Starting phenix.real_space_refine
on Tue Mar  3 22:57:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zk9_14759/03_2026/7zk9_14759.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zk9_14759/03_2026/7zk9_14759.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zk9_14759/03_2026/7zk9_14759.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zk9_14759/03_2026/7zk9_14759.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zk9_14759/03_2026/7zk9_14759.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zk9_14759/03_2026/7zk9_14759.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.13, per 1000 atoms: 0.24
  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: 0.85
  Conformation dependent library (CDL) restraints added in 320.7 milliseconds
  

  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: 0.29
  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: 1.26

  Time building geometry restraints manager: 1.09 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:             1.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.200
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.360
-------------------------------------------------------------------------------
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= 0.531
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (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
 ARG   0.009   0.001   ARG A 589 
 TYR   0.022   0.001   TYR A 924 
 PHE   0.019   0.002   PHE A 100 
 TRP   0.009   0.001   TRP A 704 
 HIS   0.002   0.000   HIS A1151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00905 ( 9166)
  covalent geometry    : angle       1.00228 (12393)
  hydrogen bonds       : bond        0.14435 (  577)
  hydrogen bonds       : angle       6.02113 ( 1701)

*********************** 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  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9266 (mt) cc_final: 0.8920 (tp)
REVERT: A   75 THR cc_start: 0.9537 (p) cc_final: 0.9332 (p)
REVERT: A   76 ASP cc_start: 0.8951 (m-30) cc_final: 0.8526 (m-30)
REVERT: A  100 PHE cc_start: 0.8316 (m-10) cc_final: 0.8050 (m-10)
REVERT: A  103 LEU cc_start: 0.9472 (tp) cc_final: 0.9058 (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: 0.8250 (mmm)
REVERT: A  191 GLN cc_start: 0.9292 (tm-30) cc_final: 0.8920 (tm-30)
REVERT: A  209 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8332 (mptt)
REVERT: A  295 MET cc_start: 0.8575 (ttm) cc_final: 0.8271 (ttm)
REVERT: A  446 MET cc_start: 0.4325 (tpt) cc_final: 0.4123 (mmt)
REVERT: A  471 GLN cc_start: 0.8887 (pt0) cc_final: 0.8550 (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: 0.7264 (mtt)
REVERT: A  828 ARG cc_start: 0.9099 (tpt170) cc_final: 0.8712 (tpt90)
REVERT: A  872 MET cc_start: 0.7337 (mmp) cc_final: 0.7127 (mmm)
REVERT: A  928 MET cc_start: 0.9013 (mpp) cc_final: 0.8753 (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: 0.8088 (t80)
REVERT: A  960 VAL cc_start: 0.9389 (t) cc_final: 0.9160 (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: 0.0778
  time to fit residues: 32.1564
Evaluate side-chains
  231 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 228
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    0.0570
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0470
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:   20.0000
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.7598

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.123776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.091089 restraints weight = 23869.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.094534 restraints weight = 14693.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.097019 restraints weight = 10439.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.098682 restraints weight = 8064.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.100029 restraints weight = 6677.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9166  Z= 0.137
  Angle     :  0.591   9.047  12393  Z= 0.321
  Chirality :  0.042   0.170   1423
  Planarity :  0.004   0.040   1578
  Dihedral  :  4.986  38.741   1274
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  4.75 %
    Favored  : 95.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.25), residues: 1153
  helix:  1.20 (0.19), residues: 749
  sheet: -0.91 (0.73), residues: 49
  loop : -2.04 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 589 
 TYR   0.023   0.001   TYR A 924 
 PHE   0.024   0.002   PHE A 131 
 TRP   0.013   0.001   TRP A 704 
 HIS   0.003   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 9166)
  covalent geometry    : angle       0.59136 (12393)
  hydrogen bonds       : bond        0.05050 (  577)
  hydrogen bonds       : angle       4.84373 ( 1701)

