Starting phenix.real_space_refine
on Thu Jul 31 15:36:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g5k_29747/07_2025/8g5k_29747.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g5k_29747/07_2025/8g5k_29747.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g5k_29747/07_2025/8g5k_29747.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g5k_29747/07_2025/8g5k_29747.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g5k_29747/07_2025/8g5k_29747.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g5k_29747/07_2025/8g5k_29747.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.029
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: 5
    Type Number    sf(0)   Gaussians
     P      37      5.49       5
     S      78      5.16       5
     C    8572      2.51       5
     N    2391      2.21       5
     O    2551      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13629
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 905, 7079
          Classifications: {'peptide': 905}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 60, 'TRANS': 844}
          Chain breaks: 5
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 136
          Unresolved non-hydrogen angles: 170
          Unresolved non-hydrogen dihedrals: 118
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 103
    Chain: "B"
      Number of atoms: 2934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 368, 2934
          Classifications: {'peptide': 368}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 15, 'TRANS': 352}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 35
    Chain: "C"
      Number of atoms: 2855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 364, 2855
          Classifications: {'peptide': 364}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 18, 'TRANS': 345}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 80
          Unresolved non-hydrogen angles: 100
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 48
    Chain: "P"
      Number of atoms: 394
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 18, 373
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
      Conformer: "B"
        Number of residues, atoms: 18, 373
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
          bond proxies already assigned to first conformer: 395
    Chain: "T"
      Number of atoms: 367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 367
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" P  A DA P  27 " occ=0.50
      ... (40 atoms not shown)
      pdb=" C4 B DA P  27 " occ=0.50
  Time building chain proxies: 8.87, per 1000 atoms: 0.65
  Number of scatterers: 13629
  At special positions: 0
  Unit cell: (91.686, 101.598, 139.594, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      78     16.00
     P      37     15.00
     O    2551      8.00
     N    2391      7.00
     C    8572      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: 3.35
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3046

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 9 sheets defined
      34.5% alpha, 10.1% beta
      17 base pairs and 29 stacking pairs defined.
    Time for finding SS restraints: 4.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 99 through 109
      removed outlier: 4.096A  pdb=" N   LYS A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 146
      removed outlier: 3.773A  pdb=" N   GLN A 146 " --> pdb=" O   LEU A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 160
    Processing helix  chain 'A' and resid 223 through 227
      removed outlier: 4.408A  pdb=" N   GLN A 226 " --> pdb=" O   TRP A 223 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ARG A 227 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 223 through 227'
    Processing helix  chain 'A' and resid 270 through 276
    Processing helix  chain 'A' and resid 294 through 301
    Processing helix  chain 'A' and resid 305 through 315
    Processing helix  chain 'A' and resid 345 through 351
      removed outlier: 3.649A  pdb=" N   ASP A 349 " --> pdb=" O   TRP A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 364
      removed outlier: 3.694A  pdb=" N   LEU A 362 " --> pdb=" O   GLU A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 380
    Processing helix  chain 'A' and resid 381 through 387
    Processing helix  chain 'A' and resid 388 through 418
      removed outlier: 3.703A  pdb=" N   LEU A 392 " --> pdb=" O   ASN A 388 " (cutoff:3.500A)
      Proline residue:  A 412  - end of helix
    Processing helix  chain 'A' and resid 420 through 432
      removed outlier: 4.135A  pdb=" N   LEU A 424 " --> pdb=" O   HIS A 420 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   VAL A 432 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 472
    Processing helix  chain 'A' and resid 542 through 552
    Processing helix  chain 'A' and resid 570 through 576
    Processing helix  chain 'A' and resid 793 through 809
      removed outlier: 4.699A  pdb=" N   PHE A 800 " --> pdb=" O   LYS A 796 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   TRP A 801 " --> pdb=" O   MET A 797 " (cutoff:3.500A)
      removed outlier: 5.766A  pdb=" N   LYS A 806 " --> pdb=" O   ARG A 802 " (cutoff:3.500A)
      removed outlier: 5.784A  pdb=" N   ARG A 807 " --> pdb=" O   ASN A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 904
    Processing helix  chain 'A' and resid 914 through 919
    Processing helix  chain 'A' and resid 933 through 940
    Processing helix  chain 'A' and resid 945 through 955
    Processing helix  chain 'A' and resid 958 through 968
      removed outlier: 3.667A  pdb=" N   GLN A 968 " --> pdb=" O   ARG A 964 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 973 through 980
    Processing helix  chain 'A' and resid 982 through 989
      removed outlier: 3.959A  pdb=" N   TYR A 986 " --> pdb=" O   ALA A 982 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1058 through 1067
    Processing helix  chain 'A' and resid 1093 through 1115
      removed outlier: 3.921A  pdb=" N   VAL A1097 " --> pdb=" O   MET A1093 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ALA A1115 " --> pdb=" O   LEU A1111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1169
    Processing helix  chain 'B' and resid 69 through 77
    Processing helix  chain 'B' and resid 100 through 105
      removed outlier: 4.184A  pdb=" N   GLU B 105 " --> pdb=" O   PRO B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 119
    Processing helix  chain 'B' and resid 186 through 192
    Processing helix  chain 'B' and resid 192 through 197
      removed outlier: 3.564A  pdb=" N   LEU B 197 " --> pdb=" O   TYR B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 265
      removed outlier: 3.760A  pdb=" N   ASP B 253 " --> pdb=" O   ASN B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 271
      No H-bonds generated for 'chain 'B' and resid 269 through 271'
    Processing helix  chain 'B' and resid 281 through 283
      No H-bonds generated for 'chain 'B' and resid 281 through 283'
    Processing helix  chain 'B' and resid 308 through 315
    Processing helix  chain 'B' and resid 319 through 323
      removed outlier: 3.507A  pdb=" N   HIS B 323 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 353
    Processing helix  chain 'B' and resid 394 through 407
      removed outlier: 3.881A  pdb=" N   VAL B 398 " --> pdb=" O   GLU B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 424 through 435
    Processing helix  chain 'B' and resid 445 through 450
      removed outlier: 3.618A  pdb=" N   GLU B 449 " --> pdb=" O   GLU B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 470 through 485
    Processing helix  chain 'C' and resid 100 through 120
      removed outlier: 4.120A  pdb=" N   SER C 117 " --> pdb=" O   GLU C 113 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   VAL C 118 " --> pdb=" O   TRP C 114 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 185 through 192
      removed outlier: 3.959A  pdb=" N   ALA C 189 " --> pdb=" O   LEU C 185 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 192 through 200
      removed outlier: 3.695A  pdb=" N   VAL C 200 " --> pdb=" O   CYS C 196 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 247 through 266
      removed outlier: 4.088A  pdb=" N   PHE C 266 " --> pdb=" O   TRP C 262 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 308 through 315
    Processing helix  chain 'C' and resid 345 through 350
    Processing helix  chain 'C' and resid 396 through 401
    Processing helix  chain 'C' and resid 402 through 406
    Processing helix  chain 'C' and resid 415 through 419
    Processing helix  chain 'C' and resid 427 through 435
      removed outlier: 3.808A  pdb=" N   ASP C 433 " --> pdb=" O   TYR C 429 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLU C 434 " --> pdb=" O   SER C 430 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 479 through 485
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 215
      removed outlier: 3.769A  pdb=" N   VAL A 213 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ASP A 198 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   LEU A 195 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 436
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1130 through 1132
    Processing sheet with id=AA4, first strand: chain 'B' and resid 126 through 127
      removed outlier: 6.600A  pdb=" N   PHE B 126 " --> pdb=" O   ALA B 209 " (cutoff:3.500A)
      removed outlier: 9.114A  pdb=" N   ILE B 211 " --> pdb=" O   PHE B 126 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   ILE B 300 " --> pdb=" O   ASP B 341 " (cutoff:3.500A)
      removed outlier: 5.632A  pdb=" N   LEU B 299 " --> pdb=" O   TYR B 291 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   TYR B 291 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLU B 301 " --> pdb=" O   LEU B 289 " (cutoff:3.500A)
      removed outlier: 4.890A  pdb=" N   LYS B 285 " --> pdb=" O   ASN B 305 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 324 through 326
    Processing sheet with id=AA6, first strand: chain 'B' and resid 413 through 415
      removed outlier: 7.076A  pdb=" N   VAL B 383 " --> pdb=" O   TRP B 414 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   ALA B 384 " --> pdb=" O   VAL B 441 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   VAL B 443 " --> pdb=" O   ALA B 384 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   ASP B 386 " --> pdb=" O   VAL B 443 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 125 through 127
      removed outlier: 6.308A  pdb=" N   PHE C 126 " --> pdb=" O   ALA C 209 " (cutoff:3.500A)
      removed outlier: 8.591A  pdb=" N   ILE C 211 " --> pdb=" O   PHE C 126 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 125 through 127
      removed outlier: 6.308A  pdb=" N   PHE C 126 " --> pdb=" O   ALA C 209 " (cutoff:3.500A)
      removed outlier: 8.591A  pdb=" N   ILE C 211 " --> pdb=" O   PHE C 126 " (cutoff:3.500A)
      removed outlier: 5.953A  pdb=" N   ILE C 300 " --> pdb=" O   ASP C 341 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   LYS C 297 " --> pdb=" O   PHE C 293 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   PHE C 293 " --> pdb=" O   LYS C 297 " (cutoff:3.500A)
      removed outlier: 5.635A  pdb=" N   LEU C 299 " --> pdb=" O   TYR C 291 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   TYR C 291 " --> pdb=" O   LEU C 299 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLU C 301 " --> pdb=" O   LEU C 289 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 325 through 326

