Starting phenix.real_space_refine
on Thu Feb 13 15:38:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zk9_14759/02_2025/7zk9_14759.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zk9_14759/02_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_14759/02_2025/7zk9_14759.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zk9_14759/02_2025/7zk9_14759.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zk9_14759/02_2025/7zk9_14759.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zk9_14759/02_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-5592/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: 5.68, per 1000 atoms: 0.63
  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: 2.48
  Conformation dependent library (CDL) restraints added in 1.1 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: 0.98
  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: 3.12

  Time building geometry restraints manager: 2.84 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:             1.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.180
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.960
-------------------------------------------------------------------------------
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  : 0.971 
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: 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: 0.1806
  time to fit residues: 72.8472
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  : 1.052 
-------------------------------------------------------------------------------
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 = 0.124310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.091922 restraints weight = 23284.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.095400 restraints weight = 14359.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.097803 restraints weight = 10172.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.1468

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   8.890  12393  Z= 0.317
  Chirality :  0.042   0.174   1423
  Planarity :  0.004   0.059   1578
  Dihedral  :  4.919  38.470   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   0.007   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  : 1.078 
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: 0.8542 (pmm) cc_final: 0.8296 (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: 0.8728 (mptt)
REVERT: A  228 TRP cc_start: 0.8828 (m100) cc_final: 0.8515 (m100)
REVERT: A  720 LEU cc_start: 0.9411 (mm) cc_final: 0.8934 (mm)
REVERT: A  754 LEU cc_start: 0.9009 (mt) cc_final: 0.8718 (mt)
REVERT: A  787 MET cc_start: 0.7736 (mmt) cc_final: 0.7524 (mtt)
REVERT: A  828 ARG cc_start: 0.9001 (tpt170) cc_final: 0.8538 (tpt90)
REVERT: A  872 MET cc_start: 0.7385 (mmp) cc_final: 0.7144 (mmm)
REVERT: A  902 THR cc_start: 0.9549 (p) cc_final: 0.9345 (t)
REVERT: A  928 MET cc_start: 0.9013 (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: 0.9192 (t80)
REVERT: A  953 PHE cc_start: 0.8678 (m-80) cc_final: 0.8470 (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: 0.9238 (t)
REVERT: A 1080 GLU cc_start: 0.7962 (pm20) cc_final: 0.7498 (pm20)
REVERT: A 1205 GLU cc_start: 0.9020 (tt0) cc_final: 0.8742 (tp30)
  outliers start: 2
  outliers final: 1
  residues processed: 268
  average time/residue: 0.1823
  time to fit residues: 70.1471
Evaluate side-chains
  232 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 231
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
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:   10.0000
   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:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 104 optimal weight:    8.9990
   chunk 47 optimal weight:    9.9990
   overall best weight:    1.9584