*********************** 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
  264 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 262
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 ILE cc_start: 0.9379 (mt) cc_final: 0.9147 (tp)
REVERT: A   76 ASP cc_start: 0.9063 (m-30) cc_final: 0.8552 (m-30)
REVERT: A   99 MET cc_start: 0.8522 (pmm) cc_final: 0.8294 (pmm)
REVERT: A  100 PHE cc_start: 0.8268 (m-10) cc_final: 0.7936 (m-10)
REVERT: A  103 LEU cc_start: 0.9538 (tp) cc_final: 0.9214 (tp)
REVERT: A  124 VAL cc_start: 0.9464 (m) cc_final: 0.9199 (p)
REVERT: A  209 LYS cc_start: 0.8968 (ptpp) cc_final: 0.8702 (mptt)
REVERT: A  406 LEU cc_start: 0.8925 (mm) cc_final: 0.8706 (mm)
REVERT: A  446 MET cc_start: 0.4351 (tpt) cc_final: 0.4012 (mmt)
REVERT: A  498 LYS cc_start: 0.8488 (tptt) cc_final: 0.8252 (mtmm)
REVERT: A  720 LEU cc_start: 0.9411 (mm) cc_final: 0.8935 (mm)
REVERT: A  754 LEU cc_start: 0.9040 (mt) cc_final: 0.8746 (mt)
REVERT: A  787 MET cc_start: 0.7731 (mmt) cc_final: 0.7507 (mtt)
REVERT: A  792 MET cc_start: 0.9260 (mpp) cc_final: 0.9039 (mpp)
REVERT: A  872 MET cc_start: 0.7389 (mmp) cc_final: 0.7132 (mmm)
REVERT: A  902 THR cc_start: 0.9564 (p) cc_final: 0.9361 (t)
REVERT: A  928 MET cc_start: 0.9036 (mpp) cc_final: 0.8812 (mpp)
REVERT: A  930 LYS cc_start: 0.8774 (ttpt) cc_final: 0.8078 (pttp)
REVERT: A  938 PHE cc_start: 0.9466 (t80) cc_final: 0.9219 (t80)
REVERT: A  953 PHE cc_start: 0.8709 (m-80) cc_final: 0.8461 (m-80)
REVERT: A  955 PHE cc_start: 0.8757 (t80) cc_final: 0.7989 (t80)
REVERT: A  960 VAL cc_start: 0.9438 (t) cc_final: 0.9184 (t)
REVERT: A 1152 GLN cc_start: 0.9160 (pt0) cc_final: 0.8947 (pp30)
REVERT: A 1205 GLU cc_start: 0.9007 (tt0) cc_final: 0.8705 (tp30)
  outliers start: 2
  outliers final: 1
  residues processed: 263
  average time/residue: 0.0733
  time to fit residues: 28.6899
Evaluate side-chains
  225 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 224
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   chunk 60 optimal weight:    5.9990
   chunk 98 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 91 optimal weight:   10.0000
   chunk 55 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    2.1990

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.119387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.087154 restraints weight = 24312.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.090534 restraints weight = 14734.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.092946 restraints weight = 10335.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.094659 restraints weight = 7933.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.095831 restraints weight = 6521.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9166  Z= 0.176
  Angle     :  0.587   9.616  12393  Z= 0.326
  Chirality :  0.041   0.142   1423
  Planarity :  0.004   0.039   1578
  Dihedral  :  5.043  41.731   1274
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.80 %
    Favored  : 95.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.25), residues: 1153
  helix:  1.12 (0.19), residues: 753
  sheet: -0.94 (0.76), residues: 49
  loop : -2.04 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 589 
 TYR   0.023   0.002   TYR A 924 
 PHE   0.067   0.002   PHE A 934 
 TRP   0.013   0.001   TRP A 704 
 HIS   0.006   0.001   HIS A1253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 9166)
  covalent geometry    : angle       0.58694 (12393)
  hydrogen bonds       : bond        0.04750 (  577)
  hydrogen bonds       : angle       4.67494 ( 1701)

*********************** 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: 2
    poor density    : 264
  time to evaluate  : 0.372 
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: 0.8995 (pmm) cc_final: 0.8643 (pmm)
REVERT: A   58 ILE cc_start: 0.9485 (mt) cc_final: 0.9267 (tp)
REVERT: A   73 ASP cc_start: 0.8708 (t70) cc_final: 0.8384 (t0)
REVERT: A   75 THR cc_start: 0.9557 (p) cc_final: 0.9341 (p)
REVERT: A   76 ASP cc_start: 0.9025 (m-30) cc_final: 0.8528 (m-30)
REVERT: A   99 MET cc_start: 0.8447 (pmm) cc_final: 0.8182 (pmm)
REVERT: A  100 PHE cc_start: 0.8220 (m-10) cc_final: 0.7960 (m-10)
REVERT: A  103 LEU cc_start: 0.9572 (tp) cc_final: 0.9120 (tp)
REVERT: A  196 PHE cc_start: 0.9136 (t80) cc_final: 0.8907 (t80)
REVERT: A  209 LYS cc_start: 0.9011 (ptpp) cc_final: 0.8781 (mptt)
REVERT: A  359 TYR cc_start: 0.8870 (t80) cc_final: 0.8020 (t80)
REVERT: A  438 ARG cc_start: 0.8716 (mtt180) cc_final: 0.8418 (mtt180)
REVERT: A  506 TYR cc_start: 0.8015 (m-10) cc_final: 0.7607 (m-10)
REVERT: A  720 LEU cc_start: 0.9480 (mm) cc_final: 0.8907 (mm)
REVERT: A  749 ASN cc_start: 0.8789 (m-40) cc_final: 0.8478 (m-40)
REVERT: A  754 LEU cc_start: 0.9110 (mt) cc_final: 0.8853 (mt)
REVERT: A  787 MET cc_start: 0.7994 (mmt) cc_final: 0.7647 (mtt)
REVERT: A  828 ARG cc_start: 0.9089 (tpt170) cc_final: 0.8650 (tpt90)
REVERT: A  872 MET cc_start: 0.7444 (mmp) cc_final: 0.7090 (mmm)
REVERT: A  938 PHE cc_start: 0.9449 (t80) cc_final: 0.9231 (t80)
REVERT: A  953 PHE cc_start: 0.8746 (m-80) cc_final: 0.8442 (m-80)
REVERT: A  955 PHE cc_start: 0.8767 (t80) cc_final: 0.7988 (t80)
REVERT: A 1104 TRP cc_start: 0.9079 (t60) cc_final: 0.8783 (t60)
  outliers start: 2
  outliers final: 0
  residues processed: 265
  average time/residue: 0.0772
  time to fit residues: 30.4998
Evaluate side-chains
  222 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 36 optimal weight:   10.0000
   chunk 58 optimal weight:    7.9990
   chunk 86 optimal weight:    0.2980
   chunk 32 optimal weight:   10.0000
   chunk 54 optimal weight:    0.3980
   chunk 79 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 92 optimal weight:    9.9990
   chunk 101 optimal weight:    5.9990
   chunk 105 optimal weight:    0.3980
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 168 ASN
A1132 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.119187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.086927 restraints weight = 24402.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.090266 restraints weight = 14709.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.092617 restraints weight = 10337.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.094290 restraints weight = 7971.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.095435 restraints weight = 6582.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   9166  Z= 0.160
  Angle     :  0.581  10.091  12393  Z= 0.321
  Chirality :  0.041   0.166   1423
  Planarity :  0.004   0.040   1578
  Dihedral  :  4.923  34.113   1274
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 14.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  4.01 %
    Favored  : 95.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.25), residues: 1153
  helix:  1.14 (0.19), residues: 754
  sheet: -0.94 (0.77), residues: 49
  loop : -2.06 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1081 
 TYR   0.038   0.002   TYR A 306 
 PHE   0.034   0.002   PHE A 934 
 TRP   0.020   0.001   TRP A 694 
 HIS   0.005   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 9166)
  covalent geometry    : angle       0.58120 (12393)
  hydrogen bonds       : bond        0.04647 (  577)
  hydrogen bonds       : angle       4.58416 ( 1701)