    422 hydrogen bonds defined for protein.
    1218 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      46 hydrogen bonds
      92 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      30 stacking parallelities
  Total time for adding SS restraints: 4.45

  Time building geometry restraints manager: 3.99 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: 4176
        1.34 -     1.46: 2886
        1.46 -     1.58: 6790
        1.58 -     1.70: 72
        1.70 -     1.82: 123
  Bond restraints: 14047
  Sorted by residual:
  bond pdb=" CG  PRO A 241 "
       pdb=" CD  PRO A 241 "
    ideal  model  delta    sigma   weight residual
    1.503  1.360  0.143 3.40e-02 8.65e+02 1.77e+01
  bond pdb=" N   VAL A 353 "
       pdb=" CA  VAL A 353 "
    ideal  model  delta    sigma   weight residual
    1.459  1.499 -0.040 1.29e-02 6.01e+03 9.61e+00
  bond pdb=" N   GLU B 282 "
       pdb=" CA  GLU B 282 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.29e-02 6.01e+03 7.74e+00
  bond pdb=" N   ILE A 313 "
       pdb=" CA  ILE A 313 "
    ideal  model  delta    sigma   weight residual
    1.462  1.494 -0.032 1.18e-02 7.18e+03 7.39e+00
  bond pdb=" C3'  DA P  10 "
       pdb=" O3'  DA P  10 "
    ideal  model  delta    sigma   weight residual
    1.422  1.499 -0.077 3.00e-02 1.11e+03 6.55e+00
  ... (remaining 14042 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.20: 19095
        5.20 -    10.40: 111
       10.40 -    15.60: 14
       15.60 -    20.80: 2
       20.80 -    26.00: 2
  Bond angle restraints: 19224
  Sorted by residual:
  angle pdb=" C3'  DG P  24 "
        pdb=" O3'  DG P  24 "
        pdb=" P    DC P  25 "
      ideal   model   delta    sigma   weight residual
     120.20  106.52   13.68 1.50e+00 4.44e-01 8.32e+01
  angle pdb=" O3'  DA P  10 "
        pdb=" P    DG P  11 "
        pdb=" OP2  DG P  11 "
      ideal   model   delta    sigma   weight residual
     108.00   82.00   26.00 3.00e+00 1.11e-01 7.51e+01
  angle pdb=" N   PRO A 241 "
        pdb=" CD  PRO A 241 "
        pdb=" CG  PRO A 241 "
      ideal   model   delta    sigma   weight residual
     103.20   90.30   12.90 1.50e+00 4.44e-01 7.40e+01
  angle pdb=" N   PRO A 241 "
        pdb=" CA  PRO A 241 "
        pdb=" CB  PRO A 241 "
      ideal   model   delta    sigma   weight residual
     103.25   94.97    8.28 1.05e+00 9.07e-01 6.22e+01
  angle pdb=" O3'  DA P  10 "
        pdb=" P    DG P  11 "
        pdb=" OP1  DG P  11 "
      ideal   model   delta    sigma   weight residual
     108.00   84.73   23.27 3.00e+00 1.11e-01 6.01e+01
  ... (remaining 19219 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.44: 8017
       35.44 -    70.88: 209
       70.88 -   106.32: 12
      106.32 -   141.76: 2
      141.76 -   177.20: 3
  Dihedral angle restraints: 8243
    sinusoidal: 3527
      harmonic: 4716
  Sorted by residual:
  dihedral pdb=" CD  ARG A 309 "
           pdb=" NE  ARG A 309 "
           pdb=" CZ  ARG A 309 "
           pdb=" NH1 ARG A 309 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   74.98  -74.98     1      1.00e+01 1.00e-02 7.11e+01
  dihedral pdb=" CA  LEU B 106 "
           pdb=" C   LEU B 106 "
           pdb=" N   ARG B 107 "
           pdb=" CA  ARG B 107 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.04   25.96     0      5.00e+00 4.00e-02 2.70e+01
  dihedral pdb=" CA  PHE B  78 "
           pdb=" C   PHE B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.14   21.86     0      5.00e+00 4.00e-02 1.91e+01
  ... (remaining 8240 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.416: 2091
       0.416 -    0.831: 5
       0.831 -    1.247: 0
       1.247 -    1.662: 0
       1.662 -    2.078: 1
  Chirality restraints: 2097
  Sorted by residual:
  chirality pdb=" P    DG P  11 "
            pdb=" OP1  DG P  11 "
            pdb=" OP2  DG P  11 "
            pdb=" O5'  DG P  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35    0.27    2.08 2.00e-01 2.50e+01 1.08e+02
  chirality pdb=" P    DG T   4 "
            pdb=" OP1  DG T   4 "
            pdb=" OP2  DG T   4 "
            pdb=" O5'  DG T   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35    2.98   -0.64 2.00e-01 2.50e+01 1.02e+01
  chirality pdb=" P    DG P  24 "
            pdb=" OP1  DG P  24 "
            pdb=" OP2  DG P  24 "
            pdb=" O5'  DG P  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.82   -0.48 2.00e-01 2.50e+01 5.73e+00
  ... (remaining 2094 not shown)

