Starting phenix.real_space_refine
on Tue Mar  3 15:06:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o2w_12700/03_2026/7o2w_12700.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o2w_12700/03_2026/7o2w_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_12700/03_2026/7o2w_12700.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o2w_12700/03_2026/7o2w_12700.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o2w_12700/03_2026/7o2w_12700.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o2w_12700/03_2026/7o2w_12700.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: {'ARG:plan': 4, 'GLU:plan': 7, 'GLN:plan1': 6, 'ASN:plan1': 4, 'ASP:plan': 5, 'PHE:plan': 1}
          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: {'ASN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 97
  Time building chain proxies: 1.52, per 1000 atoms: 0.24
  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: 0.70
  Conformation dependent library (CDL) restraints added in 261.1 milliseconds
  

  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: 0.14
  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: 0.88

  Time building geometry restraints manager: 0.89 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:             1.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.580
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.740
-------------------------------------------------------------------------------
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 : 28.66
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.012   0.001   ARG A 129 
 TYR   0.026   0.003   TYR B 157 
 PHE   0.028   0.003   PHE B 345 
 TRP   0.043   0.003   TRP B 767 
 HIS   0.009   0.002   HIS A 307 

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

*********************** 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  : 0.232 
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: 0.7252 (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: 0.0797
  time to fit residues: 15.2782
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  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:    0.6980
   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 281 GLN
A 322 HIS
B 162 GLN
** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.136772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.111502 restraints weight = 17446.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.114901 restraints weight = 9564.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.117165 restraints weight = 6525.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.118622 restraints weight = 5034.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.119539 restraints weight = 4224.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6569  Z= 0.183
  Angle     :  0.851   7.946   8919  Z= 0.442
  Chirality :  0.048   0.187   1048
  Planarity :  0.005   0.048   1121
  Dihedral  :  6.682  31.825    893
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 16.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.98 %
    Favored  : 88.02 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 13.60 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.38 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.20 (0.28), residues: 818
  helix: -0.69 (0.25), residues: 376
  sheet: -3.61 (0.55), residues: 73
  loop : -3.41 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 129 
 TYR   0.021   0.002   TYR A  32 
 PHE   0.022   0.002   PHE B 345 
 TRP   0.015   0.002   TRP B 767 
 HIS   0.009   0.001   HIS A 460 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 6569)
  covalent geometry    : angle       0.85055 ( 8919)
  hydrogen bonds       : bond        0.06406 (  257)
  hydrogen bonds       : angle       6.03512 (  741)

*********************** 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
  150 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 PHE cc_start: 0.7754 (t80) cc_final: 0.7491 (t80)
REVERT: A   61 PHE cc_start: 0.9066 (t80) cc_final: 0.8825 (t80)
REVERT: A   81 ASP cc_start: 0.7460 (m-30) cc_final: 0.7183 (m-30)
REVERT: A  151 GLN cc_start: 0.7728 (pm20) cc_final: 0.7149 (pm20)
REVERT: A  190 MET cc_start: 0.8971 (mpp) cc_final: 0.8291 (mpp)
REVERT: A  406 HIS cc_start: 0.7412 (m90) cc_final: 0.7173 (m90)
REVERT: B  201 ASP cc_start: 0.9286 (t70) cc_final: 0.8976 (t0)
REVERT: B  361 LEU cc_start: 0.9245 (mt) cc_final: 0.8991 (mt)
REVERT: B  861 TYR cc_start: 0.8483 (t80) cc_final: 0.8056 (t80)
REVERT: B  883 ARG cc_start: 0.5981 (tpt170) cc_final: 0.5562 (tpt-90)
REVERT: B  885 MET cc_start: 0.8823 (mpp) cc_final: 0.8571 (mpp)
  outliers start: 15
  outliers final: 7
  residues processed: 141
  average time/residue: 0.0673
  time to fit residues: 13.1141
Evaluate side-chains
  128 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 121
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
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 54 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0470
   chunk 48 optimal weight:    0.8980
   chunk 5 optimal weight:    7.9990
   chunk 34 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 75 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.6878