*********************** 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  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.9063 (pmm) cc_final: 0.8687 (pmm)
REVERT: A   58 ILE cc_start: 0.9488 (mt) cc_final: 0.9250 (tp)
REVERT: A   66 LEU cc_start: 0.8698 (tp) cc_final: 0.8449 (tp)
REVERT: A   99 MET cc_start: 0.8448 (pmm) cc_final: 0.8215 (pmm)
REVERT: A  100 PHE cc_start: 0.8558 (m-10) cc_final: 0.8179 (m-80)
REVERT: A  103 LEU cc_start: 0.9586 (tp) cc_final: 0.9078 (tp)
REVERT: A  107 MET cc_start: 0.9483 (mmp) cc_final: 0.9058 (mmp)
REVERT: A  359 TYR cc_start: 0.8816 (t80) cc_final: 0.7964 (t80)
REVERT: A  720 LEU cc_start: 0.9457 (mm) cc_final: 0.8814 (mm)
REVERT: A  749 ASN cc_start: 0.8796 (m-40) cc_final: 0.8498 (m-40)
REVERT: A  754 LEU cc_start: 0.9087 (mt) cc_final: 0.8818 (mt)
REVERT: A  787 MET cc_start: 0.7979 (mmt) cc_final: 0.7639 (mtt)
REVERT: A  828 ARG cc_start: 0.9060 (tpt170) cc_final: 0.8688 (tpt90)
REVERT: A  872 MET cc_start: 0.7465 (mmp) cc_final: 0.7094 (mmm)
REVERT: A  928 MET cc_start: 0.9064 (mpp) cc_final: 0.8759 (mpp)
REVERT: A  930 LYS cc_start: 0.8784 (ttpt) cc_final: 0.8382 (pttp)
REVERT: A  938 PHE cc_start: 0.9417 (t80) cc_final: 0.9214 (t80)
REVERT: A  953 PHE cc_start: 0.8686 (m-80) cc_final: 0.8391 (m-80)
REVERT: A  955 PHE cc_start: 0.8743 (t80) cc_final: 0.7951 (t80)
REVERT: A 1109 LEU cc_start: 0.9369 (mt) cc_final: 0.9018 (mt)
REVERT: A 1129 TYR cc_start: 0.7922 (t80) cc_final: 0.7639 (t80)
REVERT: A 1196 ASP cc_start: 0.9065 (t0) cc_final: 0.8409 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 256
  average time/residue: 0.0729
  time to fit residues: 28.2282
Evaluate side-chains
  218 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 54 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 47 optimal weight:   10.0000
   chunk 93 optimal weight:    5.9990
   chunk 35 optimal weight:   20.0000
   chunk 34 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 108 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 168 ASN
A 483 ASN
A1132 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.117150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.084506 restraints weight = 24543.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.087822 restraints weight = 14791.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.090180 restraints weight = 10360.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.091779 restraints weight = 7987.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.092908 restraints weight = 6615.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9166  Z= 0.194
  Angle     :  0.599  10.395  12393  Z= 0.333
  Chirality :  0.042   0.171   1423
  Planarity :  0.004   0.042   1578
  Dihedral  :  5.002  35.309   1274
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 15.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.06 %
    Favored  : 96.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.25), residues: 1153
  helix:  1.03 (0.18), residues: 757
  sheet: -0.91 (0.78), residues: 49
  loop : -2.11 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1081 
 TYR   0.025   0.002   TYR A 924 
 PHE   0.031   0.002   PHE A 934 
 TRP   0.022   0.002   TRP A 694 
 HIS   0.006   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 9166)
  covalent geometry    : angle       0.59871 (12393)
  hydrogen bonds       : bond        0.04714 (  577)
  hydrogen bonds       : angle       4.62354 ( 1701)

