Starting phenix.real_space_refine
on Sat Jun  7 05:29:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bhx_44556/06_2025/9bhx_44556.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bhx_44556/06_2025/9bhx_44556.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bhx_44556/06_2025/9bhx_44556.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bhx_44556/06_2025/9bhx_44556.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bhx_44556/06_2025/9bhx_44556.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bhx_44556/06_2025/9bhx_44556.cif"
  }
  resolution = 3.94
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.010
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      33      5.16       5
     C    5316      2.51       5
     N    1486      2.21       5
     O    1541      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8376
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 8376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1048, 8376
          Classifications: {'peptide': 1048}
          Link IDs: {'PCIS': 2, 'PTRANS': 73, 'TRANS': 972}
          Chain breaks: 2
  Time building chain proxies: 5.96, per 1000 atoms: 0.71
  Number of scatterers: 8376
  At special positions: 0
  Unit cell: (80.704, 93.184, 161.408, 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      33     16.00
     O    1541      8.00
     N    1486      7.00
     C    5316      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 220 " - pdb=" SG  CYS A 257 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 224 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 239 " - pdb=" SG  CYS A 248 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 270 " - pdb=" SG  CYS A 290 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 274 " - pdb=" SG  CYS A 286 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 387 " - pdb=" SG  CYS A 393 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 981 " - pdb=" SG  CYS A 991 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.04
  Conformation dependent library (CDL) restraints added in 963.5 milliseconds
  

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1952

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 20 sheets defined
      7.7% alpha, 28.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 216 through 228
    Processing helix  chain 'A' and resid 248 through 267
      removed outlier: 5.347A  pdb=" N   TYR A 261 " --> pdb=" O   CYS A 257 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   ARG A 262 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   GLU A 266 " --> pdb=" O   ARG A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 274
    Processing helix  chain 'A' and resid 283 through 309
      removed outlier: 3.728A  pdb=" N   VAL A 309 " --> pdb=" O   ILE A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 815 through 819
      removed outlier: 3.538A  pdb=" N   GLN A 819 " --> pdb=" O   PRO A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1070
    Processing helix  chain 'A' and resid 1202 through 1206
      removed outlier: 3.521A  pdb=" N   VAL A1206 " --> pdb=" O   PRO A1203 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 380 through 381
      removed outlier: 3.899A  pdb=" N   PHE A 380 " --> pdb=" O   TYR A 351 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ASN A 348 " --> pdb=" O   GLU A 410 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   LEU A 411 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   LEU A 421 " --> pdb=" O   LEU A 411 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 380 through 381
      removed outlier: 3.899A  pdb=" N   PHE A 380 " --> pdb=" O   TYR A 351 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ASN A 348 " --> pdb=" O   GLU A 410 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 442 through 445
      removed outlier: 6.023A  pdb=" N   ILE A 443 " --> pdb=" O   HIS A 459 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   HIS A 459 " --> pdb=" O   ILE A 443 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   HIS A 445 " --> pdb=" O   HIS A 457 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 489
      removed outlier: 3.977A  pdb=" N   GLY A 470 " --> pdb=" O   ILE A 513 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ILE A 513 " --> pdb=" O   GLY A 470 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 554 through 556
      removed outlier: 3.714A  pdb=" N   SER A 543 " --> pdb=" O   LEU A 814 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ALA A 810 " --> pdb=" O   VAL A 547 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 573 through 575
      removed outlier: 7.509A  pdb=" N   LEU A 588 " --> pdb=" O   ALA A 574 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 627 through 631
      removed outlier: 3.885A  pdb=" N   ARG A 627 " --> pdb=" O   ALA A 640 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ASP A 631 " --> pdb=" O   ARG A 636 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ARG A 636 " --> pdb=" O   ASP A 631 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   ILE A 653 " --> pdb=" O   GLU A 668 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   GLU A 668 " --> pdb=" O   ILE A 653 " (cutoff:3.500A)
      removed outlier: 7.305A  pdb=" N   SER A 655 " --> pdb=" O   VAL A 666 " (cutoff:3.500A)
      removed outlier: 7.711A  pdb=" N   VAL A 666 " --> pdb=" O   SER A 655 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 676 through 680
      removed outlier: 3.878A  pdb=" N   GLN A 676 " --> pdb=" O   ARG A 689 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 770 through 772
    Processing sheet with id=AB1, first strand: chain 'A' and resid 829 through 835
      removed outlier: 5.895A  pdb=" N   SER A 830 " --> pdb=" O   LYS A 845 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   LYS A 845 " --> pdb=" O   SER A 830 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 876 through 881
      removed outlier: 3.886A  pdb=" N   ASN A 880 " --> pdb=" O   TYR A 863 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   TYR A 863 " --> pdb=" O   ASN A 880 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ARG A 900 " --> pdb=" O   GLU A 866 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 949 through 950
      removed outlier: 3.533A  pdb=" N   HIS A 940 " --> pdb=" O   GLU A 949 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ARG A 928 " --> pdb=" O   LEU A1183 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   LEU A1183 " --> pdb=" O   ARG A 928 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ARG A 930 " --> pdb=" O   LEU A1181 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   LEU A1181 " --> pdb=" O   ARG A 930 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ALA A 932 " --> pdb=" O   SER A1179 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 963 through 964
      removed outlier: 3.678A  pdb=" N   TYR A 972 " --> pdb=" O   HIS A 980 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   HIS A 980 " --> pdb=" O   TYR A 972 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU A 997 " --> pdb=" O   LEU A 979 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1000 through 1006
      removed outlier: 4.499A  pdb=" N   SER A1002 " --> pdb=" O   THR A1015 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ARG A1011 " --> pdb=" O   ASP A1006 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   TRP A1014 " --> pdb=" O   VAL A1023 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   VAL A1023 " --> pdb=" O   TRP A1014 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   VAL A1022 " --> pdb=" O   LEU A1035 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1042 through 1045
      removed outlier: 3.889A  pdb=" N   TYR A1074 " --> pdb=" O   LEU A1060 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   ARG A1062 " --> pdb=" O   THR A1072 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   THR A1072 " --> pdb=" O   ARG A1062 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1082 through 1089
      removed outlier: 5.534A  pdb=" N   ILE A1083 " --> pdb=" O   LYS A1100 " (cutoff:3.500A)
      removed outlier: 5.775A  pdb=" N   LYS A1100 " --> pdb=" O   ILE A1083 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   SER A1085 " --> pdb=" O   LEU A1098 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1082 through 1089
      removed outlier: 5.534A  pdb=" N   ILE A1083 " --> pdb=" O   LYS A1100 " (cutoff:3.500A)
      removed outlier: 5.775A  pdb=" N   LYS A1100 " --> pdb=" O   ILE A1083 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   SER A1085 " --> pdb=" O   LEU A1098 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1137 through 1139
      removed outlier: 3.656A  pdb=" N   TRP A1147 " --> pdb=" O   ARG A1156 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1207 through 1208
      removed outlier: 3.530A  pdb=" N   PHE A1216 " --> pdb=" O   LEU A1255 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 1242 through 1248