-------------------------------------------------------------------------------
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 = 0.3821 r_free = 0.3821 target = 0.120215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.089037 restraints weight = 23818.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.092412 restraints weight = 14259.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.094869 restraints weight = 9912.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   9166  Z= 0.232
  Angle     :  0.577   9.422  12393  Z= 0.318
  Chirality :  0.041   0.147   1423
  Planarity :  0.004   0.039   1578
  Dihedral  :  4.900  40.863   1274
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  3.38 %
    Favored  : 96.30 %
  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:  0.22 (0.25), residues: 1153
  helix:  1.19 (0.19), residues: 753
  sheet: -0.70 (0.79), residues: 43
  loop : -2.05 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 704 
 HIS   0.005   0.001   HIS A  60 
 PHE   0.051   0.002   PHE A 934 
 TYR   0.023   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
  266 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 263
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9477 (mt) cc_final: 0.9262 (tp)
REVERT: A   73 ASP cc_start: 0.8661 (t70) cc_final: 0.8328 (t0)
REVERT: A   74 MET cc_start: 0.9320 (tpp) cc_final: 0.8989 (tpt)
REVERT: A   76 ASP cc_start: 0.9026 (m-30) cc_final: 0.8541 (m-30)
REVERT: A   99 MET cc_start: 0.8486 (pmm) cc_final: 0.8188 (pmm)
REVERT: A  100 PHE cc_start: 0.8207 (m-10) cc_final: 0.7959 (m-10)
REVERT: A  103 LEU cc_start: 0.9564 (tp) cc_final: 0.9157 (tp)
REVERT: A  209 LYS cc_start: 0.8978 (ptpp) cc_final: 0.8777 (mptt)
REVERT: A  228 TRP cc_start: 0.8850 (m100) cc_final: 0.8513 (m100)
REVERT: A  359 TYR cc_start: 0.8805 (t80) cc_final: 0.7974 (t80)
REVERT: A  720 LEU cc_start: 0.9458 (mm) cc_final: 0.8906 (mm)
REVERT: A  749 ASN cc_start: 0.8743 (m-40) cc_final: 0.8439 (m-40)
REVERT: A  754 LEU cc_start: 0.9102 (mt) cc_final: 0.8839 (mt)
REVERT: A  787 MET cc_start: 0.8007 (mmt) cc_final: 0.7661 (mtt)
REVERT: A  872 MET cc_start: 0.7467 (mmp) cc_final: 0.7119 (mmm)
REVERT: A  928 MET cc_start: 0.8995 (mpp) cc_final: 0.8795 (mpp)
REVERT: A  938 PHE cc_start: 0.9443 (t80) cc_final: 0.9221 (t80)
REVERT: A  953 PHE cc_start: 0.8747 (m-80) cc_final: 0.8471 (m-80)
REVERT: A  955 PHE cc_start: 0.8801 (t80) cc_final: 0.8024 (t80)
REVERT: A 1080 GLU cc_start: 0.7795 (pm20) cc_final: 0.7476 (pm20)
REVERT: A 1104 TRP cc_start: 0.8979 (t60) cc_final: 0.8760 (t60)
REVERT: A 1105 LEU cc_start: 0.9702 (tp) cc_final: 0.9439 (tp)
REVERT: A 1109 LEU cc_start: 0.9348 (mt) cc_final: 0.9040 (mt)
REVERT: A 1196 ASP cc_start: 0.9069 (t0) cc_final: 0.8335 (t0)
  outliers start: 3
  outliers final: 0
  residues processed: 264
  average time/residue: 0.1814
  time to fit residues: 69.2360
Evaluate side-chains
  224 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 55 optimal weight:    9.9990
   chunk 88 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 69 optimal weight:    0.8980
   chunk 103 optimal weight:   10.0000
   chunk 32 optimal weight:    8.9990
   chunk 56 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   chunk 108 optimal weight:    0.0020
   overall best weight:    2.3592

-------------------------------------------------------------------------------
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 = 0.3795 r_free = 0.3795 target = 0.119056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.086588 restraints weight = 24124.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.089945 restraints weight = 14644.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.092217 restraints weight = 10311.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9166  Z= 0.247
  Angle     :  0.592  10.375  12393  Z= 0.329
  Chirality :  0.041   0.178   1423
  Planarity :  0.004   0.038   1578
  Dihedral  :  5.041  40.800   1274
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.70 %
    Favored  : 96.09 %
  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:  0.14 (0.25), residues: 1153
  helix:  1.09 (0.19), residues: 759
  sheet: -0.97 (0.77), residues: 49
  loop : -2.01 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 694 
 HIS   0.006   0.001   HIS A  60 
 PHE   0.035   0.002   PHE A 204 
 TYR   0.023   0.002   TYR A 924 
 ARG   0.004   0.000   ARG A1081 