  Planarity restraints: 2340
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 309 "   -1.061 9.50e-02 1.11e+02   4.76e-01 1.36e+02
        pdb=" NE  ARG A 309 "    0.064 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 309 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 309 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 309 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C 315 "    0.055 5.00e-02 4.00e+02   8.42e-02 1.13e+01
        pdb=" N   PRO C 316 "   -0.146 5.00e-02 4.00e+02
        pdb=" CA  PRO C 316 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO C 316 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 782 "   -0.051 5.00e-02 4.00e+02   7.40e-02 8.76e+00
        pdb=" N   PRO A 783 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO A 783 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 783 "   -0.041 5.00e-02 4.00e+02
  ... (remaining 2337 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1523
        2.76 -     3.29: 13100
        3.29 -     3.83: 22253
        3.83 -     4.36: 25644
        4.36 -     4.90: 43282
  Nonbonded interactions: 105802
  Sorted by model distance:
  nonbonded pdb=" O   GLU C 113 "
            pdb=" OG1 THR C 116 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OG1 THR A 885 "
            pdb=" O   ASP A1186 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OG1 THR A 586 "
            pdb=" OG  SER A 590 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OG  SER B 457 "
            pdb=" O   THR B 460 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   PRO C 380 "
            pdb=" OG  SER C 412 "
     model   vdw
     2.313 3.040
  ... (remaining 105797 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
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 68 through 73 or (resid 74 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 75 through 77 or (resid 78 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 79 through 83 or (resid 84 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 85 through 219 or ( \ 
resid 220 through 221 and (name N or name CA or name C or name O or name CB )) o \ 
r resid 228 through 327 or (resid 328 and (name N or name CA or name C or name O \ 
 or name CB )) or resid 329 through 353 or (resid 354 and (name N or name CA or  \ 
name C or name O or name CB )) or resid 355 through 357 or resid 372 or (resid 3 \ 
73 and (name N or name CA or name C or name O or name CB )) or resid 374 through \ 
 384 or (resid 385 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 386 through 388 or (resid 389 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 390 through 428 or (resid 429 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 430 through 433 or (resid 434 through 435 a \ 
nd (name N or name CA or name C or name O or name CB )) or resid 436 through 444 \ 
 or (resid 445 and (name N or name CA or name C or name O or name CB )) or resid \ 
 446 through 454 or (resid 455 and (name N or name CA or name C or name O or nam \ 
e CB )) or resid 456 through 485))
  selection = (chain 'C' and (resid 68 through 122 or (resid 123 through 124 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 125 or (resid 126 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 127 through 133 or resid 17 \ 
9 or (resid 180 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 181 through 200 or (resid 201 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 202 through 221 or (resid 228 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 229 through 245 or (resid 246 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 247 through 485))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             2.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.620
  Check model and map are aligned:         0.130
  Set scattering table:                    0.120
  Process input model:                     36.500
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5598
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      :  0.005   0.143  14047  Z= 0.242
  Angle     :  1.073  25.995  19224  Z= 0.550
  Chirality :  0.075   2.078   2097
  Planarity :  0.012   0.476   2340
  Dihedral  : 15.614 177.202   5197
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.63 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  1.03 %
    Favored  : 98.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.20), residues: 1611
  helix: -0.02 (0.22), residues: 545
  sheet: -0.32 (0.37), residues: 177
  loop : -2.18 (0.19), residues: 889

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 607 
 HIS   0.011   0.001   HIS C 309 
 PHE   0.030   0.002   PHE A 197 
 TYR   0.027   0.001   TYR C 417 
 ARG   0.007   0.000   ARG B 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13107 (  462)
  hydrogen bonds       : angle       5.86470 ( 1310)
  covalent geometry    : bond        0.00468 (14047)
  covalent geometry    : angle       1.07339 (19224)

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

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

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 263
  time to evaluate  : 1.356 
Fit side-chains
REVERT: A  207 THR cc_start: 0.7723 (p) cc_final: 0.7482 (p)
REVERT: A  416 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6380 (tp30)
REVERT: A  544 MET cc_start: 0.6746 (mmm) cc_final: 0.6337 (mmm)
REVERT: A 1097 VAL cc_start: 0.6574 (m) cc_final: 0.6254 (p)
REVERT: A 1102 GLN cc_start: 0.7216 (mt0) cc_final: 0.6886 (mt0)
REVERT: A 1156 THR cc_start: 0.7953 (m) cc_final: 0.7272 (p)
REVERT: B  458 ARG cc_start: 0.8022 (ttp-170) cc_final: 0.7389 (ttp-170)
REVERT: C  300 ILE cc_start: 0.8106 (mm) cc_final: 0.7787 (mt)
  outliers start: 4
  outliers final: 0
  residues processed: 266
  average time/residue: 1.1699
  time to fit residues: 342.4159
Evaluate side-chains
  220 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 1.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 138 optimal weight:    1.9990
   chunk 124 optimal weight:    0.3980
   chunk 68 optimal weight:    4.9990
   chunk 42 optimal weight:    0.2980
   chunk 83 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0370
   chunk 128 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 95 optimal weight:    0.6980
   chunk 148 optimal weight:    2.9990
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
A 106 HIS
A 360 HIS
** A 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 409 GLN
** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 472 GLN
A 550 GLN
A 906 HIS
A 932 HIS
A 968 GLN
A 970 ASN
** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 292 ASN
B 323 HIS
B 404 ASN
C 133 HIS
C 422 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.213439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.190986 restraints weight = 20034.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.4354 rms_B_bonded: 2.23
r_work: 0.4257 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.4257
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4261
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4261 r_free = 0.4261    target_work(ls_wunit_k1) = 0.182         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4261 r_free = 0.4261    target_work(ls_wunit_k1) = 0.182         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4261
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6150
moved from start:          0.1565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14047  Z= 0.141
  Angle     :  0.735  26.348  19224  Z= 0.350
  Chirality :  0.061   1.988   2097
  Planarity :  0.005   0.064   2340
  Dihedral  : 16.775 177.071   2149
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.57 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  :  9.68 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.20), residues: 1611
  helix:  0.57 (0.23), residues: 521
  sheet: -0.17 (0.37), residues: 171
  loop : -2.00 (0.19), residues: 919