*********************** 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
  254 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 252
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.9111 (pmm) cc_final: 0.8799 (pmm)
REVERT: A   49 TYR cc_start: 0.8834 (m-10) cc_final: 0.8514 (m-80)
REVERT: A   58 ILE cc_start: 0.9515 (mt) cc_final: 0.9290 (tp)
REVERT: A   66 LEU cc_start: 0.8731 (tp) cc_final: 0.8438 (tp)
REVERT: A   74 MET cc_start: 0.9541 (ttt) cc_final: 0.9290 (ttp)
REVERT: A   99 MET cc_start: 0.8451 (pmm) cc_final: 0.8203 (pmm)
REVERT: A  100 PHE cc_start: 0.8640 (m-10) cc_final: 0.8223 (m-80)
REVERT: A  103 LEU cc_start: 0.9610 (tp) cc_final: 0.9128 (tp)
REVERT: A  107 MET cc_start: 0.9495 (mmp) cc_final: 0.9116 (mmm)
REVERT: A  237 ASP cc_start: 0.8670 (m-30) cc_final: 0.8202 (p0)
REVERT: A  359 TYR cc_start: 0.8818 (t80) cc_final: 0.7949 (t80)
REVERT: A  438 ARG cc_start: 0.8747 (mtt180) cc_final: 0.8547 (mtt180)
REVERT: A  720 LEU cc_start: 0.9461 (mm) cc_final: 0.8803 (mm)
REVERT: A  749 ASN cc_start: 0.8921 (m-40) cc_final: 0.8600 (m-40)
REVERT: A  754 LEU cc_start: 0.9156 (mt) cc_final: 0.8905 (mt)
REVERT: A  872 MET cc_start: 0.7445 (mmp) cc_final: 0.7084 (mmm)
REVERT: A  938 PHE cc_start: 0.9420 (t80) cc_final: 0.9175 (t80)
REVERT: A  953 PHE cc_start: 0.8712 (m-80) cc_final: 0.8323 (m-80)
REVERT: A  969 ASN cc_start: 0.8748 (m110) cc_final: 0.8531 (m110)
REVERT: A 1104 TRP cc_start: 0.9235 (t60) cc_final: 0.8884 (t60)
REVERT: A 1105 LEU cc_start: 0.9728 (tp) cc_final: 0.9384 (tp)
REVERT: A 1109 LEU cc_start: 0.9362 (mt) cc_final: 0.9018 (mt)
REVERT: A 1129 TYR cc_start: 0.8099 (t80) cc_final: 0.7848 (t80)
REVERT: A 1196 ASP cc_start: 0.9056 (t0) cc_final: 0.8457 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 253
  average time/residue: 0.0715
  time to fit residues: 27.5416
Evaluate side-chains
  212 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 39 optimal weight:   10.0000
   chunk 49 optimal weight:    4.9990
   chunk 104 optimal weight:    0.0870
   chunk 34 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 45 optimal weight:   10.0000
   chunk 42 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0170
   overall best weight:    0.9800

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

Flipped N/Q/H residues before XYZ refinement:
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1132 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 = 0.120057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.087371 restraints weight = 24208.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.090786 restraints weight = 14594.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.093238 restraints weight = 10208.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.094857 restraints weight = 7892.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.096177 restraints weight = 6552.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9166  Z= 0.133
  Angle     :  0.583  12.884  12393  Z= 0.314
  Chirality :  0.042   0.190   1423
  Planarity :  0.004   0.041   1578
  Dihedral  :  4.811  35.705   1274
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 14.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.25), residues: 1153
  helix:  1.19 (0.19), residues: 757
  sheet: -0.98 (0.76), residues: 49
  loop : -2.00 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 206 
 TYR   0.022   0.002   TYR A 924 
 PHE   0.025   0.002   PHE A 934 
 TRP   0.027   0.002   TRP A 694 
 HIS   0.005   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9166)
  covalent geometry    : angle       0.58343 (12393)
  hydrogen bonds       : bond        0.04493 (  577)
  hydrogen bonds       : angle       4.44165 ( 1701)