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.138503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.113097 restraints weight = 17322.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.116570 restraints weight = 9569.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.118925 restraints weight = 6499.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.120480 restraints weight = 4976.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.121355 restraints weight = 4148.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.4062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7000
moved from start:          0.2746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   6569  Z= 0.150
  Angle     :  0.755   7.242   8919  Z= 0.388
  Chirality :  0.045   0.207   1048
  Planarity :  0.004   0.044   1121
  Dihedral  :  6.164  29.880    893
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.25 %
    Favored  : 88.75 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 18.13 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.92 (0.28), residues: 818
  helix: -0.39 (0.25), residues: 377
  sheet: -3.58 (0.50), residues: 89
  loop : -3.27 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 802 
 TYR   0.017   0.001   TYR A  32 
 PHE   0.027   0.002   PHE B 117 
 TRP   0.012   0.001   TRP B 767 
 HIS   0.006   0.001   HIS A 460 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 6569)
  covalent geometry    : angle       0.75461 ( 8919)
  hydrogen bonds       : bond        0.04973 (  257)
  hydrogen bonds       : angle       5.29246 (  741)

*********************** 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
  172 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 142
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 PHE cc_start: 0.7749 (t80) cc_final: 0.7396 (t80)
REVERT: A   44 ILE cc_start: 0.7315 (mp) cc_final: 0.7080 (mm)
REVERT: A   61 PHE cc_start: 0.9114 (t80) cc_final: 0.8858 (t80)
REVERT: A   81 ASP cc_start: 0.7383 (m-30) cc_final: 0.7118 (m-30)
REVERT: A  151 GLN cc_start: 0.7761 (pm20) cc_final: 0.7179 (pm20)
REVERT: A  179 GLU cc_start: 0.8521 (mp0) cc_final: 0.8290 (mp0)
REVERT: A  464 PHE cc_start: 0.7863 (m-10) cc_final: 0.7617 (m-10)
REVERT: B  149 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7547 (t80)
REVERT: B  201 ASP cc_start: 0.9307 (t70) cc_final: 0.9052 (t0)
REVERT: B  235 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.5966 (mm-30)
REVERT: B  861 TYR cc_start: 0.8398 (t80) cc_final: 0.8123 (t80)
REVERT: B  883 ARG cc_start: 0.6103 (tpt170) cc_final: 0.5731 (tpt-90)
  outliers start: 30
  outliers final: 18
  residues processed: 152
  average time/residue: 0.0624
  time to fit residues: 13.3047
Evaluate side-chains
  151 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
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  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  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  349 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  912 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 68 optimal weight:    0.0050
   chunk 37 optimal weight:    2.9990
   chunk 70 optimal weight:    0.1980
   chunk 50 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.8396

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.138663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.113150 restraints weight = 17459.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.116475 restraints weight = 9851.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.118745 restraints weight = 6816.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.120250 restraints weight = 5305.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.121129 restraints weight = 4453.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7030
moved from start:          0.3064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6569  Z= 0.148
  Angle     :  0.762   9.026   8919  Z= 0.387
  Chirality :  0.045   0.178   1048
  Planarity :  0.004   0.041   1121
  Dihedral  :  5.946  28.335    893
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 13.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.86 %
    Favored  : 88.14 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 20.09 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.84 (0.28), residues: 818
  helix: -0.35 (0.25), residues: 383
  sheet: -3.53 (0.50), residues: 89
  loop : -3.24 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 129 
 TYR   0.015   0.001   TYR A  32 
 PHE   0.026   0.002   PHE B 117 
 TRP   0.011   0.001   TRP B 767 
 HIS   0.005   0.001   HIS B 721 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6569)
  covalent geometry    : angle       0.76216 ( 8919)
  hydrogen bonds       : bond        0.04543 (  257)
  hydrogen bonds       : angle       4.99258 (  741)