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 607 
 HIS   0.006   0.001   HIS C 133 
 PHE   0.023   0.002   PHE A 749 
 TYR   0.023   0.001   TYR B 206 
 ARG   0.006   0.001   ARG C 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03827 (  462)
  hydrogen bonds       : angle       4.59627 ( 1310)
  covalent geometry    : bond        0.00311 (14047)
  covalent geometry    : angle       0.73532 (19224)

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

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

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 235
  time to evaluate  : 1.498 
Fit side-chains
REVERT: A  100 VAL cc_start: 0.7337 (OUTLIER) cc_final: 0.7124 (m)
REVERT: A  220 TRP cc_start: 0.5137 (m100) cc_final: 0.4598 (m100)
REVERT: A  434 TYR cc_start: 0.7554 (t80) cc_final: 0.7051 (t80)
REVERT: A  465 ASP cc_start: 0.6906 (m-30) cc_final: 0.6678 (m-30)
REVERT: A  544 MET cc_start: 0.6883 (mmm) cc_final: 0.6625 (mmm)
REVERT: A  953 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.6123 (mtm110)
REVERT: A 1057 MET cc_start: 0.3975 (mmm) cc_final: 0.1783 (ptm)
REVERT: A 1107 ASP cc_start: 0.6399 (m-30) cc_final: 0.6154 (m-30)
REVERT: B  256 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7245 (tp)
REVERT: B  404 ASN cc_start: 0.7487 (m-40) cc_final: 0.7252 (m-40)
REVERT: B  458 ARG cc_start: 0.7966 (ttp-170) cc_final: 0.7761 (ttp-170)
REVERT: C  300 ILE cc_start: 0.8241 (mm) cc_final: 0.7967 (mt)
  outliers start: 33
  outliers final: 9
  residues processed: 245
  average time/residue: 1.2088
  time to fit residues: 326.1192
Evaluate side-chains
  228 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 216
  time to evaluate  : 1.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  873 GLU
Chi-restraints excluded: chain A residue  953 ARG
Chi-restraints excluded: chain A residue 1104 SER
Chi-restraints excluded: chain A residue 1141 VAL
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain B residue  337 SER
Chi-restraints excluded: chain C residue  411 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 157 optimal weight:    0.9990
   chunk 95 optimal weight:    0.2980
   chunk 73 optimal weight:    1.9990
   chunk 117 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 141 optimal weight:    1.9990
   chunk 149 optimal weight:    4.9990
   chunk 109 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0170
   chunk 81 optimal weight:    0.6980
   chunk 121 optimal weight:    0.9990
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
A 298 HIS
A 404 HIS
** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 971 HIS
** B  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 375 HIS
C 133 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.208129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.184940 restraints weight = 20062.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.4287 rms_B_bonded: 2.30
r_work: 0.4186 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.4186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4191
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4191 r_free = 0.4191    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4191 r_free = 0.4191    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4191
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6294
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14047  Z= 0.149
  Angle     :  0.714  25.926  19224  Z= 0.343
  Chirality :  0.062   2.000   2097
  Planarity :  0.005   0.049   2340
  Dihedral  : 16.719 177.781   2149
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  9.12 %
    Favored  : 90.81 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 12.55 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.21), residues: 1611
  helix:  0.55 (0.23), residues: 533
  sheet: -0.10 (0.36), residues: 189
  loop : -1.97 (0.20), residues: 889

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 607 
 HIS   0.009   0.001   HIS A 805 
 PHE   0.026   0.002   PHE A 749 
 TYR   0.026   0.001   TYR B 193 
 ARG   0.008   0.001   ARG A 866 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03655 (  462)
  hydrogen bonds       : angle       4.47314 ( 1310)
  covalent geometry    : bond        0.00330 (14047)
  covalent geometry    : angle       0.71370 (19224)

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

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

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 239
  time to evaluate  : 1.483 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7820 (mmt-90)
REVERT: A  297 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.6805 (mtm)
REVERT: A  416 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6857 (tp30)
REVERT: A  465 ASP cc_start: 0.6930 (m-30) cc_final: 0.6664 (m-30)
REVERT: A  486 TRP cc_start: 0.7905 (p-90) cc_final: 0.7638 (p-90)
REVERT: A  544 MET cc_start: 0.6940 (mmm) cc_final: 0.6626 (mmm)
REVERT: A  803 ASN cc_start: 0.7565 (t0) cc_final: 0.7311 (t0)
REVERT: A  953 ARG cc_start: 0.6495 (OUTLIER) cc_final: 0.6137 (mtm110)
REVERT: A  969 PHE cc_start: 0.7481 (m-10) cc_final: 0.7207 (m-10)
REVERT: B  186 LEU cc_start: 0.7694 (mp) cc_final: 0.7493 (mp)
REVERT: B  260 LEU cc_start: 0.7636 (tp) cc_final: 0.7363 (mt)
REVERT: B  285 LYS cc_start: 0.6984 (mmmt) cc_final: 0.6590 (tptp)
REVERT: B  404 ASN cc_start: 0.7731 (m-40) cc_final: 0.7495 (m110)
REVERT: B  442 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7601 (tp)
REVERT: C  300 ILE cc_start: 0.8337 (mm) cc_final: 0.8100 (mt)
REVERT: C  346 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6277 (mtp)
REVERT: C  462 MET cc_start: 0.3956 (pp-130) cc_final: 0.3292 (pp-130)
  outliers start: 43
  outliers final: 13
  residues processed: 256
  average time/residue: 1.1688
  time to fit residues: 329.7004
Evaluate side-chains
  249 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 231
  time to evaluate  : 1.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 ARG
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  404 HIS
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  491 ASP
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  953 ARG
Chi-restraints excluded: chain A residue 1104 SER
Chi-restraints excluded: chain A residue 1141 VAL
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  442 LEU
Chi-restraints excluded: chain C residue  314 MET
Chi-restraints excluded: chain C residue  346 MET
Chi-restraints excluded: chain C residue  411 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 86 optimal weight:    2.9990
   chunk 158 optimal weight:    9.9990
   chunk 22 optimal weight:    4.9990
   chunk 142 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 151 optimal weight:    0.0980
   chunk 91 optimal weight:    3.9990
   chunk 137 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 911 HIS
** B  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.200871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.175507 restraints weight = 28112.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.4165 rms_B_bonded: 2.87
r_work: 0.4045 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4050
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4050 r_free = 0.4050    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4050 r_free = 0.4050    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4050
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6556
moved from start:          0.3311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074  14047  Z= 0.234
  Angle     :  0.788  26.013  19224  Z= 0.386
  Chirality :  0.064   1.995   2097
  Planarity :  0.005   0.049   2340
  Dihedral  : 16.920 177.737   2149
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 10.24 %
    Favored  : 89.63 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 14.97 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.20), residues: 1611
  helix:  0.08 (0.22), residues: 541
  sheet: -0.13 (0.37), residues: 181
  loop : -2.02 (0.20), residues: 889