    224 hydrogen bonds defined for protein.
    594 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.40

  Time building geometry restraints manager: 2.44 seconds

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

  Histogram of bond lengths:
        0.81 -     1.11: 1
        1.11 -     1.41: 3625
        1.41 -     1.72: 4930
        1.72 -     2.02: 51
        2.02 -     2.33: 1
  Bond restraints: 8608
  Sorted by residual:
  bond pdb=" CG  PRO A 460 "
       pdb=" CD  PRO A 460 "
    ideal  model  delta    sigma   weight residual
    1.503  0.806  0.697 3.40e-02 8.65e+02 4.20e+02
  bond pdb=" N   PRO A1111 "
       pdb=" CD  PRO A1111 "
    ideal  model  delta    sigma   weight residual
    1.473  1.719 -0.246 1.40e-02 5.10e+03 3.09e+02
  bond pdb=" CB  PRO A 460 "
       pdb=" CG  PRO A 460 "
    ideal  model  delta    sigma   weight residual
    1.492  2.328 -0.836 5.00e-02 4.00e+02 2.79e+02
  bond pdb=" N   PRO A 460 "
       pdb=" CD  PRO A 460 "
    ideal  model  delta    sigma   weight residual
    1.473  1.606 -0.133 1.40e-02 5.10e+03 9.01e+01
  bond pdb=" C   HIS A 459 "
       pdb=" N   PRO A 460 "
    ideal  model  delta    sigma   weight residual
    1.331  1.427 -0.096 1.27e-02 6.20e+03 5.74e+01
  ... (remaining 8603 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    21.22: 11717
       21.22 -    42.44: 3
       42.44 -    63.65: 0
       63.65 -    84.87: 0
       84.87 -   106.09: 1
  Bond angle restraints: 11721
  Sorted by residual:
  angle pdb=" CB  PRO A 460 "
        pdb=" CG  PRO A 460 "
        pdb=" CD  PRO A 460 "
      ideal   model   delta    sigma   weight residual
     106.10    0.01  106.09 3.20e+00 9.77e-02 1.10e+03
  angle pdb=" CA  PRO A 460 "
        pdb=" N   PRO A 460 "
        pdb=" CD  PRO A 460 "
      ideal   model   delta    sigma   weight residual
     112.00   84.63   27.37 1.40e+00 5.10e-01 3.82e+02
  angle pdb=" CA  PRO A1111 "
        pdb=" N   PRO A1111 "
        pdb=" CD  PRO A1111 "
      ideal   model   delta    sigma   weight residual
     112.00   90.00   22.00 1.40e+00 5.10e-01 2.47e+02
  angle pdb=" CA  PRO A 460 "
        pdb=" CB  PRO A 460 "
        pdb=" CG  PRO A 460 "
      ideal   model   delta    sigma   weight residual
     104.50   85.23   19.27 1.90e+00 2.77e-01 1.03e+02
  angle pdb=" N   PRO A 460 "
        pdb=" CA  PRO A 460 "
        pdb=" CB  PRO A 460 "
      ideal   model   delta    sigma   weight residual
     103.25   95.72    7.53 8.80e-01 1.29e+00 7.32e+01
  ... (remaining 11716 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4345
       17.98 -    35.96: 641
       35.96 -    53.95: 142
       53.95 -    71.93: 20
       71.93 -    89.91: 14
  Dihedral angle restraints: 5162
    sinusoidal: 2132
      harmonic: 3030
  Sorted by residual:
  dihedral pdb=" CB  CYS A 239 "
           pdb=" SG  CYS A 239 "
           pdb=" SG  CYS A 248 "
           pdb=" CB  CYS A 248 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -155.35   69.35     1      1.00e+01 1.00e-02 6.21e+01
  dihedral pdb=" CA  PRO A 923 "
           pdb=" C   PRO A 923 "
           pdb=" N   LEU A 924 "
           pdb=" CA  LEU A 924 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.84   22.16     0      5.00e+00 4.00e-02 1.96e+01
  dihedral pdb=" CA  GLN A 898 "
           pdb=" C   GLN A 898 "
           pdb=" N   LEU A 899 "
           pdb=" CA  LEU A 899 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.45  -21.55     0      5.00e+00 4.00e-02 1.86e+01
  ... (remaining 5159 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1083
       0.065 -    0.130: 153
       0.130 -    0.195: 5
       0.195 -    0.260: 2
       0.260 -    0.325: 1
  Chirality restraints: 1244
  Sorted by residual:
  chirality pdb=" CA  PRO A 460 "
            pdb=" N   PRO A 460 "
            pdb=" C   PRO A 460 "
            pdb=" CB  PRO A 460 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.39    0.32 2.00e-01 2.50e+01 2.64e+00
  chirality pdb=" CA  GLU A 434 "
            pdb=" N   GLU A 434 "
            pdb=" C   GLU A 434 "
            pdb=" CB  GLU A 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CA  PRO A 433 "
            pdb=" N   PRO A 433 "
            pdb=" C   PRO A 433 "
            pdb=" CB  PRO A 433 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 1241 not shown)