*********************** 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
  182 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 148
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 PHE cc_start: 0.7821 (t80) cc_final: 0.7418 (t80)
REVERT: A   44 ILE cc_start: 0.7399 (mp) cc_final: 0.7157 (mm)
REVERT: A   61 PHE cc_start: 0.9101 (t80) cc_final: 0.8858 (t80)
REVERT: A   81 ASP cc_start: 0.7323 (m-30) cc_final: 0.7049 (m-30)
REVERT: A  151 GLN cc_start: 0.7628 (pm20) cc_final: 0.7209 (pm20)
REVERT: A  179 GLU cc_start: 0.8515 (mp0) cc_final: 0.8249 (mp0)
REVERT: A  299 MET cc_start: 0.5671 (tmm) cc_final: 0.5425 (tpp)
REVERT: B  149 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7495 (t80)
REVERT: B  168 GLN cc_start: 0.8608 (tp-100) cc_final: 0.8125 (tp-100)
REVERT: B  201 ASP cc_start: 0.9311 (t70) cc_final: 0.9075 (t0)
REVERT: B  235 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.5990 (mm-30)
REVERT: B  897 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7019 (mm-30)
REVERT: B  900 ARG cc_start: 0.8506 (mtm180) cc_final: 0.8233 (mtm180)
  outliers start: 34
  outliers final: 20
  residues processed: 164
  average time/residue: 0.0681
  time to fit residues: 15.2938
Evaluate side-chains
  156 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
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  376 LEU
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  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  897 GLU
Chi-restraints excluded: chain B residue  912 HIS
Chi-restraints excluded: chain B residue  913 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 82 optimal weight:    8.9990
   chunk 46 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 78 optimal weight:    0.0980
   chunk 73 optimal weight:    0.5980
   chunk 54 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0770
   overall best weight:    0.9140

-------------------------------------------------------------------------------
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**
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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.139066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.113374 restraints weight = 17543.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.116818 restraints weight = 9884.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.119144 restraints weight = 6757.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.120535 restraints weight = 5212.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.121697 restraints weight = 4415.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.4069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7023
moved from start:          0.3272

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= 0.150
  Angle     :  0.771  12.108   8919  Z= 0.388
  Chirality :  0.045   0.163   1048
  Planarity :  0.004   0.040   1121
  Dihedral  :  5.794  27.411    893
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 15.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.98 %
    Favored  : 88.02 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 21.45 %
    Favored  : 72.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.82 (0.29), residues: 818
  helix: -0.35 (0.26), residues: 391
  sheet: -3.49 (0.51), residues: 89
  loop : -3.28 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 129 
 TYR   0.017   0.002   TYR B 844 
 PHE   0.017   0.002   PHE A 464 
 TRP   0.010   0.001   TRP B 767 
 HIS   0.005   0.001   HIS B 721 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6569)
  covalent geometry    : angle       0.77109 ( 8919)
  hydrogen bonds       : bond        0.04326 (  257)
  hydrogen bonds       : angle       4.95521 (  741)

*********************** 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
  181 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 141
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 PHE cc_start: 0.7874 (t80) cc_final: 0.7480 (t80)
REVERT: A   44 ILE cc_start: 0.7429 (mp) cc_final: 0.7191 (mm)
REVERT: A   61 PHE cc_start: 0.9095 (t80) cc_final: 0.8828 (t80)
REVERT: A   81 ASP cc_start: 0.7307 (m-30) cc_final: 0.7047 (m-30)
REVERT: A  151 GLN cc_start: 0.7680 (pm20) cc_final: 0.7242 (pm20)
REVERT: A  179 GLU cc_start: 0.8524 (mp0) cc_final: 0.8233 (mp0)
REVERT: A  235 VAL cc_start: 0.6091 (OUTLIER) cc_final: 0.5804 (p)
REVERT: A  299 MET cc_start: 0.5789 (tmm) cc_final: 0.5566 (tpp)
REVERT: B  149 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.7463 (t80)
REVERT: B  168 GLN cc_start: 0.8586 (tp-100) cc_final: 0.8084 (tp-100)
REVERT: B  235 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6004 (mm-30)
REVERT: B  878 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7057 (tp30)
REVERT: B  883 ARG cc_start: 0.6073 (tpt170) cc_final: 0.5124 (tpp-160)
REVERT: B  897 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6969 (mm-30)
REVERT: B  900 ARG cc_start: 0.8424 (mtm180) cc_final: 0.8085 (mtm180)
  outliers start: 40
  outliers final: 22
  residues processed: 163
  average time/residue: 0.0676
  time to fit residues: 15.1758
Evaluate side-chains
  156 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
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  235 VAL
Chi-restraints excluded: chain A residue  237 VAL
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  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 60 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   chunk 52 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0270
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.7440