*********************** 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
  253 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 253
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.9126 (pmm) cc_final: 0.8827 (pmm)
REVERT: A   58 ILE cc_start: 0.9461 (mt) cc_final: 0.9254 (tp)
REVERT: A   67 MET cc_start: 0.9420 (tpt) cc_final: 0.9211 (tpp)
REVERT: A   74 MET cc_start: 0.9464 (ttt) cc_final: 0.9186 (ttp)
REVERT: A   99 MET cc_start: 0.8408 (pmm) cc_final: 0.8199 (pmm)
REVERT: A  103 LEU cc_start: 0.9592 (tp) cc_final: 0.9101 (tp)
REVERT: A  107 MET cc_start: 0.9513 (mmp) cc_final: 0.9116 (mmm)
REVERT: A  237 ASP cc_start: 0.8656 (m-30) cc_final: 0.8141 (p0)
REVERT: A  295 MET cc_start: 0.8554 (ttm) cc_final: 0.8287 (ttm)
REVERT: A  359 TYR cc_start: 0.8723 (t80) cc_final: 0.7870 (t80)
REVERT: A  446 MET cc_start: 0.4598 (tpt) cc_final: 0.4201 (mmt)
REVERT: A  720 LEU cc_start: 0.9431 (mm) cc_final: 0.8774 (mm)
REVERT: A  749 ASN cc_start: 0.8825 (m-40) cc_final: 0.8526 (m-40)
REVERT: A  754 LEU cc_start: 0.9088 (mt) cc_final: 0.8813 (mt)
REVERT: A  787 MET cc_start: 0.7866 (mmt) cc_final: 0.7505 (mtt)
REVERT: A  872 MET cc_start: 0.7420 (mmp) cc_final: 0.7085 (mmm)
REVERT: A  928 MET cc_start: 0.9022 (mpp) cc_final: 0.8770 (mpp)
REVERT: A  938 PHE cc_start: 0.9410 (t80) cc_final: 0.9189 (t80)
REVERT: A  953 PHE cc_start: 0.8692 (m-80) cc_final: 0.8368 (m-80)
REVERT: A  955 PHE cc_start: 0.8721 (t80) cc_final: 0.7865 (t80)
REVERT: A  969 ASN cc_start: 0.8761 (m110) cc_final: 0.8504 (m110)
REVERT: A 1104 TRP cc_start: 0.9195 (t60) cc_final: 0.8878 (t60)
REVERT: A 1105 LEU cc_start: 0.9716 (tp) cc_final: 0.9328 (tp)
REVERT: A 1109 LEU cc_start: 0.9341 (mt) cc_final: 0.8997 (mt)
REVERT: A 1129 TYR cc_start: 0.7720 (t80) cc_final: 0.7485 (t80)
REVERT: A 1196 ASP cc_start: 0.9064 (t0) cc_final: 0.8472 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 253
  average time/residue: 0.0708
  time to fit residues: 27.5209
Evaluate side-chains
  220 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 104 optimal weight:    8.9990
   chunk 78 optimal weight:    0.7980
   chunk 53 optimal weight:   20.0000
   chunk 16 optimal weight:    5.9990
   chunk 108 optimal weight:    4.9990
   chunk 102 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 43 optimal weight:    6.9990
   chunk 31 optimal weight:    7.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1077 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 = 0.3784 r_free = 0.3784 target = 0.118440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.085484 restraints weight = 24712.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.088886 restraints weight = 15088.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.091240 restraints weight = 10569.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.092921 restraints weight = 8178.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.094129 restraints weight = 6770.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9166  Z= 0.181
  Angle     :  0.611  12.775  12393  Z= 0.338
  Chirality :  0.043   0.204   1423
  Planarity :  0.004   0.049   1578
  Dihedral  :  4.922  33.834   1274
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.25), residues: 1153
  helix:  1.08 (0.19), residues: 756
  sheet: -0.78 (0.93), residues: 34
  loop : -1.93 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1121 
 TYR   0.023   0.002   TYR A 924 
 PHE   0.022   0.002   PHE A 204 
 TRP   0.027   0.002   TRP A 694 
 HIS   0.006   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 9166)
  covalent geometry    : angle       0.61094 (12393)
  hydrogen bonds       : bond        0.04599 (  577)
  hydrogen bonds       : angle       4.60255 ( 1701)

*********************** 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
  246 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.9125 (pmm) cc_final: 0.8726 (pmm)
REVERT: A   58 ILE cc_start: 0.9483 (mt) cc_final: 0.9278 (tp)
REVERT: A   67 MET cc_start: 0.9429 (tpt) cc_final: 0.9188 (tpp)
REVERT: A   74 MET cc_start: 0.9511 (ttt) cc_final: 0.9271 (ttp)
REVERT: A  103 LEU cc_start: 0.9596 (tp) cc_final: 0.9113 (tp)
REVERT: A  107 MET cc_start: 0.9502 (mmp) cc_final: 0.9099 (mmm)
REVERT: A  195 THR cc_start: 0.8825 (m) cc_final: 0.8547 (m)
REVERT: A  335 LEU cc_start: 0.8922 (mt) cc_final: 0.8583 (mt)
REVERT: A  359 TYR cc_start: 0.8649 (t80) cc_final: 0.7905 (t80)
REVERT: A  446 MET cc_start: 0.4687 (tpt) cc_final: 0.4356 (mmt)
REVERT: A  720 LEU cc_start: 0.9455 (mm) cc_final: 0.8803 (mm)
REVERT: A  749 ASN cc_start: 0.8920 (m-40) cc_final: 0.8600 (m-40)
REVERT: A  754 LEU cc_start: 0.9134 (mt) cc_final: 0.8869 (mt)
REVERT: A  787 MET cc_start: 0.8008 (mmt) cc_final: 0.7629 (mtt)
REVERT: A  928 MET cc_start: 0.9060 (mpp) cc_final: 0.8791 (mpp)
REVERT: A  938 PHE cc_start: 0.9402 (t80) cc_final: 0.9171 (t80)
REVERT: A  953 PHE cc_start: 0.8700 (m-80) cc_final: 0.8371 (m-80)
REVERT: A  955 PHE cc_start: 0.8771 (t80) cc_final: 0.7928 (t80)
REVERT: A  969 ASN cc_start: 0.8789 (m110) cc_final: 0.8531 (m110)
REVERT: A 1109 LEU cc_start: 0.9367 (mt) cc_final: 0.9029 (mt)
REVERT: A 1196 ASP cc_start: 0.9101 (t0) cc_final: 0.8526 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 246
  average time/residue: 0.0754
  time to fit residues: 28.1748
Evaluate side-chains
  213 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 111 optimal weight:    5.9990
   chunk 94 optimal weight:    0.4980
   chunk 17 optimal weight:    0.0870
   chunk 41 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 104 optimal weight:   10.0000
   chunk 77 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9980
   chunk 98 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9990
   overall best weight:    1.3162

