Starting phenix.real_space_refine
on Thu Jul 24 17:08:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o2w_12700/07_2025/7o2w_12700.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o2w_12700/07_2025/7o2w_12700.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7o2w_12700/07_2025/7o2w_12700.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o2w_12700/07_2025/7o2w_12700.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o2w_12700/07_2025/7o2w_12700.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o2w_12700/07_2025/7o2w_12700.cif"
  }
  resolution = 3.8
  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=   0.000
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      31      5.16       5
     C    4149      2.51       5
     N    1094      2.21       5
     O    1157      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6431
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3151
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 418, 3151
          Classifications: {'peptide': 418}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 398}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 169
          Unresolved non-hydrogen angles: 198
          Unresolved non-hydrogen dihedrals: 142
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 4, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 105
    Chain: "B"
      Number of atoms: 3280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 422, 3280
          Classifications: {'peptide': 422}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'CIS': 2, 'PTRANS': 13, 'TRANS': 406}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 159
          Unresolved non-hydrogen angles: 193
          Unresolved non-hydrogen dihedrals: 130
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 97
  Time building chain proxies: 5.37, per 1000 atoms: 0.84
  Number of scatterers: 6431
  At special positions: 0
  Unit cell: (77.4, 121.26, 125.56, 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      31     16.00
     O    1157      8.00
     N    1094      7.00
     C    4149      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.41
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1598

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 3 sheets defined
      53.8% alpha, 1.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 55 through 72
      removed outlier: 3.540A  pdb=" N   THR A  66 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ASN A  68 " --> pdb=" O   ASN A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 143
      Proline residue:  A 126  - end of helix
      removed outlier: 4.457A  pdb=" N   ARG A 129 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   VAL A 130 " --> pdb=" O   PRO A 126 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ILE A 138 " --> pdb=" O   ARG A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 172
    Processing helix  chain 'A' and resid 172 through 193
      removed outlier: 3.742A  pdb=" N   GLU A 179 " --> pdb=" O   MET A 175 " (cutoff:3.500A)
      Proline residue:  A 182  - end of helix
      removed outlier: 3.683A  pdb=" N   GLU A 185 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   MET A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   LYS A 191 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 230
      removed outlier: 3.544A  pdb=" N   THR A 230 " --> pdb=" O   SER A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 249
      removed outlier: 3.959A  pdb=" N   VAL A 248 " --> pdb=" O   VAL A 244 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ARG A 249 " --> pdb=" O   ASN A 245 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 244 through 249'
    Processing helix  chain 'A' and resid 256 through 260
    Processing helix  chain 'A' and resid 284 through 289
      removed outlier: 3.901A  pdb=" N   SER A 287 " --> pdb=" O   LEU A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 300
      removed outlier: 4.081A  pdb=" N   MET A 299 " --> pdb=" O   PHE A 295 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   TYR A 300 " --> pdb=" O   ARG A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 334
      removed outlier: 4.497A  pdb=" N   SER A 334 " --> pdb=" O   ARG A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 385
      removed outlier: 4.064A  pdb=" N   PHE A 385 " --> pdb=" O   LEU A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 388
      No H-bonds generated for 'chain 'A' and resid 386 through 388'
    Processing helix  chain 'A' and resid 392 through 419
      removed outlier: 3.681A  pdb=" N   THR A 396 " --> pdb=" O   SER A 392 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU A 412 " --> pdb=" O   LYS A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 437
      removed outlier: 3.903A  pdb=" N   ILE A 435 " --> pdb=" O   ARG A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 454
      removed outlier: 3.772A  pdb=" N   ASN A 446 " --> pdb=" O   GLU A 442 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ILE A 447 " --> pdb=" O   GLY A 443 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   GLU A 453 " --> pdb=" O   MET A 449 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   LYS A 454 " --> pdb=" O   ALA A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 465
    Processing helix  chain 'B' and resid 146 through 150
    Processing helix  chain 'B' and resid 162 through 167
      removed outlier: 3.737A  pdb=" N   MET B 166 " --> pdb=" O   GLN B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 213
      removed outlier: 3.877A  pdb=" N   LEU B 172 " --> pdb=" O   GLN B 168 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   SER B 177 " --> pdb=" O   SER B 173 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ARG B 178 " --> pdb=" O   ALA B 174 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ARG B 188 " --> pdb=" O   LYS B 184 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLU B 196 " --> pdb=" O   ALA B 192 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   THR B 205 " --> pdb=" O   ASP B 201 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ARG B 206 " --> pdb=" O   LEU B 202 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   THR B 211 " --> pdb=" O   THR B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 249
      removed outlier: 3.673A  pdb=" N   GLN B 228 " --> pdb=" O   PHE B 224 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   ALA B 233 " --> pdb=" O   ALA B 229 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ASN B 234 " --> pdb=" O   ILE B 230 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLU B 235 " --> pdb=" O   GLU B 231 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ALA B 237 " --> pdb=" O   ALA B 233 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LYS B 241 " --> pdb=" O   ALA B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 331