-------------------------------------------------------------------------------
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 = 0.4340 r_free = 0.4340 target = 0.140111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.114527 restraints weight = 17452.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.118036 restraints weight = 9802.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.120393 restraints weight = 6687.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.121996 restraints weight = 5146.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.122937 restraints weight = 4283.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.4088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7003
moved from start:          0.3538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6569  Z= 0.145
  Angle     :  0.798  18.408   8919  Z= 0.396
  Chirality :  0.045   0.181   1048
  Planarity :  0.004   0.041   1121
  Dihedral  :  5.684  26.605    893
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 14.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.61 %
    Favored  : 88.39 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.84 (0.29), residues: 818
  helix: -0.36 (0.26), residues: 399
  sheet: -3.51 (0.50), residues: 93
  loop : -3.34 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 129 
 TYR   0.013   0.001   TYR A  32 
 PHE   0.016   0.002   PHE A 464 
 TRP   0.006   0.001   TRP B 767 
 HIS   0.006   0.001   HIS A 460 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 6569)
  covalent geometry    : angle       0.79778 ( 8919)
  hydrogen bonds       : bond        0.04139 (  257)
  hydrogen bonds       : angle       4.96385 (  741)

*********************** 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
  182 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 142
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 PHE cc_start: 0.7903 (t80) cc_final: 0.7520 (t80)
REVERT: A   44 ILE cc_start: 0.7435 (mp) cc_final: 0.7200 (mm)
REVERT: A   61 PHE cc_start: 0.9098 (t80) cc_final: 0.8837 (t80)
REVERT: A   77 SER cc_start: 0.4488 (OUTLIER) cc_final: 0.4199 (m)
REVERT: A  151 GLN cc_start: 0.7677 (pm20) cc_final: 0.7252 (pm20)
REVERT: A  179 GLU cc_start: 0.8539 (mp0) cc_final: 0.8181 (mp0)
REVERT: A  235 VAL cc_start: 0.5980 (OUTLIER) cc_final: 0.5718 (p)
REVERT: A  299 MET cc_start: 0.5794 (tmm) cc_final: 0.5590 (tpp)
REVERT: B  149 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.7472 (t80)
REVERT: B  235 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6082 (mm-30)
REVERT: B  878 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7103 (tp30)
REVERT: B  883 ARG cc_start: 0.5973 (tpt170) cc_final: 0.5151 (tpp-160)
REVERT: B  897 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6942 (mm-30)
  outliers start: 40
  outliers final: 24
  residues processed: 164
  average time/residue: 0.0705
  time to fit residues: 15.7858
Evaluate side-chains
  163 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 133
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
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  235 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  303 TYR
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  418 ASP
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  353 LEU
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  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 55 optimal weight:    9.9990
   chunk 43 optimal weight:    7.9990
   chunk 3 optimal weight:    0.0070
   chunk 0 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 74 optimal weight:    0.2980
   chunk 46 optimal weight:    9.9990
   chunk 78 optimal weight:    0.9980
   overall best weight:    0.6602

-------------------------------------------------------------------------------
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 = 0.4350 r_free = 0.4350 target = 0.140966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.115414 restraints weight = 17234.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.118910 restraints weight = 9675.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.121284 restraints weight = 6599.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.122679 restraints weight = 5069.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.123918 restraints weight = 4274.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.4103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6983
moved from start:          0.3697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6569  Z= 0.142
  Angle     :  0.791  16.371   8919  Z= 0.394
  Chirality :  0.045   0.162   1048
  Planarity :  0.004   0.040   1121
  Dihedral  :  5.561  26.271    893
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.76 %
    Favored  : 89.24 %
  Rotamer:
    Outliers :  6.50 %
    Allowed  : 23.72 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.87 (0.29), residues: 818
  helix: -0.37 (0.26), residues: 400
  sheet: -3.48 (0.50), residues: 93
  loop : -3.40 (0.31), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 359 
 TYR   0.012   0.001   TYR A  32 
 PHE   0.012   0.002   PHE A  30 
 TRP   0.006   0.001   TRP B 767 
 HIS   0.005   0.001   HIS B 766 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 6569)
  covalent geometry    : angle       0.79057 ( 8919)
  hydrogen bonds       : bond        0.04154 (  257)
  hydrogen bonds       : angle       4.88005 (  741)