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

Flipped N/Q/H residues before XYZ refinement:
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1077 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 = 0.3810 r_free = 0.3810 target = 0.120384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.087182 restraints weight = 24393.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.090639 restraints weight = 14785.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.093034 restraints weight = 10380.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.094666 restraints weight = 8029.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.095936 restraints weight = 6687.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.3111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9166  Z= 0.141
  Angle     :  0.598  12.584  12393  Z= 0.323
  Chirality :  0.042   0.186   1423
  Planarity :  0.004   0.048   1578
  Dihedral  :  4.886  34.136   1274
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.25), residues: 1153
  helix:  1.10 (0.19), residues: 756
  sheet: -1.01 (0.76), residues: 49
  loop : -1.89 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1081 
 TYR   0.023   0.002   TYR A 924 
 PHE   0.021   0.002   PHE A 934 
 TRP   0.032   0.002   TRP A 694 
 HIS   0.005   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 9166)
  covalent geometry    : angle       0.59785 (12393)
  hydrogen bonds       : bond        0.04461 (  577)
  hydrogen bonds       : angle       4.50814 ( 1701)

*********************** 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
  253 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 253
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.9123 (pmm) cc_final: 0.8796 (pmm)
REVERT: A   67 MET cc_start: 0.9399 (tpt) cc_final: 0.9135 (tpp)
REVERT: A  103 LEU cc_start: 0.9592 (tp) cc_final: 0.9099 (tp)
REVERT: A  107 MET cc_start: 0.9521 (mmp) cc_final: 0.9137 (mmm)
REVERT: A  195 THR cc_start: 0.8771 (m) cc_final: 0.8514 (m)
REVERT: A  237 ASP cc_start: 0.8682 (m-30) cc_final: 0.8165 (p0)
REVERT: A  335 LEU cc_start: 0.8897 (mt) cc_final: 0.8567 (mt)
REVERT: A  359 TYR cc_start: 0.8656 (t80) cc_final: 0.7960 (t80)
REVERT: A  446 MET cc_start: 0.4630 (tpt) cc_final: 0.4317 (mmt)
REVERT: A  720 LEU cc_start: 0.9423 (mm) cc_final: 0.8747 (mm)
REVERT: A  749 ASN cc_start: 0.8895 (m-40) cc_final: 0.8573 (m-40)
REVERT: A  754 LEU cc_start: 0.9109 (mt) cc_final: 0.8840 (mt)
REVERT: A  787 MET cc_start: 0.8024 (mmt) cc_final: 0.7626 (mtt)
REVERT: A  872 MET cc_start: 0.7443 (mmp) cc_final: 0.7090 (mmm)
REVERT: A  928 MET cc_start: 0.9025 (mpp) cc_final: 0.8788 (mpp)
REVERT: A  938 PHE cc_start: 0.9394 (t80) cc_final: 0.9183 (t80)
REVERT: A  953 PHE cc_start: 0.8634 (m-80) cc_final: 0.8356 (m-80)
REVERT: A  955 PHE cc_start: 0.8731 (t80) cc_final: 0.7816 (t80)
REVERT: A 1104 TRP cc_start: 0.9199 (t60) cc_final: 0.8775 (t60)
REVERT: A 1105 LEU cc_start: 0.9713 (tp) cc_final: 0.9328 (tp)
REVERT: A 1109 LEU cc_start: 0.9341 (mt) cc_final: 0.9010 (mt)
REVERT: A 1141 ILE cc_start: 0.9416 (mm) cc_final: 0.9182 (mm)
REVERT: A 1196 ASP cc_start: 0.9036 (t0) cc_final: 0.8393 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 253
  average time/residue: 0.0710
  time to fit residues: 27.1999
Evaluate side-chains
  220 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 114 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 111 optimal weight:    5.9990
   chunk 112 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9990
   chunk 99 optimal weight:    6.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1077 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 = 0.3813 r_free = 0.3813 target = 0.120886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.087904 restraints weight = 24263.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.091335 restraints weight = 14820.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.093745 restraints weight = 10449.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.095467 restraints weight = 8088.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.096731 restraints weight = 6678.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9166  Z= 0.142
  Angle     :  0.614  10.900  12393  Z= 0.333
  Chirality :  0.042   0.217   1423
  Planarity :  0.004   0.046   1578
  Dihedral  :  4.868  33.804   1274
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 15.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.25), residues: 1153
  helix:  1.07 (0.19), residues: 758
  sheet: -0.91 (0.77), residues: 49
  loop : -1.88 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 828 
 TYR   0.028   0.002   TYR A1129 
 PHE   0.026   0.002   PHE A 200 
 TRP   0.036   0.002   TRP A 694 
 HIS   0.004   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9166)
  covalent geometry    : angle       0.61371 (12393)
  hydrogen bonds       : bond        0.04431 (  577)
  hydrogen bonds       : angle       4.52880 ( 1701)