*********************** 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
  257 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 255
  time to evaluate  : 1.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.9052 (pmm) cc_final: 0.8707 (pmm)
REVERT: A   58 ILE cc_start: 0.9492 (mt) cc_final: 0.9257 (tp)
REVERT: A   99 MET cc_start: 0.8542 (pmm) cc_final: 0.8293 (pmm)
REVERT: A  100 PHE cc_start: 0.8580 (m-10) cc_final: 0.8196 (m-80)
REVERT: A  103 LEU cc_start: 0.9602 (tp) cc_final: 0.9119 (tp)
REVERT: A  107 MET cc_start: 0.9512 (mmp) cc_final: 0.9075 (mmp)
REVERT: A  228 TRP cc_start: 0.8864 (m100) cc_final: 0.8506 (m100)
REVERT: A  359 TYR cc_start: 0.8845 (t80) cc_final: 0.7976 (t80)
REVERT: A  438 ARG cc_start: 0.8735 (mtt180) cc_final: 0.8446 (mtt180)
REVERT: A  720 LEU cc_start: 0.9483 (mm) cc_final: 0.8881 (mm)
REVERT: A  749 ASN cc_start: 0.8817 (m-40) cc_final: 0.8515 (m-40)
REVERT: A  754 LEU cc_start: 0.9129 (mt) cc_final: 0.8865 (mt)
REVERT: A  787 MET cc_start: 0.7911 (mmt) cc_final: 0.7610 (mtt)
REVERT: A  872 MET cc_start: 0.7430 (mmp) cc_final: 0.7049 (mmm)
REVERT: A  928 MET cc_start: 0.9086 (mpp) cc_final: 0.8810 (mpp)
REVERT: A  930 LYS cc_start: 0.8762 (ttpt) cc_final: 0.8388 (pttp)
REVERT: A  938 PHE cc_start: 0.9424 (t80) cc_final: 0.9213 (t80)
REVERT: A  953 PHE cc_start: 0.8685 (m-80) cc_final: 0.8395 (m-80)
REVERT: A  955 PHE cc_start: 0.8771 (t80) cc_final: 0.7989 (t80)
REVERT: A 1080 GLU cc_start: 0.7923 (pm20) cc_final: 0.7587 (pm20)
REVERT: A 1109 LEU cc_start: 0.9369 (mt) cc_final: 0.9024 (mt)
REVERT: A 1196 ASP cc_start: 0.9072 (t0) cc_final: 0.8417 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 256
  average time/residue: 0.1733
  time to fit residues: 65.4871
Evaluate side-chains
  224 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 17 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 58 optimal weight:   20.0000
   chunk 37 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 33 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 112 optimal weight:    5.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3833 r_free = 0.3833 target = 0.121982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.089508 restraints weight = 23578.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.092967 restraints weight = 14139.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.095363 restraints weight = 9928.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.2565

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= 0.172
  Angle     :  0.567   9.416  12393  Z= 0.304
  Chirality :  0.041   0.166   1423
  Planarity :  0.004   0.038   1578
  Dihedral  :  4.842  38.789   1274
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.11 %
    Favored  : 97.78 %
  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:  1.27 (0.19), residues: 755
  sheet: -0.93 (0.78), residues: 49
  loop : -1.97 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 694 
 HIS   0.005   0.001   HIS A  60 
 PHE   0.028   0.002   PHE A 934 
 TYR   0.024   0.002   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
  256 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 255
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.8997 (pmm) cc_final: 0.8710 (pmm)
REVERT: A   58 ILE cc_start: 0.9452 (mt) cc_final: 0.9216 (tp)
REVERT: A   74 MET cc_start: 0.9420 (ttt) cc_final: 0.9110 (ttp)
REVERT: A   99 MET cc_start: 0.8466 (pmm) cc_final: 0.8235 (pmm)
REVERT: A  100 PHE cc_start: 0.8557 (m-10) cc_final: 0.8137 (m-80)
REVERT: A  103 LEU cc_start: 0.9580 (tp) cc_final: 0.9051 (tp)
REVERT: A  107 MET cc_start: 0.9496 (mmp) cc_final: 0.9017 (mmp)
REVERT: A  228 TRP cc_start: 0.8818 (m100) cc_final: 0.8432 (m100)
REVERT: A  359 TYR cc_start: 0.8752 (t80) cc_final: 0.7906 (t80)
REVERT: A  438 ARG cc_start: 0.8730 (mtt180) cc_final: 0.8381 (mtt180)
REVERT: A  720 LEU cc_start: 0.9464 (mm) cc_final: 0.8796 (mm)
REVERT: A  749 ASN cc_start: 0.8746 (m-40) cc_final: 0.8435 (m-40)
REVERT: A  754 LEU cc_start: 0.9093 (mt) cc_final: 0.8819 (mt)
REVERT: A  787 MET cc_start: 0.7782 (mmt) cc_final: 0.7512 (mtt)
REVERT: A  872 MET cc_start: 0.7431 (mmp) cc_final: 0.7077 (mmm)
REVERT: A  928 MET cc_start: 0.8986 (mpp) cc_final: 0.8762 (mpp)
REVERT: A  953 PHE cc_start: 0.8658 (m-80) cc_final: 0.8381 (m-80)
REVERT: A  955 PHE cc_start: 0.8766 (t80) cc_final: 0.7893 (t80)
REVERT: A  965 MET cc_start: 0.8299 (tmm) cc_final: 0.8066 (tmm)
REVERT: A  969 ASN cc_start: 0.8727 (m110) cc_final: 0.8508 (m110)
REVERT: A 1104 TRP cc_start: 0.9098 (t60) cc_final: 0.8798 (t60)
REVERT: A 1105 LEU cc_start: 0.9717 (tp) cc_final: 0.9465 (tp)
REVERT: A 1196 ASP cc_start: 0.9066 (t0) cc_final: 0.8421 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 256
  average time/residue: 0.1657
  time to fit residues: 62.7607
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  : 1.042 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 93 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9990
   chunk 49 optimal weight:   20.0000
   chunk 56 optimal weight:   50.0000
   chunk 80 optimal weight:    0.9990
   chunk 101 optimal weight:    5.9990
   overall best weight:    1.7588