*********************** 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
  183 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 140
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 PHE cc_start: 0.7929 (t80) cc_final: 0.7540 (t80)
REVERT: A   44 ILE cc_start: 0.7437 (mp) cc_final: 0.7198 (mm)
REVERT: A   61 PHE cc_start: 0.9086 (t80) cc_final: 0.8851 (t80)
REVERT: A  151 GLN cc_start: 0.7676 (pm20) cc_final: 0.7150 (pm20)
REVERT: A  179 GLU cc_start: 0.8619 (mp0) cc_final: 0.8164 (mp0)
REVERT: A  235 VAL cc_start: 0.5877 (OUTLIER) cc_final: 0.5623 (p)
REVERT: A  299 MET cc_start: 0.5841 (tmm) cc_final: 0.5597 (tpp)
REVERT: B  149 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.7440 (t80)
REVERT: B  235 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6088 (mm-30)
REVERT: B  348 ASP cc_start: 0.6457 (t70) cc_final: 0.6083 (m-30)
REVERT: B  861 TYR cc_start: 0.8202 (t80) cc_final: 0.7928 (t80)
REVERT: B  878 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7077 (tp30)
REVERT: B  897 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6984 (mm-30)
  outliers start: 43
  outliers final: 27
  residues processed: 164
  average time/residue: 0.0699
  time to fit residues: 15.7924
Evaluate side-chains
  162 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 130
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
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  176 LEU
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  376 LEU
Chi-restraints excluded: chain A residue  383 GLN
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  205 THR
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  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  909 LEU
Chi-restraints excluded: chain B residue  912 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 82 optimal weight:    7.9990
   chunk 3 optimal weight:    0.7980
   chunk 44 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0570
   chunk 12 optimal weight:    0.4980
   chunk 14 optimal weight:    0.3980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.7500

-------------------------------------------------------------------------------
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 = 0.4351 r_free = 0.4351 target = 0.140982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.115494 restraints weight = 17164.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.119047 restraints weight = 9579.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.121486 restraints weight = 6465.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.123107 restraints weight = 4928.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.124135 restraints weight = 4086.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.4107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6979
moved from start:          0.3880

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= 0.145
  Angle     :  0.804  16.603   8919  Z= 0.394
  Chirality :  0.045   0.168   1048
  Planarity :  0.004   0.040   1121
  Dihedral  :  5.499  26.728    893
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 14.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.25 %
    Favored  : 88.75 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 25.23 %
    Favored  : 69.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.78 (0.29), residues: 818
  helix: -0.30 (0.26), residues: 400
  sheet: -3.46 (0.50), residues: 93
  loop : -3.34 (0.32), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 802 
 TYR   0.012   0.001   TYR A  32 
 PHE   0.012   0.002   PHE A  30 
 TRP   0.006   0.001   TRP B 767 
 HIS   0.005   0.001   HIS B 766 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6569)
  covalent geometry    : angle       0.80447 ( 8919)
  hydrogen bonds       : bond        0.03997 (  257)
  hydrogen bonds       : angle       4.88315 (  741)

*********************** 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
  175 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 140
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 PHE cc_start: 0.7983 (t80) cc_final: 0.7618 (t80)
REVERT: A   44 ILE cc_start: 0.7436 (mp) cc_final: 0.7196 (mm)
REVERT: A   61 PHE cc_start: 0.9107 (t80) cc_final: 0.8853 (t80)
REVERT: A  151 GLN cc_start: 0.7649 (pm20) cc_final: 0.7097 (pm20)
REVERT: A  179 GLU cc_start: 0.8648 (mp0) cc_final: 0.8140 (mp0)
REVERT: A  235 VAL cc_start: 0.5993 (OUTLIER) cc_final: 0.5713 (p)
REVERT: A  299 MET cc_start: 0.5842 (tmm) cc_final: 0.5605 (tpp)
REVERT: B  149 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7403 (t80)
REVERT: B  235 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6083 (mm-30)
REVERT: B  861 TYR cc_start: 0.8180 (t80) cc_final: 0.7688 (t80)
REVERT: B  878 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7126 (tp30)
REVERT: B  883 ARG cc_start: 0.6071 (tpt170) cc_final: 0.4020 (tpt-90)
REVERT: B  897 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6939 (mm-30)
  outliers start: 35
  outliers final: 26
  residues processed: 157
  average time/residue: 0.0684
  time to fit residues: 14.6417
Evaluate side-chains
  167 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 136
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
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  176 LEU
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  376 LEU
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  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  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  909 LEU
Chi-restraints excluded: chain B residue  912 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0170
   chunk 67 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 57 optimal weight:    6.9990
   chunk 40 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.7220