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 607 
 HIS   0.030   0.002   HIS A 404 
 PHE   0.024   0.002   PHE A 749 
 TYR   0.030   0.002   TYR B 206 
 ARG   0.008   0.001   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04380 (  462)
  hydrogen bonds       : angle       4.71232 ( 1310)
  covalent geometry    : bond        0.00531 (14047)
  covalent geometry    : angle       0.78842 (19224)

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

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

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 246
  time to evaluate  : 1.418 
Fit side-chains
REVERT: A  141 LEU cc_start: 0.7546 (mm) cc_final: 0.7322 (mp)
REVERT: A  465 ASP cc_start: 0.6888 (m-30) cc_final: 0.6674 (m-30)
REVERT: A  486 TRP cc_start: 0.8178 (p-90) cc_final: 0.7844 (p-90)
REVERT: A  544 MET cc_start: 0.6965 (mmm) cc_final: 0.6613 (mmm)
REVERT: A  803 ASN cc_start: 0.7590 (t0) cc_final: 0.7360 (t0)
REVERT: A  898 ILE cc_start: 0.7562 (mm) cc_final: 0.7327 (mm)
REVERT: A  953 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.6234 (mtm110)
REVERT: A 1057 MET cc_start: 0.4144 (mmm) cc_final: 0.3940 (mmp)
REVERT: A 1102 GLN cc_start: 0.7854 (mt0) cc_final: 0.7579 (mt0)
REVERT: A 1111 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8219 (mp)
REVERT: B  132 HIS cc_start: 0.6020 (OUTLIER) cc_final: 0.4292 (t-170)
REVERT: B  256 LEU cc_start: 0.7779 (tm) cc_final: 0.7520 (tp)
REVERT: B  285 LYS cc_start: 0.7335 (mmmt) cc_final: 0.5696 (mmmm)
REVERT: B  404 ASN cc_start: 0.7963 (m-40) cc_final: 0.7716 (m110)
REVERT: C  300 ILE cc_start: 0.8454 (mm) cc_final: 0.8211 (mt)
REVERT: C  346 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.6610 (mtp)
REVERT: C  349 TYR cc_start: 0.5721 (m-10) cc_final: 0.5218 (m-10)
REVERT: C  382 LYS cc_start: 0.5526 (OUTLIER) cc_final: 0.5099 (mppt)
REVERT: C  462 MET cc_start: 0.4499 (pp-130) cc_final: 0.4242 (pp-130)
  outliers start: 43
  outliers final: 19
  residues processed: 262
  average time/residue: 1.1574
  time to fit residues: 333.6472
Evaluate side-chains
  261 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 237
  time to evaluate  : 1.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 MET
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  491 ASP
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  953 ARG
Chi-restraints excluded: chain A residue 1104 SER
Chi-restraints excluded: chain A residue 1111 LEU
Chi-restraints excluded: chain A residue 1141 VAL
Chi-restraints excluded: chain A residue 1164 PHE
Chi-restraints excluded: chain B residue  132 HIS
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  331 VAL
Chi-restraints excluded: chain B residue  337 SER
Chi-restraints excluded: chain B residue  431 LYS
Chi-restraints excluded: chain B residue  442 LEU
Chi-restraints excluded: chain C residue  236 GLU
Chi-restraints excluded: chain C residue  298 GLU
Chi-restraints excluded: chain C residue  346 MET
Chi-restraints excluded: chain C residue  382 LYS
Chi-restraints excluded: chain C residue  411 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 123 optimal weight:    0.8980
   chunk 97 optimal weight:    0.8980
   chunk 72 optimal weight:    4.9990
   chunk 101 optimal weight:    0.3980
   chunk 28 optimal weight:    0.6980
   chunk 50 optimal weight:    0.5980
   chunk 91 optimal weight:    0.0170
   chunk 143 optimal weight:    3.9990
   chunk 63 optimal weight:    0.5980
   chunk 147 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.4618

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

Flipped N/Q/H residues before XYZ refinement:
** B  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 305 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 = 0.4482 r_free = 0.4482 target = 0.202514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.179668 restraints weight = 19429.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.4217 rms_B_bonded: 2.25
r_work: 0.4113 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4120 r_free = 0.4120    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4120 r_free = 0.4120    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6436
moved from start:          0.3430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14047  Z= 0.139
  Angle     :  0.702  25.976  19224  Z= 0.342
  Chirality :  0.061   1.993   2097
  Planarity :  0.005   0.046   2340
  Dihedral  : 16.754 177.616   2149
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  9.56 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 17.17 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.21), residues: 1611
  helix:  0.27 (0.23), residues: 547
  sheet: -0.12 (0.37), residues: 179
  loop : -2.04 (0.20), residues: 885

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 607 
 HIS   0.006   0.001   HIS A 404 
 PHE   0.021   0.002   PHE A 749 
 TYR   0.024   0.001   TYR B 206 
 ARG   0.007   0.000   ARG C 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03563 (  462)
  hydrogen bonds       : angle       4.45659 ( 1310)
  covalent geometry    : bond        0.00307 (14047)
  covalent geometry    : angle       0.70223 (19224)

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

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

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 239
  time to evaluate  : 1.428 
Fit side-chains
REVERT: A  245 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7188 (mp)
REVERT: A  390 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.6717 (tt0)
REVERT: A  465 ASP cc_start: 0.6785 (m-30) cc_final: 0.6529 (m-30)
REVERT: A  486 TRP cc_start: 0.8106 (p-90) cc_final: 0.7833 (p-90)
REVERT: A  544 MET cc_start: 0.6910 (mmm) cc_final: 0.6566 (mmm)
REVERT: A  898 ILE cc_start: 0.7435 (mm) cc_final: 0.7211 (mm)
REVERT: A  953 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.6152 (ttp80)
REVERT: A 1075 LEU cc_start: 0.7777 (mt) cc_final: 0.7567 (mt)
REVERT: A 1111 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8079 (mp)
REVERT: B  256 LEU cc_start: 0.7765 (tm) cc_final: 0.7508 (tp)
REVERT: B  404 ASN cc_start: 0.7916 (m-40) cc_final: 0.7691 (m110)
REVERT: B  442 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7564 (tt)
REVERT: C  300 ILE cc_start: 0.8366 (mm) cc_final: 0.8101 (mt)
REVERT: C  346 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6452 (mtp)
REVERT: C  382 LYS cc_start: 0.5298 (OUTLIER) cc_final: 0.4930 (mppt)
  outliers start: 40
  outliers final: 14
  residues processed: 255
  average time/residue: 1.1160
  time to fit residues: 314.4329
Evaluate side-chains
  247 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 226
  time to evaluate  : 1.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 MET
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  491 ASP
Chi-restraints excluded: chain A residue  542 ASP
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  953 ARG
Chi-restraints excluded: chain A residue 1104 SER
Chi-restraints excluded: chain A residue 1111 LEU
Chi-restraints excluded: chain A residue 1141 VAL
Chi-restraints excluded: chain A residue 1164 PHE
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain B residue  331 VAL
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  442 LEU
Chi-restraints excluded: chain C residue  346 MET
Chi-restraints excluded: chain C residue  382 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0040
   chunk 60 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0470
   chunk 146 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.5490