-------------------------------------------------------------------------------
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 = 0.120392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.087911 restraints weight = 23955.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.091343 restraints weight = 14531.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.093700 restraints weight = 10189.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.2683

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= 0.214
  Angle     :  0.584  12.400  12393  Z= 0.319
  Chirality :  0.041   0.188   1423
  Planarity :  0.004   0.048   1578
  Dihedral  :  4.865  38.351   1274
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 14.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  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:  0.37 (0.25), residues: 1153
  helix:  1.27 (0.19), residues: 758
  sheet: -0.74 (0.93), residues: 34
  loop : -1.90 (0.31), residues: 361

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   0.021   0.002   PHE A 204 
 TYR   0.024   0.002   TYR A 924 
 ARG   0.003   0.000   ARG A1081 

*********************** 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
  249 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.9050 (pmm) cc_final: 0.8786 (pmm)
REVERT: A   49 TYR cc_start: 0.8799 (m-10) cc_final: 0.8478 (m-80)
REVERT: A   58 ILE cc_start: 0.9468 (mt) cc_final: 0.9244 (tp)
REVERT: A   99 MET cc_start: 0.8471 (pmm) cc_final: 0.8228 (pmm)
REVERT: A  100 PHE cc_start: 0.8620 (m-10) cc_final: 0.8187 (m-80)
REVERT: A  103 LEU cc_start: 0.9592 (tp) cc_final: 0.9103 (tp)
REVERT: A  107 MET cc_start: 0.9525 (mmp) cc_final: 0.9156 (mmm)
REVERT: A  228 TRP cc_start: 0.8853 (m100) cc_final: 0.8612 (m100)
REVERT: A  293 ILE cc_start: 0.9110 (tp) cc_final: 0.8905 (tp)
REVERT: A  359 TYR cc_start: 0.8615 (t80) cc_final: 0.7934 (t80)
REVERT: A  438 ARG cc_start: 0.8783 (mtt180) cc_final: 0.8573 (mtt180)
REVERT: A  720 LEU cc_start: 0.9433 (mm) cc_final: 0.8778 (mm)
REVERT: A  749 ASN cc_start: 0.8844 (m-40) cc_final: 0.8544 (m-40)
REVERT: A  754 LEU cc_start: 0.9092 (mt) cc_final: 0.8825 (mt)
REVERT: A  787 MET cc_start: 0.7834 (mmt) cc_final: 0.7511 (mtt)
REVERT: A  872 MET cc_start: 0.7473 (mmp) cc_final: 0.7115 (mmm)
REVERT: A  928 MET cc_start: 0.9034 (mpp) cc_final: 0.8823 (mpp)
REVERT: A  953 PHE cc_start: 0.8718 (m-80) cc_final: 0.8398 (m-80)
REVERT: A  955 PHE cc_start: 0.8792 (t80) cc_final: 0.7947 (t80)
REVERT: A 1104 TRP cc_start: 0.9191 (t60) cc_final: 0.8868 (t60)
REVERT: A 1105 LEU cc_start: 0.9723 (tp) cc_final: 0.9345 (tp)
REVERT: A 1109 LEU cc_start: 0.9325 (mt) cc_final: 0.8971 (mt)
REVERT: A 1196 ASP cc_start: 0.9075 (t0) cc_final: 0.8437 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 249
  average time/residue: 0.1671
  time to fit residues: 61.7590
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  : 1.119 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 70 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 36 optimal weight:    8.9990
   chunk 57 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 98 optimal weight:    8.9990
   chunk 102 optimal weight:    9.9990
   chunk 79 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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 = 0.3815 r_free = 0.3815 target = 0.120608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.087847 restraints weight = 24321.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.091287 restraints weight = 14636.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.093695 restraints weight = 10248.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.2827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9166  Z= 0.199