-------------------------------------------------------------------------------
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 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 = 0.4354 r_free = 0.4354 target = 0.141166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.115757 restraints weight = 17530.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.119275 restraints weight = 9743.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.121681 restraints weight = 6602.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.123341 restraints weight = 5063.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.124507 restraints weight = 4185.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
moved from start:          0.4022

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     :  0.809  16.320   8919  Z= 0.395
  Chirality :  0.045   0.161   1048
  Planarity :  0.004   0.040   1121
  Dihedral  :  5.449  26.712    893
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 15.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.88 %
    Favored  : 89.12 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 25.38 %
    Favored  : 69.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.72 (0.29), residues: 818
  helix: -0.29 (0.26), residues: 401
  sheet: -3.39 (0.51), residues: 93
  loop : -3.27 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 129 
 TYR   0.014   0.001   TYR B 803 
 PHE   0.031   0.002   PHE A 464 
 TRP   0.006   0.001   TRP B 767 
 HIS   0.005   0.001   HIS B 766 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6569)
  covalent geometry    : angle       0.80905 ( 8919)
  hydrogen bonds       : bond        0.04012 (  257)
  hydrogen bonds       : angle       4.83697 (  741)

*********************** 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: 36
    poor density    : 143
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 PHE cc_start: 0.8054 (t80) cc_final: 0.7692 (t80)
REVERT: A   44 ILE cc_start: 0.7447 (mp) cc_final: 0.7210 (mm)
REVERT: A   61 PHE cc_start: 0.9109 (t80) cc_final: 0.8870 (t80)
REVERT: A  151 GLN cc_start: 0.7637 (pm20) cc_final: 0.7046 (pm20)
REVERT: A  179 GLU cc_start: 0.8629 (mp0) cc_final: 0.8119 (mp0)
REVERT: A  235 VAL cc_start: 0.5908 (OUTLIER) cc_final: 0.5620 (p)
REVERT: A  327 ASN cc_start: 0.7268 (m-40) cc_final: 0.6995 (m-40)
REVERT: B  149 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7342 (t80)
REVERT: B  195 LEU cc_start: 0.8544 (tp) cc_final: 0.8229 (tp)
REVERT: B  235 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6100 (mm-30)
REVERT: B  861 TYR cc_start: 0.8125 (t80) cc_final: 0.7626 (t80)
REVERT: B  878 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7035 (tp30)
REVERT: B  883 ARG cc_start: 0.6156 (tpt170) cc_final: 0.4176 (tpt-90)
REVERT: B  897 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6921 (mm-30)
  outliers start: 36
  outliers final: 29
  residues processed: 162
  average time/residue: 0.0692
  time to fit residues: 15.0013
Evaluate side-chains
  172 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 138
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
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  176 LEU
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  376 LEU
Chi-restraints excluded: chain A residue  383 GLN
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  205 THR
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  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  853 GLN
Chi-restraints excluded: chain B residue  878 GLU
Chi-restraints excluded: chain B residue  897 GLU
Chi-restraints excluded: chain B residue  909 LEU
Chi-restraints excluded: chain B residue  912 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0370
   chunk 82 optimal weight:    3.9990
   chunk 57 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   chunk 14 optimal weight:    8.9990
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.7458