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

Flipped N/Q/H residues before XYZ refinement:
A 404 HIS
A 803 ASN
A 970 ASN
** B  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 409 ASN
** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.202024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.177998 restraints weight = 23885.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.4197 rms_B_bonded: 2.58
r_work: 0.4084 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.4084
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4091 r_free = 0.4091    target_work(ls_wunit_k1) = 0.164         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4091 r_free = 0.4091    target_work(ls_wunit_k1) = 0.164         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4091
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6484
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14047  Z= 0.146
  Angle     :  0.718  26.013  19224  Z= 0.345
  Chirality :  0.061   1.992   2097
  Planarity :  0.005   0.046   2340
  Dihedral  : 16.710 177.695   2149
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 10.24 %
    Favored  : 89.70 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.71 %
    Favored  : 78.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.21), residues: 1611
  helix:  0.38 (0.23), residues: 544
  sheet: -0.04 (0.38), residues: 178
  loop : -1.95 (0.20), residues: 889

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 607 
 HIS   0.005   0.001   HIS A 805 
 PHE   0.024   0.002   PHE A 539 
 TYR   0.025   0.001   TYR B 206 
 ARG   0.008   0.000   ARG A1187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03653 (  462)
  hydrogen bonds       : angle       4.45469 ( 1310)
  covalent geometry    : bond        0.00329 (14047)
  covalent geometry    : angle       0.71778 (19224)

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

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

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 233
  time to evaluate  : 1.737 
Fit side-chains
REVERT: A  245 ILE cc_start: 0.7406 (OUTLIER) cc_final: 0.7178 (mp)
REVERT: A  299 MET cc_start: 0.7241 (mmm) cc_final: 0.6794 (tpt)
REVERT: A  465 ASP cc_start: 0.6774 (m-30) cc_final: 0.6509 (m-30)
REVERT: A  486 TRP cc_start: 0.8119 (p-90) cc_final: 0.7850 (p-90)
REVERT: A  544 MET cc_start: 0.6973 (mmm) cc_final: 0.6657 (mmm)
REVERT: A  856 GLU cc_start: 0.7628 (tp30) cc_final: 0.7399 (tp30)
REVERT: A  898 ILE cc_start: 0.7448 (mm) cc_final: 0.7241 (mm)
REVERT: A  953 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6204 (ttp80)
REVERT: A  969 PHE cc_start: 0.7629 (m-10) cc_final: 0.7351 (m-10)
REVERT: A 1057 MET cc_start: 0.2351 (mmp) cc_final: 0.0172 (pp-130)
REVERT: A 1111 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8065 (mp)
REVERT: B  132 HIS cc_start: 0.6031 (OUTLIER) cc_final: 0.4433 (t-170)
REVERT: B  256 LEU cc_start: 0.7814 (tm) cc_final: 0.7538 (tp)
REVERT: B  442 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7579 (tt)
REVERT: C  300 ILE cc_start: 0.8385 (mm) cc_final: 0.8140 (mt)
REVERT: C  346 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6474 (mtp)
REVERT: C  349 TYR cc_start: 0.5766 (m-10) cc_final: 0.5275 (m-10)
REVERT: C  382 LYS cc_start: 0.5282 (OUTLIER) cc_final: 0.4933 (mppt)
REVERT: C  465 MET cc_start: 0.4135 (tmm) cc_final: 0.3876 (tmm)
  outliers start: 38
  outliers final: 18
  residues processed: 252
  average time/residue: 1.1675
  time to fit residues: 325.1863
Evaluate side-chains
  250 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 225
  time to evaluate  : 1.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  491 ASP
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  849 THR
Chi-restraints excluded: chain A residue  953 ARG
Chi-restraints excluded: chain A residue 1104 SER
Chi-restraints excluded: chain A residue 1111 LEU
Chi-restraints excluded: chain A residue 1141 VAL
Chi-restraints excluded: chain A residue 1164 PHE
Chi-restraints excluded: chain B residue  132 HIS
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain B residue  314 MET
Chi-restraints excluded: chain B residue  331 VAL
Chi-restraints excluded: chain B residue  337 SER
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  442 LEU
Chi-restraints excluded: chain C residue  346 MET
Chi-restraints excluded: chain C residue  382 LYS
Chi-restraints excluded: chain C residue  411 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 94 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9980
   chunk 125 optimal weight:    0.6980
   chunk 132 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0770
   chunk 65 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 157 optimal weight:    2.9990
   chunk 23 optimal weight:    0.1980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
A 277 HIS
A1102 GLN
** B  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 404 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.201603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.179099 restraints weight = 20147.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.4236 rms_B_bonded: 2.23
r_work: 0.4137 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work (final): 0.4137
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4144
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4144 r_free = 0.4144    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4144 r_free = 0.4144    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4144
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6430
moved from start:          0.3769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14047  Z= 0.139
  Angle     :  0.712  26.014  19224  Z= 0.342
  Chirality :  0.062   1.991   2097
  Planarity :  0.005   0.048   2340
  Dihedral  : 16.670 177.510   2149
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  9.93 %
    Favored  : 90.01 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 19.52 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.21), residues: 1611
  helix:  0.44 (0.23), residues: 544
  sheet: -0.04 (0.38), residues: 170
  loop : -1.94 (0.20), residues: 897

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 607 
 HIS   0.004   0.001   HIS A 805 
 PHE   0.018   0.001   PHE A 749 
 TYR   0.025   0.001   TYR B 206 
 ARG   0.007   0.000   ARG A1187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03454 (  462)
  hydrogen bonds       : angle       4.43239 ( 1310)
  covalent geometry    : bond        0.00311 (14047)
  covalent geometry    : angle       0.71207 (19224)