      removed outlier: 3.983A  pdb=" N   THR B 321 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU B 322 " --> pdb=" O   LYS B 318 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLU B 323 " --> pdb=" O   LEU B 319 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   THR B 328 " --> pdb=" O   GLU B 324 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLU B 329 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 345
      removed outlier: 3.623A  pdb=" N   LEU B 338 " --> pdb=" O   THR B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 363
      removed outlier: 3.991A  pdb=" N   LEU B 352 " --> pdb=" O   ASP B 348 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   SER B 355 " --> pdb=" O   TYR B 351 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLN B 356 " --> pdb=" O   LEU B 352 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LYS B 363 " --> pdb=" O   ARG B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 371
      removed outlier: 3.509A  pdb=" N   PHE B 370 " --> pdb=" O   HIS B 366 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU B 371 " --> pdb=" O   ILE B 367 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 366 through 371'
    Processing helix  chain 'B' and resid 701 through 703
      No H-bonds generated for 'chain 'B' and resid 701 through 703'
    Processing helix  chain 'B' and resid 704 through 715
      removed outlier: 4.569A  pdb=" N   ALA B 710 " --> pdb=" O   ALA B 706 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 719 through 730
      removed outlier: 4.160A  pdb=" N   ALA B 723 " --> pdb=" O   PHE B 719 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 739 through 749
      removed outlier: 4.322A  pdb=" N   VAL B 743 " --> pdb=" O   ASP B 739 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ARG B 744 " --> pdb=" O   GLU B 740 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   LYS B 745 " --> pdb=" O   ALA B 741 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   THR B 748 " --> pdb=" O   ARG B 744 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ALA B 749 " --> pdb=" O   LYS B 745 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 750 through 754
      removed outlier: 3.748A  pdb=" N   PHE B 753 " --> pdb=" O   LEU B 750 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 795 through 803
      removed outlier: 3.899A  pdb=" N   ALA B 799 " --> pdb=" O   GLY B 795 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 825 through 831
    Processing helix  chain 'B' and resid 840 through 863
      removed outlier: 3.694A  pdb=" N   THR B 852 " --> pdb=" O   GLN B 848 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLN B 853 " --> pdb=" O   SER B 849 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   PHE B 863 " --> pdb=" O   PHE B 859 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 877 through 890
      removed outlier: 3.590A  pdb=" N   PHE B 887 " --> pdb=" O   ARG B 883 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU B 888 " --> pdb=" O   GLN B 884 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LYS B 889 " --> pdb=" O   MET B 885 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 894 through 916
      removed outlier: 3.925A  pdb=" N   VAL B 899 " --> pdb=" O   VAL B 895 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ARG B 900 " --> pdb=" O   ASN B 896 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ALA B 906 " --> pdb=" O   VAL B 902 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LEU B 911 " --> pdb=" O   GLU B 907 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16
      removed outlier: 6.937A  pdb=" N   THR A  15 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29
      removed outlier: 3.551A  pdb=" N   SER A 113 " --> pdb=" O   THR A  29 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL A  86 " --> pdb=" O   LEU B 115 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   LEU B 115 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82

    257 hydrogen bonds defined for protein.
    741 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.36

  Time building geometry restraints manager: 2.31 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2014
        1.34 -     1.45: 988
        1.45 -     1.57: 3522
        1.57 -     1.69: 0
        1.69 -     1.81: 45
  Bond restraints: 6569
  Sorted by residual:
  bond pdb=" CG1 ILE A 325 "
       pdb=" CD1 ILE A 325 "
    ideal  model  delta    sigma   weight residual
    1.513  1.436  0.077 3.90e-02 6.57e+02 3.90e+00
  bond pdb=" CB  PHE B 372 "
       pdb=" CG  PHE B 372 "
    ideal  model  delta    sigma   weight residual
    1.502  1.465  0.037 2.30e-02 1.89e+03 2.57e+00
  bond pdb=" C   ILE A 173 "
       pdb=" N   PRO A 174 "
    ideal  model  delta    sigma   weight residual
    1.334  1.371 -0.037 2.34e-02 1.83e+03 2.54e+00
  bond pdb=" CG  GLN A 281 "
       pdb=" CD  GLN A 281 "
    ideal  model  delta    sigma   weight residual
    1.516  1.480  0.036 2.50e-02 1.60e+03 2.05e+00
  bond pdb=" CA  ASP A 203 "
       pdb=" C   ASP A 203 "
    ideal  model  delta    sigma   weight residual
    1.523  1.499  0.025 1.80e-02 3.09e+03 1.88e+00
  ... (remaining 6564 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.54: 8676
        2.54 -     5.07: 208
        5.07 -     7.61: 29
        7.61 -    10.15: 5
       10.15 -    12.69: 1
  Bond angle restraints: 8919
  Sorted by residual:
  angle pdb=" CA  ASP A 203 "
        pdb=" C   ASP A 203 "
        pdb=" N   THR A 204 "
      ideal   model   delta    sigma   weight residual
     118.27  108.50    9.77 1.59e+00 3.96e-01 3.78e+01
  angle pdb=" C   ALA B 160 "
        pdb=" N   ASP B 161 "
        pdb=" CA  ASP B 161 "
      ideal   model   delta    sigma   weight residual
     121.54  131.20   -9.66 1.91e+00 2.74e-01 2.56e+01
  angle pdb=" C   ILE A 144 "
        pdb=" N   TRP A 145 "
        pdb=" CA  TRP A 145 "
      ideal   model   delta    sigma   weight residual
     121.70  129.02   -7.32 1.80e+00 3.09e-01 1.66e+01
  angle pdb=" CA  ASP A 203 "
        pdb=" C   ASP A 203 "
        pdb=" O   ASP A 203 "
      ideal   model   delta    sigma   weight residual
     119.23  124.85   -5.62 1.54e+00 4.22e-01 1.33e+01
  angle pdb=" CA  LEU A 283 "
        pdb=" CB  LEU A 283 "
        pdb=" CG  LEU A 283 "
      ideal   model   delta    sigma   weight residual
     116.30  128.99  -12.69 3.50e+00 8.16e-02 1.31e+01
  ... (remaining 8914 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.20: 3505
       18.20 -    36.40: 339
       36.40 -    54.60: 49