  Angle     :  0.581  12.093  12393  Z= 0.316
  Chirality :  0.041   0.183   1423
  Planarity :  0.004   0.044   1578
  Dihedral  :  4.861  37.056   1274
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 14.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  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:  0.37 (0.25), residues: 1153
  helix:  1.28 (0.19), residues: 757
  sheet: -0.93 (0.76), residues: 49
  loop : -1.91 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 694 
 HIS   0.005   0.001   HIS A  60 
 PHE   0.020   0.002   PHE A 934 
 TYR   0.024   0.002   TYR A 924 
 ARG   0.004   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
  249 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.9049 (pmm) cc_final: 0.8777 (pmm)
REVERT: A   58 ILE cc_start: 0.9455 (mt) cc_final: 0.9251 (tp)
REVERT: A   99 MET cc_start: 0.8565 (pmm) cc_final: 0.8313 (pmm)
REVERT: A  100 PHE cc_start: 0.8626 (m-10) cc_final: 0.8223 (m-80)
REVERT: A  103 LEU cc_start: 0.9611 (tp) cc_final: 0.9113 (tp)
REVERT: A  107 MET cc_start: 0.9542 (mmp) cc_final: 0.9156 (mmm)
REVERT: A  228 TRP cc_start: 0.8824 (m100) cc_final: 0.8591 (m100)
REVERT: A  237 ASP cc_start: 0.8700 (m-30) cc_final: 0.8262 (p0)
REVERT: A  293 ILE cc_start: 0.9173 (tp) cc_final: 0.8972 (tp)
REVERT: A  306 TYR cc_start: 0.8524 (m-80) cc_final: 0.8203 (m-80)
REVERT: A  359 TYR cc_start: 0.8613 (t80) cc_final: 0.7919 (t80)
REVERT: A  438 ARG cc_start: 0.8765 (mtt180) cc_final: 0.8406 (ttt180)
REVERT: A  720 LEU cc_start: 0.9406 (mm) cc_final: 0.8767 (mm)
REVERT: A  749 ASN cc_start: 0.8858 (m-40) cc_final: 0.8548 (m-40)
REVERT: A  754 LEU cc_start: 0.9124 (mt) cc_final: 0.8850 (mt)
REVERT: A  787 MET cc_start: 0.7894 (mmt) cc_final: 0.7553 (mtt)
REVERT: A  872 MET cc_start: 0.7494 (mmp) cc_final: 0.7146 (mmm)
REVERT: A  915 MET cc_start: 0.9478 (mtm) cc_final: 0.9055 (mtm)
REVERT: A  928 MET cc_start: 0.9037 (mpp) cc_final: 0.8815 (mpp)
REVERT: A  938 PHE cc_start: 0.9462 (t80) cc_final: 0.9245 (t80)
REVERT: A  953 PHE cc_start: 0.8681 (m-80) cc_final: 0.8352 (m-80)
REVERT: A  955 PHE cc_start: 0.8818 (t80) cc_final: 0.7952 (t80)
REVERT: A  969 ASN cc_start: 0.8826 (m110) cc_final: 0.8599 (m110)
REVERT: A 1104 TRP cc_start: 0.9211 (t60) cc_final: 0.8875 (t60)
REVERT: A 1105 LEU cc_start: 0.9725 (tp) cc_final: 0.9366 (tp)
REVERT: A 1109 LEU cc_start: 0.9317 (mt) cc_final: 0.8992 (mt)
REVERT: A 1196 ASP cc_start: 0.9117 (t0) cc_final: 0.8577 (t0)
REVERT: A 1205 GLU cc_start: 0.8982 (tt0) cc_final: 0.8772 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 249
  average time/residue: 0.1678
  time to fit residues: 61.5861
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  : 1.033 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 95 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 98 optimal weight:    0.0010
   chunk 112 optimal weight:    6.9990
   chunk 91 optimal weight:   10.0000
   chunk 29 optimal weight:    0.0670
   overall best weight:    1.0128

-------------------------------------------------------------------------------
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 = 0.3838 r_free = 0.3838 target = 0.122115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.089338 restraints weight = 24517.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.092870 restraints weight = 14918.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.095372 restraints weight = 10439.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.2970

