt)
REVERT: A  787 MET cc_start: 0.7793 (mmt) cc_final: 0.7463 (mtt)
REVERT: A  872 MET cc_start: 0.7435 (mmp) cc_final: 0.7108 (mmm)
REVERT: A  908 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.8025 (mmm-85)
REVERT: A  910 GLN cc_start: 0.8527 (tp40) cc_final: 0.8125 (mm-40)
REVERT: A  928 MET cc_start: 0.8999 (mpp) cc_final: 0.8782 (mpp)
REVERT: A  953 PHE cc_start: 0.8639 (m-80) cc_final: 0.8368 (m-80)
REVERT: A  955 PHE cc_start: 0.8796 (t80) cc_final: 0.7896 (t80)
REVERT: A 1080 GLU cc_start: 0.8122 (pm20) cc_final: 0.7729 (pm20)
REVERT: A 1104 TRP cc_start: 0.9194 (t60) cc_final: 0.8848 (t60)
REVERT: A 1105 LEU cc_start: 0.9721 (tp) cc_final: 0.9351 (tp)
REVERT: A 1109 LEU cc_start: 0.9340 (mt) cc_final: 0.8991 (mt)
REVERT: A 1196 ASP cc_start: 0.9073 (t0) cc_final: 0.8425 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 265
  average time/residue: 0.1742
  time to fit residues: 67.0702
Evaluate side-chains
  223 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 113 optimal weight:   20.0000
   chunk 26 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9990
   chunk 112 optimal weight:    5.9990
   chunk 108 optimal weight:    0.0050
   chunk 94 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.122931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.090266 restraints weight = 23897.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.093810 restraints weight = 14358.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.096213 restraints weight = 10013.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9166  Z= 0.174
  Angle     :  0.595  10.812  12393  Z= 0.318
  Chirality :  0.041   0.192   1423
  Planarity :  0.004   0.049   1578
  Dihedral  :  4.676  33.820   1274
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  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:  0.42 (0.25), residues: 1153
  helix:  1.29 (0.19), residues: 755
  sheet: -0.94 (0.77), residues: 49
  loop : -1.79 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 694 
 HIS   0.004   0.001   HIS A  60 
 PHE   0.025   0.002   PHE A 200 
 TYR   0.022   0.002   TYR A 924 
 ARG   0.019   0.001   ARG A 828 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 1.070 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.9030 (pmm) cc_final: 0.8800 (pmm)
REVERT: A   50 MET cc_start: 0.8673 (mtp) cc_final: 0.8311 (mmm)
REVERT: A   99 MET cc_start: 0.8547 (pmm) cc_final: 0.8332 (pmm)
REVERT: A  100 PHE cc_start: 0.8583 (m-10) cc_final: 0.8185 (m-80)
REVERT: A  103 LEU cc_start: 0.9595 (tp) cc_final: 0.9125 (tp)
REVERT: A  107 MET cc_start: 0.9564 (mmp) cc_final: 0.9199 (mmm)
REVERT: A  228 TRP cc_start: 0.8808 (m100) cc_final: 0.8564 (m100)
REVERT: A  237 ASP cc_start: 0.8680 (m-30) cc_final: 0.8190 (p0)
REVERT: A  251 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8128 (mt-10)
REVERT: A  306 TYR cc_start: 0.8562 (m-80) cc_final: 0.8164 (m-80)
REVERT: A  359 TYR cc_start: 0.8616 (t80) cc_final: 0.7879 (t80)
REVERT: A  720 LEU cc_start: 0.9374 (mm) cc_final: 0.8736 (mm)
REVERT: A  749 ASN cc_start: 0.8803 (m-40) cc_final: 0.8492 (m-40)
REVERT: A  754 LEU cc_start: 0.9104 (mt) cc_final: 0.8833 (mt)
REVERT: A  787 MET cc_start: 0.7796 (mmt) cc_final: 0.7420 (mtt)
REVERT: A  825 THR cc_start: 0.8741 (m) cc_final: 0.8489 (m)
REVERT: A  872 MET cc_start: 0.7447 (mmp) cc_final: 0.7120 (mmm)
REVERT: A  910 GLN cc_start: 0.8482 (tp40) cc_final: 0.8108 (mm-40)
REVERT: A  928 MET cc_start: 0.8996 (mpp) cc_final: 0.8746 (mpp)
REVERT: A  938 PHE cc_start: 0.9442 (t80) cc_final: 0.9241 (t80)
REVERT: A  953 PHE cc_start: 0.8657 (m-80) cc_final: 0.8397 (m-80)
REVERT: A  955 PHE cc_start: 0.8770 (t80) cc_final: 0.7874 (t80)
REVERT: A 1039 ASN cc_start: 0.6900 (p0) cc_final: 0.6310 (p0)
REVERT: A 1080 GLU cc_start: 0.8328 (pm20) cc_final: 0.7971 (pm20)
REVERT: A 1109 LEU cc_start: 0.9367 (mt) cc_final: 0.8999 (mt)
REVERT: A 1196 ASP cc_start: 0.9161 (t0) cc_final: 0.8675 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 252
  average time/residue: 0.1756
  time to fit residues: 64.8027
Evaluate side-chains
  226 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 109 optimal weight:    0.0570
   chunk 103 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    1.3504