  Planarity restraints: 1542
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A1187 "    0.095 5.00e-02 4.00e+02   1.39e-01 3.09e+01
        pdb=" N   PRO A1188 "   -0.240 5.00e-02 4.00e+02
        pdb=" CA  PRO A1188 "    0.072 5.00e-02 4.00e+02
        pdb=" CD  PRO A1188 "    0.073 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A1110 "    0.102 5.00e-02 4.00e+02   1.28e-01 2.64e+01
        pdb=" N   PRO A1111 "   -0.220 5.00e-02 4.00e+02
        pdb=" CA  PRO A1111 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A1111 "    0.067 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A1140 "   -0.088 5.00e-02 4.00e+02   1.26e-01 2.54e+01
        pdb=" N   PRO A1141 "    0.217 5.00e-02 4.00e+02
        pdb=" CA  PRO A1141 "   -0.063 5.00e-02 4.00e+02
        pdb=" CD  PRO A1141 "   -0.067 5.00e-02 4.00e+02
  ... (remaining 1539 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.31: 21
        2.31 -     2.96: 3994
        2.96 -     3.60: 12027
        3.60 -     4.25: 18260
        4.25 -     4.90: 29730
  Nonbonded interactions: 64032
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 550 "
            pdb=" O   GLN A 570 "
     model   vdw
     1.661 3.120
  nonbonded pdb=" NH1 ARG A 550 "
            pdb=" C   GLN A 570 "
     model   vdw
     1.724 3.350
  nonbonded pdb=" OE1 GLU A 846 "
            pdb=" OH  TYR A 863 "
     model   vdw
     1.792 3.040
  nonbonded pdb=" OD1 ASP A 657 "
            pdb=" N   LEU A 658 "
     model   vdw
     1.941 3.120
  nonbonded pdb=" O   PRO A1111 "
            pdb=" CD  PRO A1111 "
     model   vdw
     2.141 3.440
  ... (remaining 64027 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:             4.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     24.450
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
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      :  0.013   0.836   8615  Z= 0.449
  Angle     :  1.344 106.088  11735  Z= 0.588
  Chirality :  0.046   0.325   1244
  Planarity :  0.009   0.139   1542
  Dihedral  : 17.516  89.909   3189
  Min Nonbonded Distance : 1.661

Molprobity Statistics.
  All-atom Clashscore : 20.33
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  6.72 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 30.79 %
    Favored  : 68.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.25), residues: 1042
  helix:  1.02 (0.67), residues: 63
  sheet: -0.48 (0.28), residues: 333
  loop : -1.39 (0.24), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 695 
 HIS   0.008   0.001   HIS A 459 
 PHE   0.011   0.001   PHE A 735 
 TYR   0.070   0.002   TYR A 422 
 ARG   0.003   0.000   ARG A1008 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23843 (  213)
  hydrogen bonds       : angle      10.56516 (  594)
  SS BOND              : bond        0.00361 (    7)
  SS BOND              : angle       1.18933 (   14)
  covalent geometry    : bond        0.01314 ( 8608)
  covalent geometry    : angle       1.34369 (11721)

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

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

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 1
  residues processed: 102
  average time/residue: 0.2063
  time to fit residues: 29.7111
Evaluate side-chains
  98 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  889 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 617 ASN
A 648 GLN
A 697 GLN
** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.190312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.154216 restraints weight = 13666.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.153061 restraints weight = 18410.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.154418 restraints weight = 16678.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.1209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8615  Z= 0.168
  Angle     :  0.712  12.104  11735  Z= 0.357
  Chirality :  0.045   0.154   1244
  Planarity :  0.006   0.070   1542
  Dihedral  :  4.950  23.169   1154
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  7.29 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 25.47 %
    Favored  : 70.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.26), residues: 1042
  helix:  1.12 (0.65), residues: 64
  sheet: -0.49 (0.26), residues: 359
  loop : -1.35 (0.25), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 695 
 HIS   0.006   0.001   HIS A 457 
 PHE   0.018   0.002   PHE A1096 
 TYR   0.014   0.002   TYR A 351 
 ARG   0.007   0.001   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04278 (  213)
  hydrogen bonds       : angle       7.25130 (  594)
  SS BOND              : bond        0.00342 (    7)
  SS BOND              : angle       0.98973 (   14)
  covalent geometry    : bond        0.00402 ( 8608)
  covalent geometry    : angle       0.71154 (11721)