       54.60 -    72.79: 2
       72.79 -    90.99: 5
  Dihedral angle restraints: 3900
    sinusoidal: 1442
      harmonic: 2458
  Sorted by residual:
  dihedral pdb=" CA  HIS B 766 "
           pdb=" C   HIS B 766 "
           pdb=" N   TRP B 767 "
           pdb=" CA  TRP B 767 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  137.61   42.39     0      5.00e+00 4.00e-02 7.19e+01
  dihedral pdb=" CA  PHE A 279 "
           pdb=" C   PHE A 279 "
           pdb=" N   VAL A 280 "
           pdb=" CA  VAL A 280 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.60   36.40     0      5.00e+00 4.00e-02 5.30e+01
  dihedral pdb=" CA  ALA A  75 "
           pdb=" C   ALA A  75 "
           pdb=" N   GLU A  76 "
           pdb=" CA  GLU A  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -149.06  -30.94     0      5.00e+00 4.00e-02 3.83e+01
  ... (remaining 3897 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 703
       0.046 -    0.092: 277
       0.092 -    0.138: 55
       0.138 -    0.184: 12
       0.184 -    0.230: 1
  Chirality restraints: 1048
  Sorted by residual:
  chirality pdb=" CA  PHE A 279 "
            pdb=" N   PHE A 279 "
            pdb=" C   PHE A 279 "
            pdb=" CB  PHE A 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CB  ILE B 158 "
            pdb=" CA  ILE B 158 "
            pdb=" CG1 ILE B 158 "
            pdb=" CG2 ILE B 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.17e-01
  chirality pdb=" CG  LEU A 283 "
            pdb=" CB  LEU A 283 "
            pdb=" CD1 LEU A 283 "
            pdb=" CD2 LEU A 283 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.60e-01
  ... (remaining 1045 not shown)

  Planarity restraints: 1121
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 767 "   -0.019 2.00e-02 2.50e+03   1.60e-02 6.38e+00
        pdb=" CG  TRP B 767 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 767 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 767 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 767 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 767 "    0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 767 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 767 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 767 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 767 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 379 "   -0.011 2.00e-02 2.50e+03   2.28e-02 5.20e+00
        pdb=" C   ALA A 379 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ALA A 379 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   PHE A 380 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 318 "    0.032 5.00e-02 4.00e+02   4.77e-02 3.64e+00
        pdb=" N   PRO A 319 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 319 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 319 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1118 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 164
        2.64 -     3.21: 7095
        3.21 -     3.77: 10074
        3.77 -     4.33: 13625
        4.33 -     4.90: 20403
  Nonbonded interactions: 51361
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 832 "
            pdb=" OG1 THR B 835 "
     model   vdw
     2.075 3.040
  nonbonded pdb=" O   GLY B 223 "
            pdb=" OG  SER B 226 "
     model   vdw
     2.112 3.040
  nonbonded pdb=" O   HIS B 766 "
            pdb=" ND1 HIS B 766 "
     model   vdw
     2.159 3.120
  nonbonded pdb=" O   TYR B 204 "
            pdb=" OG1 THR B 207 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" NZ  LYS A 273 "
            pdb=" O   TYR A 274 "
     model   vdw
     2.170 3.120
  ... (remaining 51356 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     22.510
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077   6569  Z= 0.271
  Angle     :  0.961  12.686   8919  Z= 0.511
  Chirality :  0.050   0.230   1048
  Planarity :  0.005   0.048   1121
  Dihedral  : 14.295  90.993   2302
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 28.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.89 %
    Favored  : 84.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.38 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.82 (0.27), residues: 818
  helix: -1.42 (0.27), residues: 325
  sheet: -4.01 (0.51), residues: 78
  loop : -3.23 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.003   TRP B 767 
 HIS   0.009   0.002   HIS A 307 
 PHE   0.028   0.003   PHE B 345 
 TYR   0.026   0.003   TYR B 157 
 ARG   0.012   0.001   ARG A 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.33310 (  257)
  hydrogen bonds       : angle      10.06243 (  741)
  covalent geometry    : bond        0.00613 ( 6569)
  covalent geometry    : angle       0.96081 ( 8919)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.9099 (t80) cc_final: 0.8789 (t80)
REVERT: A   81 ASP cc_start: 0.7551 (m-30) cc_final: 0.7334 (m-30)
REVERT: A  146 MET cc_start: 0.3427 (mmp) cc_final: 0.3056 (mmp)
REVERT: A  151 GLN cc_start: 0.7713 (pm20) cc_final: 0.7251 (pm20)
REVERT: A  190 MET cc_start: 0.8955 (mpp) cc_final: 0.8182 (mpp)
REVERT: A  299 MET cc_start: 0.6166 (tmm) cc_final: 0.5862 (tpp)
REVERT: A  372 HIS cc_start: 0.7321 (m90) cc_final: 0.6985 (m90)
REVERT: B  201 ASP cc_start: 0.9267 (t70) cc_final: 0.8994 (t0)
REVERT: B  861 TYR cc_start: 0.8729 (t80) cc_final: 0.8519 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.3138
  time to fit residues: 59.3175
Evaluate side-chains
  109 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 62 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0870
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0870
   chunk 39 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.5136

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

Flipped N/Q/H residues before XYZ refinement:
A 281 GLN
A 322 HIS
B 162 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.138100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.112820 restraints weight = 17205.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.116259 restraints weight = 9422.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.118520 restraints weight = 6405.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7041
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6569  Z= 0.172
  Angle     :  0.840   8.051   8919  Z= 0.436
  Chirality :  0.048   0.189   1048
  Planarity :  0.005   0.048   1121
  Dihedral  :  6.580  31.561    893
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 16.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.00 %
    Favored  : 89.00 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 13.29 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.13 (0.28), residues: 818