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1228 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.121455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.088979 restraints weight = 24462.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.092423 restraints weight = 14840.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.094877 restraints weight = 10434.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9166  Z= 0.194
  Angle     :  0.600  11.176  12393  Z= 0.323
  Chirality :  0.042   0.197   1423
  Planarity :  0.004   0.056   1578
  Dihedral  :  4.708  34.097   1274
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.11 %
    Favored  : 99.79 %
  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:  0.39 (0.25), residues: 1153
  helix:  1.26 (0.19), residues: 756
  sheet: -1.01 (0.75), residues: 49
  loop : -1.79 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 694 
 HIS   0.003   0.001   HIS A  60 
 PHE   0.023   0.002   PHE A 200 
 TYR   0.022   0.002   TYR A 273 
 ARG   0.014   0.001   ARG A 828 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 246
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.9013 (pmm) cc_final: 0.8675 (pmm)
REVERT: A   50 MET cc_start: 0.8725 (mtp) cc_final: 0.8458 (mmm)
REVERT: A  103 LEU cc_start: 0.9585 (tp) cc_final: 0.9130 (tp)
REVERT: A  107 MET cc_start: 0.9536 (mmp) cc_final: 0.9176 (mmm)
REVERT: A  228 TRP cc_start: 0.8851 (m100) cc_final: 0.8615 (m100)
REVERT: A  237 ASP cc_start: 0.8716 (m-30) cc_final: 0.8226 (p0)
REVERT: A  251 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8221 (mt-10)
REVERT: A  359 TYR cc_start: 0.8663 (t80) cc_final: 0.7941 (t80)
REVERT: A  720 LEU cc_start: 0.9400 (mm) cc_final: 0.8728 (mm)
REVERT: A  749 ASN cc_start: 0.8836 (m-40) cc_final: 0.8528 (m-40)
REVERT: A  754 LEU cc_start: 0.9106 (mt) cc_final: 0.8838 (mt)
REVERT: A  787 MET cc_start: 0.7873 (mmt) cc_final: 0.7546 (mtt)
REVERT: A  872 MET cc_start: 0.7479 (mmp) cc_final: 0.7124 (mmm)
REVERT: A  910 GLN cc_start: 0.8450 (tp40) cc_final: 0.8119 (mm-40)
REVERT: A  915 MET cc_start: 0.9415 (mtm) cc_final: 0.9125 (mtm)
REVERT: A  928 MET cc_start: 0.8999 (mpp) cc_final: 0.8773 (mpp)
REVERT: A  938 PHE cc_start: 0.9418 (t80) cc_final: 0.9205 (t80)
REVERT: A  953 PHE cc_start: 0.8611 (m-80) cc_final: 0.8376 (m-80)
REVERT: A  955 PHE cc_start: 0.8797 (t80) cc_final: 0.7915 (t80)
REVERT: A 1039 ASN cc_start: 0.6888 (p0) cc_final: 0.6298 (p0)
REVERT: A 1080 GLU cc_start: 0.8352 (pm20) cc_final: 0.7936 (pm20)
REVERT: A 1104 TRP cc_start: 0.9182 (t60) cc_final: 0.8771 (t60)
REVERT: A 1105 LEU cc_start: 0.9714 (tp) cc_final: 0.9309 (tp)
REVERT: A 1109 LEU cc_start: 0.9336 (mt) cc_final: 0.9003 (mt)
REVERT: A 1196 ASP cc_start: 0.9064 (t0) cc_final: 0.8429 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 246
  average time/residue: 0.1764
  time to fit residues: 65.4807
Evaluate side-chains
  218 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 5 optimal weight:    8.9990
   chunk 9 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 105 optimal weight:    0.6980
   chunk 109 optimal weight:   10.0000
   chunk 30 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 104 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1228 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.121521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.088686 restraints weight = 24247.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.092112 restraints weight = 14623.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.094508 restraints weight = 10276.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.3277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9166  Z= 0.193
  Angle     :  0.604  11.091  12393  Z= 0.324
  Chirality :  0.042   0.192   1423
  Planarity :  0.004   0.053   1578
  Dihedral  :  4.714  34.396   1274
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.32 %
    Favored  : 99.58 %
  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:  0.33 (0.25), residues: 1153
  helix:  1.21 (0.19), residues: 756
  sheet: -1.03 (0.76), residues: 49
  loop : -1.79 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 694 
 HIS   0.007   0.001   HIS A1003 
 PHE   0.022   0.002   PHE A 200 
 TYR   0.023   0.002   TYR A 924 
 ARG   0.017   0.001   ARG A 828 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3680.03 seconds
wall clock time: 66 minutes 41.66 seconds (4001.66 seconds total)