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

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

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 112
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 ARG cc_start: 0.8000 (pmt-80) cc_final: 0.7778 (ppt170)
REVERT: A  400 ILE cc_start: 0.7281 (tt) cc_final: 0.7044 (tt)
REVERT: A  657 ASP cc_start: 0.7540 (t0) cc_final: 0.7340 (t0)
REVERT: A 1089 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7388 (m-30)
  outliers start: 39
  outliers final: 19
  residues processed: 144
  average time/residue: 0.2091
  time to fit residues: 42.1063
Evaluate side-chains
  112 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  403 THR
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  647 ASN
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  738 ILE
Chi-restraints excluded: chain A residue  785 ILE
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  866 GLU
Chi-restraints excluded: chain A residue  878 ILE
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue  950 VAL
Chi-restraints excluded: chain A residue 1012 VAL
Chi-restraints excluded: chain A residue 1017 LEU
Chi-restraints excluded: chain A residue 1043 LEU
Chi-restraints excluded: chain A residue 1076 VAL
Chi-restraints excluded: chain A residue 1089 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 64 optimal weight:    0.4980
   chunk 3 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 96 optimal weight:    8.9990
   chunk 92 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 86 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 898 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.187458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.145450 restraints weight = 13871.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.141776 restraints weight = 17033.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.143800 restraints weight = 16287.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   8615  Z= 0.210
  Angle     :  0.716  11.063  11735  Z= 0.359
  Chirality :  0.045   0.139   1244
  Planarity :  0.006   0.065   1542
  Dihedral  :  5.119  23.284   1151
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  8.06 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  5.87 %
    Allowed  : 24.14 %
    Favored  : 69.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.26), residues: 1042
  helix:  1.17 (0.65), residues: 64
  sheet: -0.57 (0.26), residues: 368
  loop : -1.39 (0.25), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 586 
 HIS   0.005   0.001   HIS A 529 
 PHE   0.017   0.002   PHE A1096 
 TYR   0.014   0.002   TYR A 422 
 ARG   0.004   0.000   ARG A1156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03932 (  213)
  hydrogen bonds       : angle       6.76692 (  594)
  SS BOND              : bond        0.00296 (    7)
  SS BOND              : angle       0.93619 (   14)
  covalent geometry    : bond        0.00506 ( 8608)
  covalent geometry    : angle       0.71571 (11721)

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

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

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 96
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  332 ARG cc_start: 0.5217 (OUTLIER) cc_final: 0.3846 (mpp80)
REVERT: A  400 ILE cc_start: 0.7716 (tt) cc_final: 0.7509 (tt)
REVERT: A  555 GLN cc_start: 0.7498 (tm-30) cc_final: 0.7283 (tm-30)
REVERT: A  575 ASP cc_start: 0.8644 (p0) cc_final: 0.7732 (t70)
REVERT: A  688 TRP cc_start: 0.8281 (p-90) cc_final: 0.8060 (p-90)
REVERT: A  862 SER cc_start: 0.8350 (OUTLIER) cc_final: 0.7945 (p)
REVERT: A 1041 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8336 (t0)
REVERT: A 1086 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8116 (p90)
  outliers start: 53
  outliers final: 34
  residues processed: 139
  average time/residue: 0.1859
  time to fit residues: 37.4046
Evaluate side-chains
  126 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 88
  time to evaluate  : 1.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  403 THR
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  530 SER
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  656 THR
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  686 ILE
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  738 ILE
Chi-restraints excluded: chain A residue  785 ILE
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  808 CYS
Chi-restraints excluded: chain A residue  862 SER
Chi-restraints excluded: chain A residue  866 GLU
Chi-restraints excluded: chain A residue  878 ILE
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue  950 VAL
Chi-restraints excluded: chain A residue  955 LEU
Chi-restraints excluded: chain A residue  964 MET
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue  991 CYS
Chi-restraints excluded: chain A residue 1017 LEU
Chi-restraints excluded: chain A residue 1041 ASN
Chi-restraints excluded: chain A residue 1071 VAL
Chi-restraints excluded: chain A residue 1086 PHE
Chi-restraints excluded: chain A residue 1088 LEU
Chi-restraints excluded: chain A residue 1089 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 88 optimal weight:    0.0980
   chunk 102 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 568 GLN
** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.185966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.149098 restraints weight = 13584.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.147959 restraints weight = 17700.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.149608 restraints weight = 16964.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8615  Z= 0.169
  Angle     :  0.670  10.416  11735  Z= 0.334
  Chirality :  0.044   0.138   1244
  Planarity :  0.006   0.062   1542
  Dihedral  :  4.978  23.425   1151
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  7.77 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  : 24.36 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.26), residues: 1042
  helix:  1.34 (0.65), residues: 64
  sheet: -0.51 (0.27), residues: 366
  loop : -1.35 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 695 
 HIS   0.007   0.001   HIS A 746 
 PHE   0.010   0.001   PHE A1096 
 TYR   0.015   0.002   TYR A 351 
 ARG   0.005   0.000   ARG A 920 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03388 (  213)
  hydrogen bonds       : angle       6.40420 (  594)
  SS BOND              : bond        0.00276 (    7)
  SS BOND              : angle       0.88401 (   14)
  covalent geometry    : bond        0.00413 ( 8608)
  covalent geometry    : angle       0.66926 (11721)