-------------------------------------------------------------------------------
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**
** 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 = 0.4351 r_free = 0.4351 target = 0.140888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.115577 restraints weight = 17265.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.119117 restraints weight = 9622.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.121504 restraints weight = 6517.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.123178 restraints weight = 4984.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.124153 restraints weight = 4124.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6971
moved from start:          0.4096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6569  Z= 0.148
  Angle     :  0.841  16.330   8919  Z= 0.409
  Chirality :  0.045   0.162   1048
  Planarity :  0.004   0.040   1121
  Dihedral  :  5.482  25.978    893
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 15.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.12 %
    Favored  : 88.88 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 25.98 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.70 (0.29), residues: 818
  helix: -0.26 (0.26), residues: 400
  sheet: -3.40 (0.51), residues: 93
  loop : -3.28 (0.32), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 333 
 TYR   0.014   0.001   TYR B 803 
 PHE   0.013   0.002   PHE B 863 
 TRP   0.005   0.001   TRP B 780 
 HIS   0.005   0.001   HIS B 766 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6569)
  covalent geometry    : angle       0.84080 ( 8919)
  hydrogen bonds       : bond        0.03956 (  257)
  hydrogen bonds       : angle       4.84303 (  741)

********************** 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: 35
    poor density    : 137
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 PHE cc_start: 0.8050 (t80) cc_final: 0.7693 (t80)
REVERT: A   44 ILE cc_start: 0.7423 (mp) cc_final: 0.7177 (mm)
REVERT: A   61 PHE cc_start: 0.9113 (t80) cc_final: 0.8870 (t80)
REVERT: A  151 GLN cc_start: 0.7643 (pm20) cc_final: 0.7041 (pm20)
REVERT: A  179 GLU cc_start: 0.8670 (mp0) cc_final: 0.8320 (mp0)
REVERT: A  235 VAL cc_start: 0.5815 (OUTLIER) cc_final: 0.5540 (p)
REVERT: A  327 ASN cc_start: 0.7299 (m-40) cc_final: 0.7009 (m-40)
REVERT: B  149 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7388 (t80)
REVERT: B  195 LEU cc_start: 0.8543 (tp) cc_final: 0.8186 (tp)
REVERT: B  235 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6043 (mm-30)
REVERT: B  878 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.6979 (tp30)
REVERT: B  883 ARG cc_start: 0.6163 (tpt170) cc_final: 0.5413 (tpp-160)
REVERT: B  897 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6874 (mm-30)
  outliers start: 35
  outliers final: 29
  residues processed: 155
  average time/residue: 0.0733
  time to fit residues: 15.4138
Evaluate side-chains
  168 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 134
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
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  176 LEU
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  376 LEU
Chi-restraints excluded: chain A residue  383 GLN
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  205 THR
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  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  853 GLN
Chi-restraints excluded: chain B residue  878 GLU
Chi-restraints excluded: chain B residue  897 GLU
Chi-restraints excluded: chain B residue  909 LEU
Chi-restraints excluded: chain B residue  912 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 78 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 46 optimal weight:    8.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 317 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 = 0.4279 r_free = 0.4279 target = 0.135947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.110391 restraints weight = 17432.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.113674 restraints weight = 9877.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.115836 restraints weight = 6833.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.117370 restraints weight = 5344.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.118431 restraints weight = 4488.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.4018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.3892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   6569  Z= 0.222
  Angle     :  0.904  16.535   8919  Z= 0.448
  Chirality :  0.048   0.210   1048
  Planarity :  0.004   0.040   1121
  Dihedral  :  5.959  26.837    893
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 18.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.81 %
    Favored  : 86.19 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 26.59 %
    Favored  : 68.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.87 (0.29), residues: 818
  helix: -0.38 (0.26), residues: 391
  sheet: -3.49 (0.53), residues: 82
  loop : -3.35 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 206 
 TYR   0.015   0.002   TYR B 725 
 PHE   0.020   0.002   PHE B 345 
 TRP   0.012   0.002   TRP B 780 
 HIS   0.008   0.001   HIS A 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 ( 6569)
  covalent geometry    : angle       0.90369 ( 8919)
  hydrogen bonds       : bond        0.04369 (  257)
  hydrogen bonds       : angle       5.13307 (  741)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1426.14 seconds
wall clock time: 25 minutes 13.24 seconds (1513.24 seconds total)