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= 0.188
  Angle     :  0.590  12.163  12393  Z= 0.318
  Chirality :  0.042   0.199   1423
  Planarity :  0.004   0.043   1578
  Dihedral  :  4.746  34.601   1274
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  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:  0.37 (0.25), residues: 1153
  helix:  1.26 (0.19), residues: 756
  sheet: -0.96 (0.76), residues: 49
  loop : -1.85 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 694 
 HIS   0.005   0.001   HIS A  60 
 PHE   0.023   0.002   PHE A 196 
 TYR   0.039   0.002   TYR A  49 
 ARG   0.003   0.000   ARG A1081 

*********************** 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
  256 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 256
  time to evaluate  : 1.017 
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: 0.9052 (pmm) cc_final: 0.8791 (pmm)
REVERT: A   58 ILE cc_start: 0.9465 (mt) cc_final: 0.9243 (tp)
REVERT: A   99 MET cc_start: 0.8484 (pmm) cc_final: 0.8256 (pmm)
REVERT: A  100 PHE cc_start: 0.8593 (m-10) cc_final: 0.8177 (m-80)
REVERT: A  103 LEU cc_start: 0.9595 (tp) cc_final: 0.9107 (tp)
REVERT: A  107 MET cc_start: 0.9546 (mmp) cc_final: 0.9163 (mmm)
REVERT: A  228 TRP cc_start: 0.8827 (m100) cc_final: 0.8556 (m100)
REVERT: A  237 ASP cc_start: 0.8702 (m-30) cc_final: 0.8200 (p0)
REVERT: A  359 TYR cc_start: 0.8723 (t80) cc_final: 0.7889 (t80)
REVERT: A  438 ARG cc_start: 0.8816 (mtt180) cc_final: 0.8517 (ttt180)
REVERT: A  720 LEU cc_start: 0.9401 (mm) cc_final: 0.8727 (mm)
REVERT: A  749 ASN cc_start: 0.8808 (m-40) cc_final: 0.8495 (m-40)
REVERT: A  753 LEU cc_start: 0.9164 (tp) cc_final: 0.8958 (tp)
REVERT: A  754 LEU cc_start: 0.9103 (mt) cc_final: 0.8831 (mt)
REVERT: A  787 MET cc_start: 0.7901 (mmt) cc_final: 0.7553 (mtt)
REVERT: A  825 THR cc_start: 0.8722 (m) cc_final: 0.8492 (m)
REVERT: A  872 MET cc_start: 0.7479 (mmp) cc_final: 0.7129 (mmm)
REVERT: A  908 ARG cc_start: 0.8370 (mmm-85) cc_final: 0.8049 (mmm-85)
REVERT: A  910 GLN cc_start: 0.8563 (tp40) cc_final: 0.8142 (mm-40)
REVERT: A  928 MET cc_start: 0.8997 (mpp) cc_final: 0.8781 (mpp)
REVERT: A  953 PHE cc_start: 0.8607 (m-80) cc_final: 0.8327 (m-80)
REVERT: A  955 PHE cc_start: 0.8782 (t80) cc_final: 0.7930 (t80)
REVERT: A  965 MET cc_start: 0.8427 (tmm) cc_final: 0.7715 (tmm)
REVERT: A 1104 TRP cc_start: 0.9168 (t60) cc_final: 0.8839 (t60)
REVERT: A 1105 LEU cc_start: 0.9708 (tp) cc_final: 0.9335 (tp)
REVERT: A 1109 LEU cc_start: 0.9333 (mt) cc_final: 0.9024 (mt)
REVERT: A 1141 ILE cc_start: 0.9404 (mm) cc_final: 0.9180 (mm)
REVERT: A 1196 ASP cc_start: 0.9079 (t0) cc_final: 0.8435 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 256
  average time/residue: 0.1730
  time to fit residues: 65.1988
Evaluate side-chains
  215 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 48 optimal weight:   10.0000
   chunk 24 optimal weight:    0.5980
   chunk 79 optimal weight:    8.9990
   chunk 112 optimal weight:   10.0000
   chunk 108 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0050
   chunk 33 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.122927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.090373 restraints weight = 23830.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.093910 restraints weight = 14391.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.096328 restraints weight = 10090.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.3107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9166  Z= 0.179
  Angle     :  0.598  12.463  12393  Z= 0.318
  Chirality :  0.042   0.199   1423
  Planarity :  0.004   0.041   1578
  Dihedral  :  4.691  33.834   1274
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  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:  0.34 (0.25), residues: 1153
  helix:  1.25 (0.19), residues: 752
  sheet: -0.71 (0.82), residues: 43
  loop : -1.90 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 694 
 HIS   0.004   0.001   HIS A  60 
 PHE   0.025   0.002   PHE A 200 
 TYR   0.024   0.002   TYR A 924 
 ARG   0.008   0.000   ARG A1184 