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

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

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 96
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  332 ARG cc_start: 0.5396 (OUTLIER) cc_final: 0.4010 (mpp80)
REVERT: A  400 ILE cc_start: 0.7835 (tt) cc_final: 0.7616 (tt)
REVERT: A  575 ASP cc_start: 0.8641 (p0) cc_final: 0.7862 (t70)
REVERT: A  576 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8717 (pt)
REVERT: A  688 TRP cc_start: 0.8327 (p-90) cc_final: 0.8098 (p-90)
REVERT: A 1086 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.7960 (p90)
REVERT: A 1089 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7338 (m-30)
  outliers start: 58
  outliers final: 39
  residues processed: 143
  average time/residue: 0.1924
  time to fit residues: 40.2881
Evaluate side-chains
  136 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 93
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain A residue  353 PHE
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  403 THR
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  530 SER
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  556 SER
Chi-restraints excluded: chain A residue  576 ILE
Chi-restraints excluded: chain A residue  686 ILE
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  729 LEU
Chi-restraints excluded: chain A residue  738 ILE
Chi-restraints excluded: chain A residue  785 ILE
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  866 GLU
Chi-restraints excluded: chain A residue  878 ILE
Chi-restraints excluded: chain A residue  881 ILE
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue  946 GLU
Chi-restraints excluded: chain A residue  950 VAL
Chi-restraints excluded: chain A residue  955 LEU
Chi-restraints excluded: chain A residue  964 MET
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue  991 CYS
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1017 LEU
Chi-restraints excluded: chain A residue 1043 LEU
Chi-restraints excluded: chain A residue 1049 GLN
Chi-restraints excluded: chain A residue 1071 VAL
Chi-restraints excluded: chain A residue 1086 PHE
Chi-restraints excluded: chain A residue 1088 LEU
Chi-restraints excluded: chain A residue 1089 ASP
Chi-restraints excluded: chain A residue 1157 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 96 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 95 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 9 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1092 GLN
A1124 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.186001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.150872 restraints weight = 13246.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.149525 restraints weight = 17882.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.150959 restraints weight = 15871.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.2548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8615  Z= 0.147
  Angle     :  0.668  12.326  11735  Z= 0.329
  Chirality :  0.044   0.146   1244
  Planarity :  0.006   0.061   1542
  Dihedral  :  4.893  22.697   1151
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.39 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  7.20 %
    Allowed  : 24.36 %
    Favored  : 68.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.26), residues: 1042
  helix:  1.36 (0.65), residues: 64
  sheet: -0.34 (0.29), residues: 325
  loop : -1.34 (0.24), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 695 
 HIS   0.004   0.001   HIS A 445 
 PHE   0.008   0.001   PHE A 744 
 TYR   0.012   0.001   TYR A 351 
 ARG   0.006   0.000   ARG A 930 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03267 (  213)
  hydrogen bonds       : angle       6.25583 (  594)
  SS BOND              : bond        0.00267 (    7)
  SS BOND              : angle       0.85234 (   14)
  covalent geometry    : bond        0.00360 ( 8608)
  covalent geometry    : angle       0.66746 (11721)

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

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

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 101
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7812 (p0)
REVERT: A  400 ILE cc_start: 0.7818 (tt) cc_final: 0.7541 (tt)
REVERT: A  575 ASP cc_start: 0.8638 (p0) cc_final: 0.7888 (t70)
REVERT: A  576 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8720 (pt)
REVERT: A  688 TRP cc_start: 0.8232 (p-90) cc_final: 0.8003 (p-90)
REVERT: A  920 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6951 (ttp80)
REVERT: A  974 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8196 (t)
REVERT: A 1041 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8464 (t0)
REVERT: A 1086 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7827 (p90)
  outliers start: 65
  outliers final: 40
  residues processed: 155
  average time/residue: 0.2175
  time to fit residues: 48.7768
Evaluate side-chains
  138 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 92
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  353 PHE
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  403 THR
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  530 SER
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  556 SER
Chi-restraints excluded: chain A residue  576 ILE
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  686 ILE
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  729 LEU
Chi-restraints excluded: chain A residue  738 ILE
Chi-restraints excluded: chain A residue  785 ILE
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  803 LYS
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  866 GLU
Chi-restraints excluded: chain A residue  881 ILE
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  946 GLU
Chi-restraints excluded: chain A residue  950 VAL
Chi-restraints excluded: chain A residue  955 LEU
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue  982 ILE
Chi-restraints excluded: chain A residue  991 CYS
Chi-restraints excluded: chain A residue 1017 LEU
Chi-restraints excluded: chain A residue 1041 ASN
Chi-restraints excluded: chain A residue 1043 LEU
Chi-restraints excluded: chain A residue 1049 GLN
Chi-restraints excluded: chain A residue 1071 VAL
Chi-restraints excluded: chain A residue 1086 PHE
Chi-restraints excluded: chain A residue 1088 LEU
Chi-restraints excluded: chain A residue 1105 LEU
Chi-restraints excluded: chain A residue 1136 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 71 optimal weight:    0.4980
   chunk 14 optimal weight:    0.0170
   chunk 78 optimal weight:    0.9990
   chunk 91 optimal weight:    0.8980
   chunk 11 optimal weight:    0.4980
   chunk 85 optimal weight:    0.4980
   chunk 70 optimal weight:    0.2980
   overall best weight:    0.3618

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

Flipped N/Q/H residues before XYZ refinement:
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 895 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 = 0.4260 r_free = 0.4260 target = 0.185572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.147945 restraints weight = 13490.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.145189 restraints weight = 13779.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.147437 restraints weight = 15416.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8615  Z= 0.122
  Angle     :  0.651  11.658  11735  Z= 0.319
  Chirality :  0.043   0.146   1244
  Planarity :  0.005   0.059   1542
  Dihedral  :  4.755  21.740   1151
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.53 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  5.98 %
    Allowed  : 25.58 %
    Favored  : 68.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.26), residues: 1042
  helix:  1.48 (0.66), residues: 64
  sheet: -0.34 (0.29), residues: 327
  loop : -1.26 (0.24), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP A 586 
 HIS   0.005   0.001   HIS A 746 
 PHE   0.019   0.001   PHE A 337 
 TYR   0.011   0.001   TYR A 351 
 ARG   0.005   0.000   ARG A 920 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03108 (  213)
  hydrogen bonds       : angle       6.07534 (  594)
  SS BOND              : bond        0.00250 (    7)
  SS BOND              : angle       0.78388 (   14)
  covalent geometry    : bond        0.00306 ( 8608)
  covalent geometry    : angle       0.65132 (11721)