  helix: -0.61 (0.25), residues: 376
  sheet: -3.55 (0.52), residues: 79
  loop : -3.38 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 767 
 HIS   0.006   0.001   HIS B 721 
 PHE   0.020   0.002   PHE B 345 
 TYR   0.022   0.002   TYR A  32 
 ARG   0.007   0.001   ARG A 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06147 (  257)
  hydrogen bonds       : angle       5.91000 (  741)
  covalent geometry    : bond        0.00363 ( 6569)
  covalent geometry    : angle       0.84034 ( 8919)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 140
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 PHE cc_start: 0.7702 (t80) cc_final: 0.7403 (t80)
REVERT: A   61 PHE cc_start: 0.9066 (t80) cc_final: 0.8811 (t80)
REVERT: A   81 ASP cc_start: 0.7483 (m-30) cc_final: 0.7196 (m-30)
REVERT: A  151 GLN cc_start: 0.7709 (pm20) cc_final: 0.7128 (pm20)
REVERT: A  190 MET cc_start: 0.8951 (mpp) cc_final: 0.8321 (mpp)
REVERT: B  201 ASP cc_start: 0.9310 (t70) cc_final: 0.9014 (t0)
REVERT: B  361 LEU cc_start: 0.9238 (mt) cc_final: 0.9001 (mt)
REVERT: B  861 TYR cc_start: 0.8451 (t80) cc_final: 0.7975 (t80)
REVERT: B  883 ARG cc_start: 0.5996 (tpt170) cc_final: 0.5579 (tpt-90)
REVERT: B  885 MET cc_start: 0.8827 (mpp) cc_final: 0.8567 (mpp)
  outliers start: 15
  outliers final: 7
  residues processed: 147
  average time/residue: 0.1700
  time to fit residues: 34.4717
Evaluate side-chains
  130 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 123
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  460 HIS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  183 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   chunk 28 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 74 optimal weight:    7.9990
   chunk 44 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 865 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.134583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.109573 restraints weight = 17466.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.112824 restraints weight = 9907.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.114965 restraints weight = 6849.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
moved from start:          0.2482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   6569  Z= 0.207
  Angle     :  0.808   8.733   8919  Z= 0.417
  Chirality :  0.047   0.196   1048
  Planarity :  0.004   0.046   1121
  Dihedral  :  6.471  31.186    893
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 17.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.57 %
    Favored  : 86.43 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 19.18 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.38 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.12 (0.28), residues: 818
  helix: -0.58 (0.25), residues: 378
  sheet: -3.75 (0.51), residues: 81
  loop : -3.35 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 767 
 HIS   0.005   0.001   HIS A 406 
 PHE   0.030   0.003   PHE B 117 
 TYR   0.017   0.002   TYR A  32 
 ARG   0.004   0.000   ARG A 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05356 (  257)
  hydrogen bonds       : angle       5.50589 (  741)
  covalent geometry    : bond        0.00471 ( 6569)
  covalent geometry    : angle       0.80817 ( 8919)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 131
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 PHE cc_start: 0.7876 (t80) cc_final: 0.7578 (t80)
REVERT: A   44 ILE cc_start: 0.7389 (mp) cc_final: 0.7177 (mm)
REVERT: A   61 PHE cc_start: 0.9074 (t80) cc_final: 0.8872 (t80)
REVERT: A   81 ASP cc_start: 0.7347 (m-30) cc_final: 0.7109 (m-30)
REVERT: A  151 GLN cc_start: 0.7785 (pm20) cc_final: 0.7324 (pm20)
REVERT: B  149 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7439 (t80)
REVERT: B  201 ASP cc_start: 0.9288 (t70) cc_final: 0.9059 (t0)
REVERT: B  235 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.5967 (mm-30)
REVERT: B  883 ARG cc_start: 0.6142 (tpt170) cc_final: 0.5782 (tpt-90)
REVERT: B  897 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7047 (mm-30)
  outliers start: 34
  outliers final: 24
  residues processed: 145
  average time/residue: 0.1602
  time to fit residues: 31.8917
Evaluate side-chains
  145 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 118
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  460 HIS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  149 PHE
Chi-restraints excluded: chain B residue  155 MET
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  235 GLU
Chi-restraints excluded: chain B residue  328 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  714 ILE
Chi-restraints excluded: chain B residue  719 PHE
Chi-restraints excluded: chain B residue  800 LEU
Chi-restraints excluded: chain B residue  842 THR
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  862 THR
Chi-restraints excluded: chain B residue  897 GLU
Chi-restraints excluded: chain B residue  912 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 14 optimal weight:   10.0000
   chunk 56 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 313 ASN
A 400 GLN
** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 853 GLN
B 865 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.137382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.112222 restraints weight = 17277.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.115625 restraints weight = 9681.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.117831 restraints weight = 6631.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6569  Z= 0.152
  Angle     :  0.768  10.566   8919  Z= 0.395
  Chirality :  0.045   0.174   1048
  Planarity :  0.004   0.043   1121
  Dihedral  :  6.098  28.987    893
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 14.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.12 %
    Favored  : 88.88 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 21.15 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.28), residues: 818
  helix: -0.44 (0.25), residues: 384
  sheet: -3.72 (0.50), residues: 83
  loop : -3.34 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 767 
 HIS   0.006   0.001   HIS B 721 
 PHE   0.015   0.002   PHE A  30 
 TYR   0.021   0.002   TYR B 861 
 ARG   0.002   0.000   ARG A 394 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04560 (  257)
  hydrogen bonds       : angle       5.07654 (  741)
  covalent geometry    : bond        0.00337 ( 6569)
  covalent geometry    : angle       0.76779 ( 8919)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 142
  time to evaluate  : 0.725 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 PHE cc_start: 0.7849 (t80) cc_final: 0.7493 (t80)