*********************** 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
  249 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 1.003 
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: 0.9022 (pmm) cc_final: 0.8791 (pmm)
REVERT: A   50 MET cc_start: 0.8729 (mtp) cc_final: 0.8447 (mmm)
REVERT: A   58 ILE cc_start: 0.9460 (mt) cc_final: 0.9250 (tp)
REVERT: A   99 MET cc_start: 0.8501 (pmm) cc_final: 0.8248 (pmm)
REVERT: A  100 PHE cc_start: 0.8602 (m-10) cc_final: 0.8185 (m-80)
REVERT: A  103 LEU cc_start: 0.9591 (tp) cc_final: 0.9138 (tp)
REVERT: A  107 MET cc_start: 0.9534 (mmp) cc_final: 0.9184 (mmm)
REVERT: A  228 TRP cc_start: 0.8814 (m100) cc_final: 0.8566 (m100)
REVERT: A  251 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8097 (mt-10)
REVERT: A  359 TYR cc_start: 0.8635 (t80) cc_final: 0.7946 (t80)
REVERT: A  371 ILE cc_start: 0.8141 (pt) cc_final: 0.7897 (pt)
REVERT: A  720 LEU cc_start: 0.9394 (mm) cc_final: 0.8720 (mm)
REVERT: A  749 ASN cc_start: 0.8782 (m-40) cc_final: 0.8457 (m-40)
REVERT: A  754 LEU cc_start: 0.9098 (mt) cc_final: 0.8831 (mt)
REVERT: A  787 MET cc_start: 0.7824 (mmt) cc_final: 0.7497 (mtt)
REVERT: A  825 THR cc_start: 0.8680 (m) cc_final: 0.8474 (m)
REVERT: A  852 GLN cc_start: 0.7618 (mp10) cc_final: 0.7409 (mm-40)
REVERT: A  872 MET cc_start: 0.7457 (mmp) cc_final: 0.7135 (mmm)
REVERT: A  910 GLN cc_start: 0.8481 (tp40) cc_final: 0.8102 (mm-40)
REVERT: A  928 MET cc_start: 0.8905 (mpp) cc_final: 0.8699 (mpp)
REVERT: A  938 PHE cc_start: 0.9443 (t80) cc_final: 0.9217 (t80)
REVERT: A  953 PHE cc_start: 0.8622 (m-80) cc_final: 0.8346 (m-80)
REVERT: A  955 PHE cc_start: 0.8765 (t80) cc_final: 0.7866 (t80)
REVERT: A 1104 TRP cc_start: 0.9187 (t60) cc_final: 0.8851 (t60)
REVERT: A 1105 LEU cc_start: 0.9725 (tp) cc_final: 0.9358 (tp)
REVERT: A 1109 LEU cc_start: 0.9327 (mt) cc_final: 0.9010 (mt)
REVERT: A 1141 ILE cc_start: 0.9398 (mm) cc_final: 0.9183 (mm)
REVERT: A 1196 ASP cc_start: 0.9147 (t0) cc_final: 0.8647 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 249
  average time/residue: 0.1702
  time to fit residues: 62.4482
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  : 1.076 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 65 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 71 optimal weight:    0.0470
   chunk 109 optimal weight:    0.0870
   chunk 103 optimal weight:    9.9990
   chunk 27 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.5456

-------------------------------------------------------------------------------
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**
A 367 ASN
** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1228 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.123450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.091045 restraints weight = 23840.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.094487 restraints weight = 14376.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.097101 restraints weight = 10093.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.3179

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     :  0.601  12.574  12393  Z= 0.316
  Chirality :  0.042   0.195   1423
  Planarity :  0.004   0.042   1578
  Dihedral  :  4.621  34.362   1274
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.42 %
    Favored  : 99.47 %
  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:  0.39 (0.25), residues: 1153
  helix:  1.29 (0.19), residues: 751
  sheet: -0.48 (1.03), residues: 28
  loop : -1.86 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 694 
 HIS   0.004   0.000   HIS A  60 
 PHE   0.024   0.002   PHE A 200 
 TYR   0.025   0.002   TYR A 924 
 ARG   0.010   0.001   ARG A 206 