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

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

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 101
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7917 (p0)
REVERT: A  575 ASP cc_start: 0.8570 (p0) cc_final: 0.7814 (t70)
REVERT: A  688 TRP cc_start: 0.8264 (p-90) cc_final: 0.8049 (p-90)
REVERT: A  695 TRP cc_start: 0.8040 (m100) cc_final: 0.7763 (m100)
REVERT: A  920 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6961 (ttp80)
REVERT: A  974 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8130 (t)
REVERT: A 1086 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.7822 (p90)
REVERT: A 1108 TYR cc_start: 0.6829 (m-80) cc_final: 0.6529 (m-80)
  outliers start: 54
  outliers final: 40
  residues processed: 145
  average time/residue: 0.2549
  time to fit residues: 54.3296
Evaluate side-chains
  136 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 92
  time to evaluate  : 1.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  353 PHE
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  403 THR
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  556 SER
Chi-restraints excluded: chain A residue  647 ASN
Chi-restraints excluded: chain A residue  686 ILE
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  729 LEU
Chi-restraints excluded: chain A residue  738 ILE
Chi-restraints excluded: chain A residue  785 ILE
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  803 LYS
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  866 GLU
Chi-restraints excluded: chain A residue  878 ILE
Chi-restraints excluded: chain A residue  881 ILE
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  946 GLU
Chi-restraints excluded: chain A residue  950 VAL
Chi-restraints excluded: chain A residue  955 LEU
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue  991 CYS
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1017 LEU
Chi-restraints excluded: chain A residue 1043 LEU
Chi-restraints excluded: chain A residue 1049 GLN
Chi-restraints excluded: chain A residue 1071 VAL
Chi-restraints excluded: chain A residue 1086 PHE
Chi-restraints excluded: chain A residue 1136 LEU
Chi-restraints excluded: chain A residue 1197 ILE
Chi-restraints excluded: chain A residue 1248 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 96 optimal weight:    2.9990
   chunk 101 optimal weight:    8.9990
   chunk 9 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 49 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9990
   chunk 98 optimal weight:    4.9990
   overall best weight:    2.4988

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

Flipped N/Q/H residues before XYZ refinement:
** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 726 HIS ** 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 = 0.4231 r_free = 0.4231 target = 0.180959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.144993 restraints weight = 13628.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.145004 restraints weight = 20681.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.146170 restraints weight = 19426.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.3379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.073   8615  Z= 0.351
  Angle     :  0.832  11.403  11735  Z= 0.418
  Chirality :  0.049   0.177   1244
  Planarity :  0.007   0.067   1542
  Dihedral  :  5.698  26.968   1151
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 16.21
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.40 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  8.31 %
    Allowed  : 23.59 %
    Favored  : 68.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.26), residues: 1042
  helix:  1.23 (0.64), residues: 64
  sheet: -0.72 (0.28), residues: 355
  loop : -1.48 (0.24), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP A 333 
 HIS   0.014   0.002   HIS A 986 
 PHE   0.025   0.002   PHE A1096 
 TYR   0.019   0.003   TYR A1073 
 ARG   0.007   0.001   ARG A 696 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03998 (  213)
  hydrogen bonds       : angle       6.53671 (  594)
  SS BOND              : bond        0.00388 (    7)
  SS BOND              : angle       1.13991 (   14)
  covalent geometry    : bond        0.00836 ( 8608)
  covalent geometry    : angle       0.83201 (11721)

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

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

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 91
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  291 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7675 (mm-30)
REVERT: A  332 ARG cc_start: 0.6307 (OUTLIER) cc_final: 0.4690 (mpp80)
REVERT: A  388 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7797 (p0)
REVERT: A  575 ASP cc_start: 0.8784 (p0) cc_final: 0.8414 (t70)
REVERT: A  576 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8782 (pt)
REVERT: A  688 TRP cc_start: 0.8439 (p-90) cc_final: 0.8186 (p-90)
REVERT: A  712 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7729 (mt0)
REVERT: A  862 SER cc_start: 0.8292 (OUTLIER) cc_final: 0.8070 (p)
REVERT: A  920 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7120 (ttp80)
REVERT: A  974 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8351 (t)
REVERT: A 1086 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8304 (p90)
  outliers start: 75
  outliers final: 53
  residues processed: 153
  average time/residue: 0.2719
  time to fit residues: 59.5921
Evaluate side-chains
  149 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 88
  time to evaluate  : 2.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain A residue  353 PHE
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  403 THR
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  530 SER
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  550 ARG
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  556 SER
Chi-restraints excluded: chain A residue  576 ILE
Chi-restraints excluded: chain A residue  604 MET
Chi-restraints excluded: chain A residue  614 ASP
Chi-restraints excluded: chain A residue  647 ASN
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  686 ILE
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  712 GLN
Chi-restraints excluded: chain A residue  721 GLN
Chi-restraints excluded: chain A residue  729 LEU
Chi-restraints excluded: chain A residue  738 ILE
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain A residue  785 ILE
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  808 CYS
Chi-restraints excluded: chain A residue  862 SER
Chi-restraints excluded: chain A residue  866 GLU
Chi-restraints excluded: chain A residue  881 ILE
Chi-restraints excluded: chain A residue  882 ARG
Chi-restraints excluded: chain A residue  885 ILE
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  946 GLU
Chi-restraints excluded: chain A residue  950 VAL
Chi-restraints excluded: chain A residue  955 LEU
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue  982 ILE
Chi-restraints excluded: chain A residue  991 CYS
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1012 VAL
Chi-restraints excluded: chain A residue 1043 LEU
Chi-restraints excluded: chain A residue 1049 GLN
Chi-restraints excluded: chain A residue 1071 VAL
Chi-restraints excluded: chain A residue 1086 PHE
Chi-restraints excluded: chain A residue 1136 LEU
Chi-restraints excluded: chain A residue 1157 LEU
Chi-restraints excluded: chain A residue 1166 VAL
Chi-restraints excluded: chain A residue 1197 ILE
Chi-restraints excluded: chain A residue 1248 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 18 optimal weight:    0.3980
   chunk 46 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0270
   chunk 47 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 94 optimal weight:    0.8980
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 986 HIS ** 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 = 0.4209 r_free = 0.4209 target = 0.180816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.142076 restraints weight = 13572.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.139822 restraints weight = 15823.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.142060 restraints weight = 15117.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.3344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   8615  Z= 0.142
  Angle     :  0.700  12.660  11735  Z= 0.346
  Chirality :  0.044   0.146   1244
  Planarity :  0.006   0.061   1542
  Dihedral  :  5.150  25.040   1151
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.91 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  5.87 %
    Allowed  : 26.02 %
    Favored  : 68.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.26), residues: 1042
  helix:  1.28 (0.66), residues: 64
  sheet: -0.50 (0.29), residues: 331
  loop : -1.30 (0.24), residues: 647