REVERT: A   61 PHE cc_start: 0.9078 (t80) cc_final: 0.8807 (t80)
REVERT: A   81 ASP cc_start: 0.7320 (m-30) cc_final: 0.7069 (m-30)
REVERT: A   83 LYS cc_start: 0.8859 (tptm) cc_final: 0.8650 (tppp)
REVERT: A  151 GLN cc_start: 0.7712 (pm20) cc_final: 0.7279 (pm20)
REVERT: A  179 GLU cc_start: 0.8541 (mp0) cc_final: 0.8234 (mp0)
REVERT: B  149 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7430 (t80)
REVERT: B  168 GLN cc_start: 0.8637 (tp-100) cc_final: 0.8166 (tp-100)
REVERT: B  201 ASP cc_start: 0.9306 (t70) cc_final: 0.9069 (t0)
REVERT: B  235 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.5993 (mm-30)
REVERT: B  878 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.6895 (tp30)
REVERT: B  883 ARG cc_start: 0.6304 (tpt170) cc_final: 0.5892 (tpt-90)
REVERT: B  897 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6830 (mm-30)
REVERT: B  900 ARG cc_start: 0.8473 (mtm180) cc_final: 0.8072 (mtm180)
  outliers start: 33
  outliers final: 18
  residues processed: 162
  average time/residue: 0.1615
  time to fit residues: 35.4159
Evaluate side-chains
  156 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  460 HIS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  149 PHE
Chi-restraints excluded: chain B residue  155 MET
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  235 GLU
Chi-restraints excluded: chain B residue  368 THR
Chi-restraints excluded: chain B residue  714 ILE
Chi-restraints excluded: chain B residue  719 PHE
Chi-restraints excluded: chain B residue  800 LEU
Chi-restraints excluded: chain B residue  842 THR
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  878 GLU
Chi-restraints excluded: chain B residue  897 GLU
Chi-restraints excluded: chain B residue  912 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 73 optimal weight:    0.7980
   chunk 29 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 69 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 31 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 853 GLN
B 865 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.137282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.111767 restraints weight = 17416.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.115157 restraints weight = 9827.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.117427 restraints weight = 6737.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7100
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6569  Z= 0.162
  Angle     :  0.785  11.288   8919  Z= 0.396
  Chirality :  0.045   0.169   1048
  Planarity :  0.004   0.042   1121
  Dihedral  :  5.991  28.018    893
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 16.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.47 %
    Favored  : 87.53 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 21.90 %
    Favored  : 72.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.28), residues: 818
  helix: -0.45 (0.25), residues: 391
  sheet: -3.69 (0.51), residues: 83
  loop : -3.42 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 780 
 HIS   0.006   0.001   HIS B 721 
 PHE   0.015   0.002   PHE B 345 
 TYR   0.016   0.002   TYR B 844 
 ARG   0.002   0.000   ARG A 394 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04426 (  257)
  hydrogen bonds       : angle       5.05545 (  741)
  covalent geometry    : bond        0.00366 ( 6569)
  covalent geometry    : angle       0.78545 ( 8919)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 137
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 PHE cc_start: 0.7930 (t80) cc_final: 0.7578 (t80)
REVERT: A   44 ILE cc_start: 0.7408 (mp) cc_final: 0.7146 (mm)
REVERT: A   61 PHE cc_start: 0.9105 (t80) cc_final: 0.8806 (t80)
REVERT: A   81 ASP cc_start: 0.7331 (m-30) cc_final: 0.7086 (m-30)
REVERT: A  151 GLN cc_start: 0.7687 (pm20) cc_final: 0.7264 (pm20)
REVERT: A  179 GLU cc_start: 0.8554 (mp0) cc_final: 0.8225 (mp0)
REVERT: B  149 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7378 (t80)
REVERT: B  168 GLN cc_start: 0.8657 (tp-100) cc_final: 0.8157 (tp-100)
REVERT: B  201 ASP cc_start: 0.9310 (t70) cc_final: 0.9090 (t0)
REVERT: B  235 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6007 (mm-30)
REVERT: B  878 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.6905 (tp30)
REVERT: B  883 ARG cc_start: 0.5933 (tpt170) cc_final: 0.5561 (tpt-90)
REVERT: B  897 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7049 (mm-30)
REVERT: B  900 ARG cc_start: 0.8468 (mtm180) cc_final: 0.8147 (mtm180)
  outliers start: 38
  outliers final: 25
  residues processed: 158
  average time/residue: 0.1639
  time to fit residues: 34.8701
Evaluate side-chains
  157 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 128
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  460 HIS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  149 PHE
Chi-restraints excluded: chain B residue  155 MET
Chi-restraints excluded: chain B residue  167 GLN
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  235 GLU
Chi-restraints excluded: chain B residue  714 ILE
Chi-restraints excluded: chain B residue  719 PHE
Chi-restraints excluded: chain B residue  734 VAL
Chi-restraints excluded: chain B residue  772 LEU
Chi-restraints excluded: chain B residue  800 LEU
Chi-restraints excluded: chain B residue  842 THR
Chi-restraints excluded: chain B residue  878 GLU
Chi-restraints excluded: chain B residue  897 GLU
Chi-restraints excluded: chain B residue  912 HIS
Chi-restraints excluded: chain B residue  913 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 28 optimal weight:    0.2980
   chunk 76 optimal weight:    1.9990
   chunk 9 optimal weight:    8.9990
   chunk 7 optimal weight:    0.2980
   chunk 35 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 46 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 853 GLN
B 865 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.139720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.114186 restraints weight = 17001.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.117641 restraints weight = 9568.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.119939 restraints weight = 6538.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.3488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6569  Z= 0.140
  Angle     :  0.755  11.072   8919  Z= 0.381
  Chirality :  0.045   0.168   1048
  Planarity :  0.004   0.042   1121
  Dihedral  :  5.752  26.764    893
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.39 %
    Favored  : 89.61 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 23.41 %
    Favored  : 70.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.84 (0.29), residues: 818
  helix: -0.31 (0.26), residues: 392
  sheet: -3.60 (0.49), residues: 94