********************** 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
  246 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 245
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.9002 (pmm) cc_final: 0.8773 (pmm)
REVERT: A   99 MET cc_start: 0.8530 (pmm) cc_final: 0.8270 (pmm)
REVERT: A  100 PHE cc_start: 0.8607 (m-10) cc_final: 0.8188 (m-80)
REVERT: A  103 LEU cc_start: 0.9593 (tp) cc_final: 0.9158 (tp)
REVERT: A  107 MET cc_start: 0.9568 (mmp) cc_final: 0.9207 (mmm)
REVERT: A  228 TRP cc_start: 0.8785 (m100) cc_final: 0.8536 (m100)
REVERT: A  239 GLU cc_start: 0.9195 (pp20) cc_final: 0.8991 (pp20)
REVERT: A  251 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8176 (mt-10)
REVERT: A  359 TYR cc_start: 0.8570 (t80) cc_final: 0.7938 (t80)
REVERT: A  720 LEU cc_start: 0.9339 (mm) cc_final: 0.8686 (mm)
REVERT: A  749 ASN cc_start: 0.8774 (m-40) cc_final: 0.8453 (m-40)
REVERT: A  754 LEU cc_start: 0.9087 (mt) cc_final: 0.8823 (mt)
REVERT: A  787 MET cc_start: 0.7811 (mmt) cc_final: 0.7515 (mtt)
REVERT: A  825 THR cc_start: 0.8696 (m) cc_final: 0.8471 (m)
REVERT: A  872 MET cc_start: 0.7458 (mmp) cc_final: 0.7140 (mmm)
REVERT: A  910 GLN cc_start: 0.8411 (tp40) cc_final: 0.8038 (mm-40)
REVERT: A  928 MET cc_start: 0.8914 (mpp) cc_final: 0.8662 (mpp)
REVERT: A  938 PHE cc_start: 0.9472 (t80) cc_final: 0.9228 (t80)
REVERT: A  953 PHE cc_start: 0.8683 (m-80) cc_final: 0.8361 (m-80)
REVERT: A  955 PHE cc_start: 0.8796 (t80) cc_final: 0.7891 (t80)
REVERT: A  965 MET cc_start: 0.8337 (tmm) cc_final: 0.7767 (tmm)
REVERT: A 1104 TRP cc_start: 0.9206 (t60) cc_final: 0.8855 (t60)
REVERT: A 1105 LEU cc_start: 0.9732 (tp) cc_final: 0.9366 (tp)
REVERT: A 1109 LEU cc_start: 0.9302 (mt) cc_final: 0.8985 (mt)
REVERT: A 1141 ILE cc_start: 0.9382 (mm) cc_final: 0.9174 (mm)
REVERT: A 1196 ASP cc_start: 0.9198 (t0) cc_final: 0.8550 (t0)
REVERT: A 1234 GLN cc_start: 0.8743 (tp-100) cc_final: 0.8427 (mm110)
  outliers start: 1
  outliers final: 0
  residues processed: 245
  average time/residue: 0.1679
  time to fit residues: 60.8449
Evaluate side-chains
  215 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 9 optimal weight:    0.7980
   chunk 42 optimal weight:    5.9990
   chunk 105 optimal weight:    4.9990
   chunk 109 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 104 optimal weight:    0.9990
   chunk 19 optimal weight:    9.9990
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3836 r_free = 0.3836 target = 0.122354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.090230 restraints weight = 23873.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.093744 restraints weight = 14370.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.096250 restraints weight = 10071.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.3284

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= 0.175
  Angle     :  0.591  10.681  12393  Z= 0.314
  Chirality :  0.041   0.187   1423
  Planarity :  0.004   0.041   1578
  Dihedral  :  4.597  34.648   1274
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.53 %
    Favored  : 99.37 %
  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:  1.30 (0.19), residues: 751
  sheet: -0.78 (0.95), residues: 34
  loop : -1.79 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP A 694 
 HIS   0.003   0.000   HIS A  60 
 PHE   0.024   0.002   PHE A 200 
 TYR   0.022   0.002   TYR A 273 
 ARG   0.008   0.000   ARG A 206 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2927.58 seconds
wall clock time: 53 minutes 23.35 seconds (3203.35 seconds total)