*********************** 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
  248 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 247
  time to evaluate  : 0.283 
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: 0.9087 (pmm) cc_final: 0.8699 (pmm)
REVERT: A   67 MET cc_start: 0.9369 (tpt) cc_final: 0.9111 (tpp)
REVERT: A   70 ILE cc_start: 0.9404 (mt) cc_final: 0.9194 (mt)
REVERT: A  103 LEU cc_start: 0.9584 (tp) cc_final: 0.9130 (tp)
REVERT: A  107 MET cc_start: 0.9512 (mmp) cc_final: 0.9160 (mmm)
REVERT: A  237 ASP cc_start: 0.8638 (m-30) cc_final: 0.8123 (p0)
REVERT: A  335 LEU cc_start: 0.8937 (mt) cc_final: 0.8583 (mt)
REVERT: A  359 TYR cc_start: 0.8671 (t80) cc_final: 0.7975 (t80)
REVERT: A  446 MET cc_start: 0.4650 (tpt) cc_final: 0.4384 (mmt)
REVERT: A  720 LEU cc_start: 0.9409 (mm) cc_final: 0.8707 (mm)
REVERT: A  749 ASN cc_start: 0.8877 (m-40) cc_final: 0.8581 (m-40)
REVERT: A  754 LEU cc_start: 0.9093 (mt) cc_final: 0.8828 (mt)
REVERT: A  787 MET cc_start: 0.7892 (mmt) cc_final: 0.7544 (mtt)
REVERT: A  872 MET cc_start: 0.7446 (mmp) cc_final: 0.7095 (mmm)
REVERT: A  928 MET cc_start: 0.9017 (mpp) cc_final: 0.8796 (mpp)
REVERT: A  938 PHE cc_start: 0.9391 (t80) cc_final: 0.9151 (t80)
REVERT: A  953 PHE cc_start: 0.8601 (m-80) cc_final: 0.8322 (m-80)
REVERT: A  955 PHE cc_start: 0.8720 (t80) cc_final: 0.7874 (t80)
REVERT: A  965 MET cc_start: 0.8520 (tmm) cc_final: 0.7859 (tmm)
REVERT: A 1039 ASN cc_start: 0.7002 (p0) cc_final: 0.6394 (p0)
REVERT: A 1104 TRP cc_start: 0.9219 (t60) cc_final: 0.8808 (t60)
REVERT: A 1105 LEU cc_start: 0.9714 (tp) cc_final: 0.9334 (tp)
REVERT: A 1109 LEU cc_start: 0.9336 (mt) cc_final: 0.9009 (mt)
REVERT: A 1141 ILE cc_start: 0.9412 (mm) cc_final: 0.9177 (mm)
REVERT: A 1196 ASP cc_start: 0.9065 (t0) cc_final: 0.8393 (t0)
REVERT: A 1234 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8386 (mm110)
  outliers start: 1
  outliers final: 0
  residues processed: 247
  average time/residue: 0.0663
  time to fit residues: 24.7304
Evaluate side-chains
  217 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    0.8980
   chunk 80 optimal weight:    4.9990
   chunk 89 optimal weight:    0.0970
   chunk 92 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9990
   chunk 78 optimal weight:    8.9990
   chunk 86 optimal weight:    0.9990
   chunk 112 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 37 optimal weight:    0.0970
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
A 367 ASN
** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1077 GLN
A1228 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.122166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.089775 restraints weight = 23643.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.093285 restraints weight = 14287.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.095714 restraints weight = 10012.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.097488 restraints weight = 7741.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.098651 restraints weight = 6375.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9166  Z= 0.126
  Angle     :  0.614  10.720  12393  Z= 0.327
  Chirality :  0.042   0.209   1423
  Planarity :  0.004   0.058   1578
  Dihedral  :  4.759  34.073   1274
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.21 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.25), residues: 1153
  helix:  1.07 (0.19), residues: 756
  sheet: -0.99 (0.77), residues: 49
  loop : -1.77 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 828 
 TYR   0.024   0.002   TYR A 924 
 PHE   0.027   0.002   PHE A 200 
 TRP   0.038   0.002   TRP A 694 
 HIS   0.009   0.001   HIS A1003 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 9166)
  covalent geometry    : angle       0.61422 (12393)
  hydrogen bonds       : bond        0.04320 (  577)
  hydrogen bonds       : angle       4.43489 ( 1701)