  loop : -3.33 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 767 
 HIS   0.006   0.001   HIS A 460 
 PHE   0.014   0.002   PHE A  30 
 TYR   0.014   0.001   TYR A  32 
 ARG   0.003   0.000   ARG A 394 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04029 (  257)
  hydrogen bonds       : angle       4.82902 (  741)
  covalent geometry    : bond        0.00305 ( 6569)
  covalent geometry    : angle       0.75526 ( 8919)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 144
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 PHE cc_start: 0.7932 (t80) cc_final: 0.7558 (t80)
REVERT: A   61 PHE cc_start: 0.9083 (t80) cc_final: 0.8820 (t80)
REVERT: A   77 SER cc_start: 0.4348 (OUTLIER) cc_final: 0.4043 (m)
REVERT: A  151 GLN cc_start: 0.7705 (pm20) cc_final: 0.7281 (pm20)
REVERT: A  179 GLU cc_start: 0.8549 (mp0) cc_final: 0.8257 (mp0)
REVERT: A  235 VAL cc_start: 0.6090 (OUTLIER) cc_final: 0.5827 (p)
REVERT: B  149 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7441 (t80)
REVERT: B  201 ASP cc_start: 0.9305 (t70) cc_final: 0.9091 (t0)
REVERT: B  235 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6018 (mm-30)
REVERT: B  348 ASP cc_start: 0.6585 (t70) cc_final: 0.6055 (m-30)
REVERT: B  861 TYR cc_start: 0.8322 (t80) cc_final: 0.8084 (t80)
REVERT: B  878 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.6924 (tp30)
REVERT: B  897 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6939 (mm-30)
  outliers start: 40
  outliers final: 22
  residues processed: 165
  average time/residue: 0.1725
  time to fit residues: 38.2806
Evaluate side-chains
  164 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 136
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  460 HIS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  149 PHE
Chi-restraints excluded: chain B residue  155 MET
Chi-restraints excluded: chain B residue  167 GLN
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  235 GLU
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  714 ILE
Chi-restraints excluded: chain B residue  734 VAL
Chi-restraints excluded: chain B residue  767 TRP
Chi-restraints excluded: chain B residue  772 LEU
Chi-restraints excluded: chain B residue  800 LEU
Chi-restraints excluded: chain B residue  842 THR
Chi-restraints excluded: chain B residue  878 GLU
Chi-restraints excluded: chain B residue  897 GLU
Chi-restraints excluded: chain B residue  912 HIS
Chi-restraints excluded: chain B residue  913 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 43 optimal weight:    5.9990
   chunk 33 optimal weight:    0.4980
   chunk 72 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 50 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 853 GLN
B 865 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.139818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.114265 restraints weight = 17249.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.117716 restraints weight = 9712.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.119994 restraints weight = 6661.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.4042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.3642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6569  Z= 0.141
  Angle     :  0.750  10.159   8919  Z= 0.378
  Chirality :  0.045   0.165   1048
  Planarity :  0.004   0.040   1121
  Dihedral  :  5.685  26.494    893
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 15.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.61 %
    Favored  : 88.39 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 23.87 %
    Favored  : 70.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.79 (0.29), residues: 818
  helix: -0.28 (0.26), residues: 392
  sheet: -3.51 (0.50), residues: 93
  loop : -3.30 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 767 
 HIS   0.005   0.001   HIS B 766 
 PHE   0.018   0.002   PHE A 464 
 TYR   0.012   0.001   TYR A  32 
 ARG   0.003   0.000   ARG B 818 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04010 (  257)
  hydrogen bonds       : angle       4.78893 (  741)
  covalent geometry    : bond        0.00311 ( 6569)
  covalent geometry    : angle       0.74985 ( 8919)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 140
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 PHE cc_start: 0.7979 (t80) cc_final: 0.7640 (t80)
REVERT: A   61 PHE cc_start: 0.9084 (t80) cc_final: 0.8832 (t80)
REVERT: A  151 GLN cc_start: 0.7737 (pm20) cc_final: 0.7325 (pm20)
REVERT: A  179 GLU cc_start: 0.8540 (mp0) cc_final: 0.8167 (mp0)
REVERT: A  235 VAL cc_start: 0.6095 (OUTLIER) cc_final: 0.5824 (p)
REVERT: B  149 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7493 (t80)
REVERT: B  201 ASP cc_start: 0.9308 (t70) cc_final: 0.9101 (t0)
REVERT: B  235 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6008 (mm-30)
REVERT: B  348 ASP cc_start: 0.6551 (t70) cc_final: 0.6224 (m-30)
REVERT: B  861 TYR cc_start: 0.8295 (t80) cc_final: 0.8060 (t80)
REVERT: B  878 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7122 (tp30)
REVERT: B  897 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7105 (mm-30)
  outliers start: 38
  outliers final: 25
  residues processed: 161
  average time/residue: 0.1589
  time to fit residues: 35.2781
Evaluate side-chains
  164 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 134
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  368 GLN
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  383 GLN
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  460 HIS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  149 PHE
Chi-restraints excluded: chain B residue  155 MET
Chi-restraints excluded: chain B residue  167 GLN
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  235 GLU
Chi-restraints excluded: chain B residue  714 ILE
Chi-restraints excluded: chain B residue  734 VAL
Chi-restraints excluded: chain B residue  767 TRP
Chi-restraints excluded: chain B residue  772 LEU
Chi-restraints excluded: chain B residue  800 LEU
Chi-restraints excluded: chain B residue  842 THR
Chi-restraints excluded: chain B residue  878 GLU
Chi-restraints excluded: chain B residue  897 GLU
Chi-restraints excluded: chain B residue  912 HIS
Chi-restraints excluded: chain B residue  913 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 44 optimal weight:    7.9990
   chunk 54 optimal weight:    6.9990
   chunk 27 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 865 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.140234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.114602 restraints weight = 17198.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.117958 restraints weight = 9703.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.120329 restraints weight = 6671.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.4044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7042