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

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

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 225
  time to evaluate  : 1.510 
Fit side-chains
REVERT: A  245 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.7202 (mp)
REVERT: A  299 MET cc_start: 0.7133 (mmm) cc_final: 0.6829 (tpt)
REVERT: A  390 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.6556 (tm-30)
REVERT: A  465 ASP cc_start: 0.6693 (m-30) cc_final: 0.6433 (m-30)
REVERT: A  898 ILE cc_start: 0.7452 (mm) cc_final: 0.7238 (mm)
REVERT: A 1057 MET cc_start: 0.2052 (mmp) cc_final: 0.0412 (pp-130)
REVERT: A 1111 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8061 (mp)
REVERT: B  132 HIS cc_start: 0.6052 (OUTLIER) cc_final: 0.4440 (t-170)
REVERT: B  276 SER cc_start: 0.8346 (m) cc_final: 0.8057 (p)
REVERT: B  285 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.5740 (mtpp)
REVERT: B  442 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7529 (tt)
REVERT: C  300 ILE cc_start: 0.8353 (mm) cc_final: 0.8100 (mt)
REVERT: C  346 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.6432 (mtp)
REVERT: C  349 TYR cc_start: 0.5839 (m-10) cc_final: 0.5331 (m-10)
REVERT: C  465 MET cc_start: 0.4123 (tmm) cc_final: 0.3887 (tmm)
  outliers start: 36
  outliers final: 20
  residues processed: 241
  average time/residue: 1.1104
  time to fit residues: 296.3140
Evaluate side-chains
  248 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 221
  time to evaluate  : 1.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  491 ASP
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  856 GLU
Chi-restraints excluded: chain A residue  904 ASP
Chi-restraints excluded: chain A residue 1104 SER
Chi-restraints excluded: chain A residue 1111 LEU
Chi-restraints excluded: chain A residue 1141 VAL
Chi-restraints excluded: chain A residue 1164 PHE
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  132 HIS
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain B residue  285 LYS
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  314 MET
Chi-restraints excluded: chain B residue  331 VAL
Chi-restraints excluded: chain B residue  337 SER
Chi-restraints excluded: chain B residue  442 LEU
Chi-restraints excluded: chain C residue  346 MET
Chi-restraints excluded: chain C residue  411 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 125 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   chunk 101 optimal weight:    0.7980
   chunk 112 optimal weight:    0.6980
   chunk 110 optimal weight:    3.9990
   chunk 113 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
A 277 HIS
** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1102 GLN
A1171 ASN
** B  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 192 HIS
C 467 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.196708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.173910 restraints weight = 19672.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.4174 rms_B_bonded: 2.27
r_work: 0.4072 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3926 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3909
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3909 r_free = 0.3909    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3909 r_free = 0.3909    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3909
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6770
moved from start:          0.4418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067  14047  Z= 0.240
  Angle     :  0.813  25.971  19224  Z= 0.399
  Chirality :  0.065   1.997   2097
  Planarity :  0.006   0.052   2340
  Dihedral  : 16.880 177.534   2149
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 11.48 %
    Favored  : 88.45 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 19.59 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.20), residues: 1611
  helix: -0.16 (0.22), residues: 565
  sheet: -0.15 (0.39), residues: 172
  loop : -2.09 (0.20), residues: 874

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 486 
 HIS   0.011   0.002   HIS B  77 
 PHE   0.029   0.002   PHE A 749 
 TYR   0.034   0.002   TYR B 206 
 ARG   0.008   0.001   ARG A1187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04310 (  462)
  hydrogen bonds       : angle       4.79466 ( 1310)
  covalent geometry    : bond        0.00552 (14047)
  covalent geometry    : angle       0.81290 (19224)

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

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

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 230
  time to evaluate  : 1.486 
Fit side-chains
   revert: symmetry clash
REVERT: A  390 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.6748 (tm-30)
REVERT: A  447 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7137 (pp20)
REVERT: A  465 ASP cc_start: 0.7042 (m-30) cc_final: 0.6798 (m-30)
REVERT: A  544 MET cc_start: 0.7670 (mmm) cc_final: 0.7352 (mmm)
REVERT: A  904 ASP cc_start: 0.5664 (OUTLIER) cc_final: 0.5451 (p0)
REVERT: A 1057 MET cc_start: 0.2441 (mmp) cc_final: 0.0770 (pp-130)
REVERT: A 1102 GLN cc_start: 0.7990 (mt0) cc_final: 0.7758 (mt0)
REVERT: A 1111 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8221 (mp)
REVERT: B  132 HIS cc_start: 0.6315 (OUTLIER) cc_final: 0.4526 (t-170)
REVERT: B  276 SER cc_start: 0.8449 (m) cc_final: 0.8154 (p)
REVERT: B  285 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6146 (mmmt)
REVERT: B  442 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7789 (tt)
REVERT: C  300 ILE cc_start: 0.8529 (mm) cc_final: 0.8302 (mt)
REVERT: C  346 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.6973 (mtp)
REVERT: C  349 TYR cc_start: 0.6450 (m-10) cc_final: 0.5748 (m-10)
REVERT: C  465 MET cc_start: 0.4666 (OUTLIER) cc_final: 0.4431 (tmm)
  outliers start: 39
  outliers final: 18
  residues processed: 250
  average time/residue: 1.1412
  time to fit residues: 314.8140
Evaluate side-chains
  252 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 225
  time to evaluate  : 1.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  491 ASP
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  849 THR
Chi-restraints excluded: chain A residue  904 ASP
Chi-restraints excluded: chain A residue 1111 LEU
Chi-restraints excluded: chain A residue 1141 VAL
Chi-restraints excluded: chain A residue 1164 PHE
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  132 HIS
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain B residue  285 LYS
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  331 VAL
Chi-restraints excluded: chain B residue  337 SER
Chi-restraints excluded: chain B residue  442 LEU
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  346 MET
Chi-restraints excluded: chain C residue  411 ILE
Chi-restraints excluded: chain C residue  465 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 111 optimal weight:    0.9990
   chunk 156 optimal weight:    0.9980
   chunk 144 optimal weight:    0.6980
   chunk 161 optimal weight:    0.6980
   chunk 143 optimal weight:    5.9990
   chunk 155 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0970
   chunk 124 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
A 277 HIS
A 440 ASN
A1171 ASN
** B  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 330 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.198285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.175894 restraints weight = 19308.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.4176 rms_B_bonded: 2.23
r_work: 0.4073 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3930 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3936
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3936 r_free = 0.3936    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3936 r_free = 0.3936    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3936
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6722
moved from start:          0.4509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  14047  Z= 0.164
  Angle     :  0.762  25.966  19224  Z= 0.369
  Chirality :  0.063   1.993   2097
  Planarity :  0.005   0.087   2340
  Dihedral  : 16.766 176.968   2149
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 10.55 %
    Favored  : 89.39 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 20.91 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.21), residues: 1611
  helix:  0.03 (0.23), residues: 557
  sheet: -0.04 (0.40), residues: 170
  loop : -2.10 (0.20), residues: 884

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 486 
 HIS   0.005   0.001   HIS B  77 
 PHE   0.027   0.002   PHE A 749 
 TYR   0.028   0.002   TYR B 206 
 ARG   0.008   0.001   ARG A1187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03760 (  462)
  hydrogen bonds       : angle       4.61925 ( 1310)
  covalent geometry    : bond        0.00374 (14047)
  covalent geometry    : angle       0.76173 (19224)