********************** 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
  244 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 243
  time to evaluate  : 0.408 
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: 0.9068 (pmm) cc_final: 0.8807 (pmm)
REVERT: A   67 MET cc_start: 0.9345 (tpt) cc_final: 0.9006 (tpp)
REVERT: A   70 ILE cc_start: 0.9345 (mt) cc_final: 0.9144 (mt)
REVERT: A   99 MET cc_start: 0.8452 (pmm) cc_final: 0.8243 (pmm)
REVERT: A  103 LEU cc_start: 0.9568 (tp) cc_final: 0.9147 (tp)
REVERT: A  107 MET cc_start: 0.9522 (mmp) cc_final: 0.9197 (mmm)
REVERT: A  206 ARG cc_start: 0.7865 (mmm160) cc_final: 0.6682 (mmm160)
REVERT: A  237 ASP cc_start: 0.8637 (m-30) cc_final: 0.8108 (p0)
REVERT: A  251 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8043 (mt-10)
REVERT: A  359 TYR cc_start: 0.8742 (t80) cc_final: 0.7993 (t80)
REVERT: A  446 MET cc_start: 0.4870 (tpt) cc_final: 0.4590 (mmt)
REVERT: A  720 LEU cc_start: 0.9382 (mm) cc_final: 0.8733 (mm)
REVERT: A  749 ASN cc_start: 0.8785 (m-40) cc_final: 0.8485 (m-40)
REVERT: A  754 LEU cc_start: 0.9091 (mt) cc_final: 0.8819 (mt)
REVERT: A  787 MET cc_start: 0.7754 (mmt) cc_final: 0.7407 (mtt)
REVERT: A  852 GLN cc_start: 0.7550 (mp10) cc_final: 0.7265 (mm-40)
REVERT: A  872 MET cc_start: 0.7412 (mmp) cc_final: 0.7097 (mmm)
REVERT: A  910 GLN cc_start: 0.8446 (tp40) cc_final: 0.8040 (mm-40)
REVERT: A  928 MET cc_start: 0.8947 (mpp) cc_final: 0.8717 (mpp)
REVERT: A  938 PHE cc_start: 0.9395 (t80) cc_final: 0.9185 (t80)
REVERT: A  953 PHE cc_start: 0.8561 (m-80) cc_final: 0.8319 (m-80)
REVERT: A  955 PHE cc_start: 0.8708 (t80) cc_final: 0.7835 (t80)
REVERT: A  965 MET cc_start: 0.8418 (tmm) cc_final: 0.7946 (tmm)
REVERT: A 1039 ASN cc_start: 0.6894 (p0) cc_final: 0.6316 (p0)
REVERT: A 1104 TRP cc_start: 0.9182 (t60) cc_final: 0.8785 (t60)
REVERT: A 1105 LEU cc_start: 0.9722 (tp) cc_final: 0.9331 (tp)
REVERT: A 1109 LEU cc_start: 0.9304 (mt) cc_final: 0.8974 (mt)
REVERT: A 1141 ILE cc_start: 0.9369 (mm) cc_final: 0.9133 (mm)
REVERT: A 1196 ASP cc_start: 0.9016 (t0) cc_final: 0.8339 (t0)
REVERT: A 1231 SER cc_start: 0.9481 (m) cc_final: 0.9062 (m)
REVERT: A 1234 GLN cc_start: 0.8712 (tp-100) cc_final: 0.8110 (pt0)
  outliers start: 1
  outliers final: 0
  residues processed: 243
  average time/residue: 0.0828
  time to fit residues: 29.9352
Evaluate side-chains
  223 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 110 optimal weight:    7.9990
   chunk 87 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0770
   chunk 105 optimal weight:    0.0770
   chunk 13 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 42 optimal weight:    7.9990
   overall best weight:    0.5896

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

Flipped N/Q/H residues before XYZ refinement:
** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 795 GLN
A 838 ASN
A1228 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.123035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.090327 restraints weight = 23311.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.093712 restraints weight = 14353.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.096071 restraints weight = 10190.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.097854 restraints weight = 7953.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.099151 restraints weight = 6571.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.3354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9166  Z= 0.126
  Angle     :  0.604  10.047  12393  Z= 0.323
  Chirality :  0.042   0.202   1423
  Planarity :  0.004   0.056   1578
  Dihedral  :  4.698  34.362   1274
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.63 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.25), residues: 1153
  helix:  1.09 (0.19), residues: 758
  sheet: -1.02 (0.76), residues: 49
  loop : -1.79 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG A 828 
 TYR   0.038   0.002   TYR A  49 
 PHE   0.025   0.002   PHE A 131 
 TRP   0.035   0.002   TRP A 694 
 HIS   0.005   0.001   HIS A1003 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9166)
  covalent geometry    : angle       0.60365 (12393)
  hydrogen bonds       : bond        0.04270 (  577)
  hydrogen bonds       : angle       4.39262 ( 1701)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1652.76 seconds
wall clock time: 29 minutes 16.90 seconds (1756.90 seconds total)