moved from start:          0.3794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6569  Z= 0.142
  Angle     :  0.764  11.808   8919  Z= 0.382
  Chirality :  0.045   0.187   1048
  Planarity :  0.004   0.040   1121
  Dihedral  :  5.584  26.807    893
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 14.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.64 %
    Favored  : 89.36 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 24.77 %
    Favored  : 69.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.70 (0.29), residues: 818
  helix: -0.22 (0.26), residues: 393
  sheet: -3.51 (0.50), residues: 94
  loop : -3.23 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 767 
 HIS   0.005   0.001   HIS B 766 
 PHE   0.012   0.002   PHE A  30 
 TYR   0.012   0.001   TYR A  32 
 ARG   0.003   0.000   ARG A 394 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03862 (  257)
  hydrogen bonds       : angle       4.75022 (  741)
  covalent geometry    : bond        0.00313 ( 6569)
  covalent geometry    : angle       0.76394 ( 8919)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 140
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 PHE cc_start: 0.8053 (t80) cc_final: 0.7713 (t80)
REVERT: A   61 PHE cc_start: 0.9084 (t80) cc_final: 0.8825 (t80)
REVERT: A   83 LYS cc_start: 0.8567 (tptm) cc_final: 0.8361 (tppp)
REVERT: A  151 GLN cc_start: 0.7705 (pm20) cc_final: 0.7177 (pm20)
REVERT: A  179 GLU cc_start: 0.8622 (mp0) cc_final: 0.8142 (mp0)
REVERT: A  235 VAL cc_start: 0.6100 (OUTLIER) cc_final: 0.5829 (p)
REVERT: B  149 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7400 (t80)
REVERT: B  195 LEU cc_start: 0.8596 (tp) cc_final: 0.8326 (tp)
REVERT: B  201 ASP cc_start: 0.9321 (t70) cc_final: 0.9117 (t0)
REVERT: B  235 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6009 (mm-30)
REVERT: B  348 ASP cc_start: 0.6464 (t70) cc_final: 0.6173 (m-30)
REVERT: B  702 HIS cc_start: 0.7821 (OUTLIER) cc_final: 0.7277 (t-90)
REVERT: B  861 TYR cc_start: 0.8267 (t80) cc_final: 0.7758 (t80)
REVERT: B  878 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7146 (tp30)
REVERT: B  883 ARG cc_start: 0.6142 (tpt170) cc_final: 0.4113 (tpt-90)
REVERT: B  897 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7040 (mm-30)
  outliers start: 36
  outliers final: 27
  residues processed: 159
  average time/residue: 0.1689
  time to fit residues: 36.5917
Evaluate side-chains
  172 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 139
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  368 GLN
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  383 GLN
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  460 HIS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  149 PHE
Chi-restraints excluded: chain B residue  155 MET
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  235 GLU
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  702 HIS
Chi-restraints excluded: chain B residue  714 ILE
Chi-restraints excluded: chain B residue  734 VAL
Chi-restraints excluded: chain B residue  767 TRP
Chi-restraints excluded: chain B residue  772 LEU
Chi-restraints excluded: chain B residue  800 LEU
Chi-restraints excluded: chain B residue  842 THR
Chi-restraints excluded: chain B residue  878 GLU
Chi-restraints excluded: chain B residue  897 GLU
Chi-restraints excluded: chain B residue  912 HIS
Chi-restraints excluded: chain B residue  913 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 69 optimal weight:    0.0870
   chunk 4 optimal weight:    0.7980
   chunk 67 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 23 optimal weight:    0.4980
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    7.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 369 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 = 0.4360 r_free = 0.4360 target = 0.141715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.116002 restraints weight = 17350.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.119575 restraints weight = 9650.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.121965 restraints weight = 6525.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6991
moved from start:          0.4062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6569  Z= 0.131
  Angle     :  0.759  12.600   8919  Z= 0.377
  Chirality :  0.044   0.161   1048
  Planarity :  0.004   0.040   1121
  Dihedral  :  5.420  26.009    893
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.76 %
    Favored  : 89.24 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 26.13 %
    Favored  : 68.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.29), residues: 818
  helix: -0.18 (0.26), residues: 398
  sheet: -3.44 (0.51), residues: 94
  loop : -3.22 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 767 
 HIS   0.005   0.001   HIS B 721 
 PHE   0.031   0.002   PHE A 464 
 TYR   0.011   0.001   TYR A  32 
 ARG   0.002   0.000   ARG A 394 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03752 (  257)
  hydrogen bonds       : angle       4.62416 (  741)
  covalent geometry    : bond        0.00284 ( 6569)
  covalent geometry    : angle       0.75888 ( 8919)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 146
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 PHE cc_start: 0.8040 (t80) cc_final: 0.7700 (t80)
REVERT: A   61 PHE cc_start: 0.9122 (t80) cc_final: 0.8851 (t80)
REVERT: A   83 LYS cc_start: 0.8581 (tptm) cc_final: 0.8377 (tppp)
REVERT: A  151 GLN cc_start: 0.7691 (pm20) cc_final: 0.7090 (pm20)
REVERT: A  179 GLU cc_start: 0.8620 (mp0) cc_final: 0.8088 (mp0)
REVERT: A  235 VAL cc_start: 0.5976 (OUTLIER) cc_final: 0.5709 (p)
REVERT: B  149 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7403 (t80)
REVERT: B  195 LEU cc_start: 0.8558 (tp) cc_final: 0.8292 (tp)
REVERT: B  235 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6094 (mm-30)
REVERT: B  245 GLU cc_start: 0.7367 (tm-30) cc_final: 0.6619 (pt0)
REVERT: B  702 HIS cc_start: 0.7745 (OUTLIER) cc_final: 0.7217 (t-90)
REVERT: B  878 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.6966 (tp30)
REVERT: B  883 ARG cc_start: 0.6091 (tpt170) cc_final: 0.5454 (tpp-160)
REVERT: B  897 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6966 (mm-30)
  outliers start: 33
  outliers final: 23
  residues processed: 164
  average time/residue: 0.1873
  time to fit residues: 41.1692
Evaluate side-chains
  168 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 139
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  383 GLN