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 695 
 HIS   0.024   0.002   HIS A 299 
 PHE   0.007   0.001   PHE A 407 
 TYR   0.009   0.001   TYR A 351 
 ARG   0.005   0.000   ARG A 920 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03132 (  213)
  hydrogen bonds       : angle       6.27928 (  594)
  SS BOND              : bond        0.00282 (    7)
  SS BOND              : angle       0.88071 (   14)
  covalent geometry    : bond        0.00355 ( 8608)
  covalent geometry    : angle       0.69928 (11721)

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

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

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 97
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7814 (p0)
REVERT: A  575 ASP cc_start: 0.8729 (p0) cc_final: 0.8103 (t70)
REVERT: A  688 TRP cc_start: 0.8236 (p-90) cc_final: 0.7949 (p-90)
REVERT: A  695 TRP cc_start: 0.8316 (m100) cc_final: 0.8114 (m100)
REVERT: A  920 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6943 (ttp80)
REVERT: A  974 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8263 (t)
REVERT: A 1086 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.7538 (p90)
  outliers start: 53
  outliers final: 38
  residues processed: 140
  average time/residue: 0.1718
  time to fit residues: 35.3817
Evaluate side-chains
  132 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 90
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  353 PHE
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  403 THR
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  550 ARG
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  556 SER
Chi-restraints excluded: chain A residue  647 ASN
Chi-restraints excluded: chain A residue  686 ILE
Chi-restraints excluded: chain A residue  738 ILE
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain A residue  785 ILE
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  803 LYS
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  866 GLU
Chi-restraints excluded: chain A residue  881 ILE
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  946 GLU
Chi-restraints excluded: chain A residue  950 VAL
Chi-restraints excluded: chain A residue  955 LEU
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue  991 CYS
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1043 LEU
Chi-restraints excluded: chain A residue 1049 GLN
Chi-restraints excluded: chain A residue 1071 VAL
Chi-restraints excluded: chain A residue 1086 PHE
Chi-restraints excluded: chain A residue 1136 LEU
Chi-restraints excluded: chain A residue 1197 ILE
Chi-restraints excluded: chain A residue 1248 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 62 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 96 optimal weight:    0.1980
   chunk 44 optimal weight:    0.4980
   chunk 42 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 986 HIS ** 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 = 0.4218 r_free = 0.4218 target = 0.181519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.143185 restraints weight = 13781.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.142825 restraints weight = 17252.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.144967 restraints weight = 13898.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.3463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8615  Z= 0.142
  Angle     :  0.698  11.931  11735  Z= 0.344
  Chirality :  0.044   0.148   1244
  Planarity :  0.006   0.062   1542
  Dihedral  :  4.964  22.792   1151
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.16 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 27.24 %
    Favored  : 67.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.26), residues: 1042
  helix:  1.27 (0.66), residues: 64
  sheet: -0.55 (0.29), residues: 335
  loop : -1.29 (0.25), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 766 
 HIS   0.024   0.002   HIS A 299 
 PHE   0.017   0.001   PHE A 337 
 TYR   0.009   0.001   TYR A1108 
 ARG   0.005   0.000   ARG A 920 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03024 (  213)
  hydrogen bonds       : angle       6.12764 (  594)
  SS BOND              : bond        0.00255 (    7)
  SS BOND              : angle       0.84348 (   14)
  covalent geometry    : bond        0.00355 ( 8608)
  covalent geometry    : angle       0.69752 (11721)