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

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

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 229
  time to evaluate  : 1.480 
Fit side-chains
   revert: symmetry clash
REVERT: A  299 MET cc_start: 0.7412 (mmm) cc_final: 0.6971 (tpt)
REVERT: A  447 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7091 (pp20)
REVERT: A  465 ASP cc_start: 0.7029 (m-30) cc_final: 0.6764 (m-30)
REVERT: A  478 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6857 (ttp80)
REVERT: A  541 GLN cc_start: 0.6881 (tm-30) cc_final: 0.6044 (tm-30)
REVERT: A  544 MET cc_start: 0.7592 (mmm) cc_final: 0.7264 (mmm)
REVERT: A  849 THR cc_start: 0.7068 (OUTLIER) cc_final: 0.6776 (p)
REVERT: A 1057 MET cc_start: 0.2317 (mmp) cc_final: 0.0620 (pp-130)
REVERT: A 1111 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8109 (mp)
REVERT: B  132 HIS cc_start: 0.6149 (OUTLIER) cc_final: 0.4356 (t-170)
REVERT: B  276 SER cc_start: 0.8454 (m) cc_final: 0.8175 (p)
REVERT: B  285 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.5882 (mtpp)
REVERT: B  442 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7686 (tt)
REVERT: B  465 MET cc_start: 0.8073 (mpt) cc_final: 0.7863 (mpt)
REVERT: C  346 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.6823 (mtp)
REVERT: C  349 TYR cc_start: 0.6402 (m-10) cc_final: 0.5673 (m-10)
REVERT: C  375 HIS cc_start: 0.5494 (m-70) cc_final: 0.5268 (m-70)
  outliers start: 30
  outliers final: 16
  residues processed: 243
  average time/residue: 1.1618
  time to fit residues: 311.4310
Evaluate side-chains
  249 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 225
  time to evaluate  : 1.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  478 ARG
Chi-restraints excluded: chain A residue  491 ASP
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  849 THR
Chi-restraints excluded: chain A residue 1111 LEU
Chi-restraints excluded: chain A residue 1141 VAL
Chi-restraints excluded: chain A residue 1164 PHE
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  132 HIS
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain B residue  285 LYS
Chi-restraints excluded: chain B residue  331 VAL
Chi-restraints excluded: chain B residue  337 SER
Chi-restraints excluded: chain B residue  442 LEU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  338 VAL
Chi-restraints excluded: chain C residue  346 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 156 optimal weight:    9.9990
   chunk 77 optimal weight:    0.7980
   chunk 110 optimal weight:    0.0370
   chunk 57 optimal weight:    2.9990
   chunk 160 optimal weight:    6.9990
   chunk 33 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 151 optimal weight:    2.9990
   overall best weight:    0.8860

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

Flipped N/Q/H residues before XYZ refinement:
A 277 HIS
** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1102 GLN
A1171 ASN
** B  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 467 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.197030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.174652 restraints weight = 19464.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.4163 rms_B_bonded: 2.24
r_work: 0.4058 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3913 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3918
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3918 r_free = 0.3918    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3918 r_free = 0.3918    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3918
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6757
moved from start:          0.4713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075  14047  Z= 0.192
  Angle     :  0.794  25.986  19224  Z= 0.383
  Chirality :  0.064   1.993   2097
  Planarity :  0.005   0.050   2340
  Dihedral  : 16.796 177.136   2149
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 11.11 %
    Favored  : 88.76 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 20.91 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.21), residues: 1611
  helix: -0.05 (0.22), residues: 564
  sheet:  0.02 (0.40), residues: 178
  loop : -2.14 (0.20), residues: 869

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 486 
 HIS   0.008   0.001   HIS B  77 
 PHE   0.028   0.002   PHE A 749 
 TYR   0.030   0.002   TYR B 206 
 ARG   0.009   0.001   ARG A 953 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03963 (  462)
  hydrogen bonds       : angle       4.67373 ( 1310)
  covalent geometry    : bond        0.00444 (14047)
  covalent geometry    : angle       0.79350 (19224)

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

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

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3222 Ramachandran restraints generated.
    1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 220
  time to evaluate  : 1.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  299 MET cc_start: 0.7507 (mmm) cc_final: 0.7053 (tpt)
REVERT: A  390 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.6720 (tm-30)
REVERT: A  447 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7070 (pp20)
REVERT: A  465 ASP cc_start: 0.7077 (m-30) cc_final: 0.6828 (m-30)
REVERT: A  478 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6792 (ttp80)
REVERT: A  541 GLN cc_start: 0.6855 (tm-30) cc_final: 0.6023 (tm-30)
REVERT: A  544 MET cc_start: 0.7631 (mmm) cc_final: 0.7299 (mmm)
REVERT: A  849 THR cc_start: 0.7128 (OUTLIER) cc_final: 0.6833 (p)
REVERT: A 1057 MET cc_start: 0.2297 (mmp) cc_final: 0.0769 (pp-130)
REVERT: A 1072 THR cc_start: 0.6277 (OUTLIER) cc_final: 0.5958 (m)
REVERT: A 1111 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8136 (mp)
REVERT: B  132 HIS cc_start: 0.6270 (OUTLIER) cc_final: 0.4315 (t-170)
REVERT: B  276 SER cc_start: 0.8430 (m) cc_final: 0.8163 (p)
REVERT: B  285 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.5861 (mtpp)
REVERT: B  442 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7664 (tt)
REVERT: C  346 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.6856 (mtp)
REVERT: C  349 TYR cc_start: 0.6519 (m-10) cc_final: 0.5742 (m-10)
REVERT: C  375 HIS cc_start: 0.5506 (m-70) cc_final: 0.5251 (m-70)
  outliers start: 28
  outliers final: 16
  residues processed: 236
  average time/residue: 1.1447
  time to fit residues: 298.5790
Evaluate side-chains
  242 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 216
  time to evaluate  : 1.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  478 ARG
Chi-restraints excluded: chain A residue  491 ASP
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  849 THR
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1111 LEU
Chi-restraints excluded: chain A residue 1141 VAL
Chi-restraints excluded: chain A residue 1164 PHE
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  132 HIS
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain B residue  285 LYS
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  331 VAL
Chi-restraints excluded: chain B residue  337 SER
Chi-restraints excluded: chain B residue  442 LEU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  346 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 95 optimal weight:    0.5980
   chunk 134 optimal weight:    0.2980
   chunk 3 optimal weight:    0.0980
   chunk 124 optimal weight:    0.9980
   chunk 128 optimal weight:    0.7980
   chunk 160 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 156 optimal weight:    9.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 277 HIS
A 420 HIS
A1102 GLN
A1171 ASN
** B  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.199024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.177654 restraints weight = 19169.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.4194 rms_B_bonded: 2.09
r_work: 0.4095 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3960 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3966
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3966 r_free = 0.3966    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3966 r_free = 0.3966    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3966
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6682
moved from start:          0.4763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  14047  Z= 0.150
  Angle     :  0.765  25.975  19224  Z= 0.368
  Chirality :  0.062   1.991   2097
  Planarity :  0.005   0.059   2340
  Dihedral  : 16.709 176.530   2149
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 10.68 %
    Favored  : 89.20 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 20.91 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.21), residues: 1611
  helix:  0.12 (0.23), residues: 554
  sheet: -0.08 (0.39), residues: 179
  loop : -2.15 (0.20), residues: 878

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 486 
 HIS   0.005   0.001   HIS B  77 
 PHE   0.028   0.002   PHE A 749 
 TYR   0.028   0.001   TYR B 206 
 ARG   0.009   0.001   ARG A 953 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03639 (  462)
  hydrogen bonds       : angle       4.59950 ( 1310)
  covalent geometry    : bond        0.00341 (14047)
  covalent geometry    : angle       0.76485 (19224)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10677.24 seconds
wall clock time: 182 minutes 17.85 seconds (10937.85 seconds total)