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  460 HIS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  149 PHE
Chi-restraints excluded: chain B residue  155 MET
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  235 GLU
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  702 HIS
Chi-restraints excluded: chain B residue  714 ILE
Chi-restraints excluded: chain B residue  734 VAL
Chi-restraints excluded: chain B residue  767 TRP
Chi-restraints excluded: chain B residue  772 LEU
Chi-restraints excluded: chain B residue  800 LEU
Chi-restraints excluded: chain B residue  842 THR
Chi-restraints excluded: chain B residue  878 GLU
Chi-restraints excluded: chain B residue  897 GLU
Chi-restraints excluded: chain B residue  912 HIS
Chi-restraints excluded: chain B residue  913 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 67 optimal weight:    0.0370
   chunk 4 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 12 optimal weight:    6.9990
   chunk 78 optimal weight:    1.9990
   chunk 2 optimal weight:   10.0000
   chunk 30 optimal weight:    0.5980
   chunk 10 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0770
   chunk 72 optimal weight:    7.9990
   overall best weight:    0.3616

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 865 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.143004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.117493 restraints weight = 17278.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.121058 restraints weight = 9592.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.123517 restraints weight = 6496.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.4094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6963
moved from start:          0.4234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6569  Z= 0.133
  Angle     :  0.775  12.512   8919  Z= 0.385
  Chirality :  0.045   0.164   1048
  Planarity :  0.004   0.043   1121
  Dihedral  :  5.348  25.186    893
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 14.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.66 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 27.19 %
    Favored  : 68.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.29), residues: 818
  helix: -0.08 (0.26), residues: 393
  sheet: -3.38 (0.52), residues: 92
  loop : -3.08 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 780 
 HIS   0.004   0.001   HIS B 721 
 PHE   0.021   0.002   PHE B 191 
 TYR   0.012   0.001   TYR A  32 
 ARG   0.008   0.001   ARG B 359 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03690 (  257)
  hydrogen bonds       : angle       4.60949 (  741)
  covalent geometry    : bond        0.00286 ( 6569)
  covalent geometry    : angle       0.77478 ( 8919)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 PHE cc_start: 0.8030 (t80) cc_final: 0.7765 (t80)
REVERT: A   61 PHE cc_start: 0.9121 (t80) cc_final: 0.8855 (t80)
REVERT: A  151 GLN cc_start: 0.7674 (pm20) cc_final: 0.7079 (pm20)
REVERT: A  179 GLU cc_start: 0.8618 (mp0) cc_final: 0.8260 (mp0)
REVERT: A  235 VAL cc_start: 0.5916 (OUTLIER) cc_final: 0.5667 (p)
REVERT: B  149 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7393 (t80)
REVERT: B  195 LEU cc_start: 0.8554 (tp) cc_final: 0.8325 (tp)
REVERT: B  203 ASP cc_start: 0.8854 (m-30) cc_final: 0.8377 (m-30)
REVERT: B  235 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6011 (mm-30)
REVERT: B  245 GLU cc_start: 0.7355 (tm-30) cc_final: 0.6602 (pt0)
REVERT: B  702 HIS cc_start: 0.7652 (OUTLIER) cc_final: 0.7199 (t-90)
REVERT: B  878 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.6915 (tp30)
REVERT: B  883 ARG cc_start: 0.6079 (tpt170) cc_final: 0.5376 (tpp-160)
REVERT: B  897 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6954 (mm-30)
  outliers start: 27
  outliers final: 19
  residues processed: 160
  average time/residue: 0.1941
  time to fit residues: 41.3905
Evaluate side-chains
  160 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 135
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  383 GLN
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  149 PHE
Chi-restraints excluded: chain B residue  155 MET
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  235 GLU
Chi-restraints excluded: chain B residue  702 HIS
Chi-restraints excluded: chain B residue  714 ILE
Chi-restraints excluded: chain B residue  734 VAL
Chi-restraints excluded: chain B residue  767 TRP
Chi-restraints excluded: chain B residue  772 LEU
Chi-restraints excluded: chain B residue  800 LEU
Chi-restraints excluded: chain B residue  842 THR
Chi-restraints excluded: chain B residue  878 GLU
Chi-restraints excluded: chain B residue  897 GLU
Chi-restraints excluded: chain B residue  912 HIS
Chi-restraints excluded: chain B residue  913 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 67 optimal weight:    0.0870
   chunk 54 optimal weight:    0.6980
   chunk 29 optimal weight:    0.4980
   chunk 3 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0050
   chunk 9 optimal weight:   10.0000
   chunk 77 optimal weight:    0.0770
   chunk 66 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 60 optimal weight:    4.9990
   overall best weight:    0.2530

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 865 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.144685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.119211 restraints weight = 17840.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.122846 restraints weight = 9888.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.125311 restraints weight = 6672.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6933
moved from start:          0.4478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6569  Z= 0.137
  Angle     :  0.788  11.536   8919  Z= 0.392
  Chirality :  0.045   0.168   1048
  Planarity :  0.004   0.040   1121
  Dihedral  :  5.265  24.849    893
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.66 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 28.10 %
    Favored  : 67.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.39 (0.29), residues: 818
  helix: -0.01 (0.26), residues: 392
  sheet: -3.30 (0.52), residues: 92
  loop : -3.03 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 780 
 HIS   0.004   0.001   HIS B 766 
 PHE   0.019   0.002   PHE B 191 
 TYR   0.020   0.001   TYR B 844 
 ARG   0.008   0.001   ARG B 359 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03687 (  257)
  hydrogen bonds       : angle       4.64415 (  741)
  covalent geometry    : bond        0.00293 ( 6569)
  covalent geometry    : angle       0.78821 ( 8919)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3090.80 seconds
wall clock time: 54 minutes 57.39 seconds (3297.39 seconds total)