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

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

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 92
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
REVERT: A  388 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7805 (p0)
REVERT: A  575 ASP cc_start: 0.8697 (p0) cc_final: 0.8132 (t70)
REVERT: A  576 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8681 (pt)
REVERT: A  688 TRP cc_start: 0.8164 (p-90) cc_final: 0.7952 (p-90)
REVERT: A  695 TRP cc_start: 0.8219 (m100) cc_final: 0.8016 (m100)
REVERT: A  844 TRP cc_start: 0.8286 (p90) cc_final: 0.7930 (p90)
REVERT: A  920 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6865 (ttp80)
REVERT: A  974 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8311 (t)
REVERT: A 1086 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7269 (p90)
  outliers start: 47
  outliers final: 39
  residues processed: 129
  average time/residue: 0.1648
  time to fit residues: 31.4195
Evaluate side-chains
  132 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 88
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  353 PHE
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  403 THR
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  550 ARG
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  556 SER
Chi-restraints excluded: chain A residue  576 ILE
Chi-restraints excluded: chain A residue  647 ASN
Chi-restraints excluded: chain A residue  729 LEU
Chi-restraints excluded: chain A residue  738 ILE
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain A residue  785 ILE
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain A residue  866 GLU
Chi-restraints excluded: chain A residue  881 ILE
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  946 GLU
Chi-restraints excluded: chain A residue  950 VAL
Chi-restraints excluded: chain A residue  962 MET
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue  982 ILE
Chi-restraints excluded: chain A residue  991 CYS
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1043 LEU
Chi-restraints excluded: chain A residue 1049 GLN
Chi-restraints excluded: chain A residue 1071 VAL
Chi-restraints excluded: chain A residue 1086 PHE
Chi-restraints excluded: chain A residue 1136 LEU
Chi-restraints excluded: chain A residue 1248 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 78 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0970
   chunk 66 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0370
   chunk 71 optimal weight:    0.6980
   chunk 20 optimal weight:    0.3980
   chunk 50 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.4056

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 986 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.183226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.146095 restraints weight = 13487.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.143550 restraints weight = 15408.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.145833 restraints weight = 15640.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8615  Z= 0.125
  Angle     :  0.687  11.652  11735  Z= 0.335
  Chirality :  0.044   0.148   1244
  Planarity :  0.006   0.063   1542
  Dihedral  :  4.780  21.451   1151
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.72 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 27.57 %
    Favored  : 67.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.26), residues: 1042
  helix:  1.24 (0.66), residues: 64
  sheet: -0.48 (0.29), residues: 330
  loop : -1.21 (0.25), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.072   0.002   TRP A 586 
 HIS   0.024   0.001   HIS A 299 
 PHE   0.008   0.001   PHE A1086 
 TYR   0.009   0.001   TYR A1108 
 ARG   0.004   0.000   ARG A 920 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02931 (  213)
  hydrogen bonds       : angle       5.99768 (  594)
  SS BOND              : bond        0.00244 (    7)
  SS BOND              : angle       0.79070 (   14)
  covalent geometry    : bond        0.00312 ( 8608)
  covalent geometry    : angle       0.68729 (11721)

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

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

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2084 Ramachandran restraints generated.
    1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 87
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7821 (p0)
REVERT: A  575 ASP cc_start: 0.8692 (p0) cc_final: 0.8070 (t70)
REVERT: A  576 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8629 (pt)
REVERT: A  688 TRP cc_start: 0.8143 (p-90) cc_final: 0.7851 (p-90)
REVERT: A  844 TRP cc_start: 0.8173 (p90) cc_final: 0.7806 (p90)
REVERT: A  920 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6753 (ttp80)
REVERT: A  974 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8220 (t)
REVERT: A 1086 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7445 (p90)
  outliers start: 44
  outliers final: 34
  residues processed: 121
  average time/residue: 0.1883
  time to fit residues: 32.7914
Evaluate side-chains
  123 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 84
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  353 PHE
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  403 THR
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  539 ASP
Chi-restraints excluded: chain A residue  544 VAL
Chi-restraints excluded: chain A residue  550 ARG
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  556 SER
Chi-restraints excluded: chain A residue  576 ILE
Chi-restraints excluded: chain A residue  647 ASN
Chi-restraints excluded: chain A residue  738 ILE
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain A residue  785 ILE
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  803 LYS
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain A residue  866 GLU
Chi-restraints excluded: chain A residue  881 ILE
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  950 VAL
Chi-restraints excluded: chain A residue  962 MET
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue  991 CYS
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1043 LEU
Chi-restraints excluded: chain A residue 1049 GLN
Chi-restraints excluded: chain A residue 1071 VAL
Chi-restraints excluded: chain A residue 1086 PHE
Chi-restraints excluded: chain A residue 1136 LEU
Chi-restraints excluded: chain A residue 1248 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 4 optimal weight:    0.7980
   chunk 100 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 726 HIS ** 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 = 0.4177 r_free = 0.4177 target = 0.177797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.127456 restraints weight = 13549.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.130207 restraints weight = 11107.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.130664 restraints weight = 9065.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.3728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   8615  Z= 0.241
  Angle     :  0.769  11.343  11735  Z= 0.381
  Chirality :  0.046   0.145   1244
  Planarity :  0.006   0.064   1542
  Dihedral  :  5.153  24.007   1151
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.93 %
    Favored  : 90.88 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 27.13 %
    Favored  : 67.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.26), residues: 1042
  helix:  1.00 (0.64), residues: 64
  sheet: -0.75 (0.29), residues: 349
  loop : -1.27 (0.25), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.003   TRP A 586 
 HIS   0.026   0.002   HIS A 299 
 PHE   0.015   0.002   PHE A1096 
 TYR   0.026   0.002   TYR A 297 
 ARG   0.010   0.000   ARG A1019 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03410 (  213)
  hydrogen bonds       : angle       6.22520 (  594)
  SS BOND              : bond        0.00275 (    7)
  SS BOND              : angle       0.91458 (   14)
  covalent geometry    : bond        0.00583 ( 8608)
  covalent geometry    : angle       0.76886 (11721)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3215.07 seconds
wall clock time: 58 minutes 35.20 seconds (3515.20 seconds total)