Starting phenix.real_space_refine
on Wed Aug  5 14:12:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vcu_64968/08_2026/9vcu_64968.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vcu_64968/08_2026/9vcu_64968.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vcu_64968/08_2026/9vcu_64968.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vcu_64968/08_2026/9vcu_64968.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vcu_64968/08_2026/9vcu_64968.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vcu_64968/08_2026/9vcu_64968.map"
  }
  resolution = 3.84
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.030
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       2      5.49       5
     S      56      5.16       5
     C    6333      2.51       5
     N    1693      2.21       5
     O    1813      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9897
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 602, 4819
          Classifications: {'peptide': 602}
          Link IDs: {'PTRANS': 32, 'TRANS': 569}
    Chain: "B"
      Number of atoms: 5051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 635, 5051
          Classifications: {'peptide': 635}
          Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 597}
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.23, per 1000 atoms: 0.23
  Number of scatterers: 9897
  At special positions: 0
  Unit cell: (97.11, 103.75, 129.48, 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      56     16.00
     P       2     15.00
     O    1813      8.00
     N    1693      7.00
     C    6333      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 361.9 milliseconds
  

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2352

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 7 sheets defined
      56.9% alpha, 8.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 89 through 103
    Processing helix  chain 'A' and resid 104 through 112
    Processing helix  chain 'A' and resid 116 through 133
    Processing helix  chain 'A' and resid 138 through 150
    Processing helix  chain 'A' and resid 154 through 170
      removed outlier: 3.646A  pdb=" N   LEU A 158 " --> pdb=" O   HIS A 154 " (cutoff:3.500A)
      Proline residue:  A 160  - end of helix
    Processing helix  chain 'A' and resid 170 through 175
      removed outlier: 3.718A  pdb=" N   ASP A 174 " --> pdb=" O   PHE A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 183
      removed outlier: 3.902A  pdb=" N   LEU A 179 " --> pdb=" O   CYS A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 192
    Processing helix  chain 'A' and resid 212 through 223
    Processing helix  chain 'A' and resid 233 through 248
    Processing helix  chain 'A' and resid 277 through 279
      No H-bonds generated for 'chain 'A' and resid 277 through 279'
    Processing helix  chain 'A' and resid 293 through 296
    Processing helix  chain 'A' and resid 301 through 312
      removed outlier: 4.215A  pdb=" N   TRP A 305 " --> pdb=" O   ARG A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 324
      No H-bonds generated for 'chain 'A' and resid 322 through 324'
    Processing helix  chain 'A' and resid 325 through 337
    Processing helix  chain 'A' and resid 374 through 388
    Processing helix  chain 'A' and resid 400 through 412
    Processing helix  chain 'A' and resid 426 through 429
    Processing helix  chain 'A' and resid 460 through 470
    Processing helix  chain 'A' and resid 487 through 499
      removed outlier: 3.833A  pdb=" N   LYS A 499 " --> pdb=" O   LYS A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 524
      removed outlier: 3.549A  pdb=" N   ILE A 517 " --> pdb=" O   THR A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 528 through 539
    Processing helix  chain 'A' and resid 551 through 563
      removed outlier: 3.993A  pdb=" N   HIS A 563 " --> pdb=" O   GLU A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 577
    Processing helix  chain 'A' and resid 583 through 600
      removed outlier: 3.985A  pdb=" N   CYS A 587 " --> pdb=" O   GLN A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 613
    Processing helix  chain 'A' and resid 621 through 645
    Processing helix  chain 'A' and resid 651 through 671
    Processing helix  chain 'A' and resid 672 through 684
    Processing helix  chain 'B' and resid 79 through 85
    Processing helix  chain 'B' and resid 89 through 103
      removed outlier: 3.786A  pdb=" N   ARG B 103 " --> pdb=" O   LYS B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 114
      removed outlier: 3.505A  pdb=" N   TYR B 113 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 133
    Processing helix  chain 'B' and resid 138 through 150
    Processing helix  chain 'B' and resid 154 through 170
      removed outlier: 3.718A  pdb=" N   LEU B 158 " --> pdb=" O   HIS B 154 " (cutoff:3.500A)
      Proline residue:  B 160  - end of helix
    Processing helix  chain 'B' and resid 175 through 183
    Processing helix  chain 'B' and resid 187 through 191
    Processing helix  chain 'B' and resid 192 through 198
      removed outlier: 3.589A  pdb=" N   ARG B 196 " --> pdb=" O   TYR B 192 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   MET B 198 " --> pdb=" O   ASP B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 223
      removed outlier: 3.673A  pdb=" N   HIS B 216 " --> pdb=" O   GLY B 212 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   SER B 223 " --> pdb=" O   GLN B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 247
    Processing helix  chain 'B' and resid 293 through 298
      removed outlier: 3.534A  pdb=" N   ARG B 297 " --> pdb=" O   GLN B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 310
      removed outlier: 3.834A  pdb=" N   TRP B 305 " --> pdb=" O   ARG B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 324
      No H-bonds generated for 'chain 'B' and resid 322 through 324'
    Processing helix  chain 'B' and resid 325 through 337
    Processing helix  chain 'B' and resid 360 through 364
      removed outlier: 3.709A  pdb=" N   ASN B 363 " --> pdb=" O   SER B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 374 through 389
    Processing helix  chain 'B' and resid 400 through 413
      removed outlier: 3.714A  pdb=" N   ASP B 413 " --> pdb=" O   LYS B 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 470
    Processing helix  chain 'B' and resid 475 through 479
    Processing helix  chain 'B' and resid 488 through 500
    Processing helix  chain 'B' and resid 513 through 524
    Processing helix  chain 'B' and resid 529 through 540
    Processing helix  chain 'B' and resid 552 through 561
    Processing helix  chain 'B' and resid 567 through 576
    Processing helix  chain 'B' and resid 583 through 599
      removed outlier: 3.920A  pdb=" N   CYS B 587 " --> pdb=" O   GLN B 583 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 604 through 613
    Processing helix  chain 'B' and resid 622 through 643
    Processing helix  chain 'B' and resid 651 through 671
    Processing helix  chain 'B' and resid 672 through 688
      removed outlier: 3.900A  pdb=" N   LEU B 685 " --> pdb=" O   GLU B 681 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   LEU B 686 " --> pdb=" O   THR B 682 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 259 through 260
      removed outlier: 6.030A  pdb=" N   ASP A 252 " --> pdb=" O   SER A 273 " (cutoff:3.500A)
      removed outlier: 8.090A  pdb=" N   THR A 275 " --> pdb=" O   ASP A 252 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   VAL A 254 " --> pdb=" O   THR A 275 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   GLY A 227 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   CYS A 274 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   TYR A 229 " --> pdb=" O   CYS A 274 " (cutoff:3.500A)
      removed outlier: 4.749A  pdb=" N   ASP A 291 " --> pdb=" O   CYS A 230 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   GLU A 286 " --> pdb=" O   GLU A 316 " (cutoff:3.500A)
      removed outlier: 7.973A  pdb=" N   HIS A 318 " --> pdb=" O   GLU A 286 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   ALA A 288 " --> pdb=" O   HIS A 318 " (cutoff:3.500A)
      removed outlier: 8.070A  pdb=" N   CYS A 320 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   ILE A 290 " --> pdb=" O   CYS A 320 " (cutoff:3.500A)
      removed outlier: 5.961A  pdb=" N   LYS A 201 " --> pdb=" O   VAL A 317 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   LEU A 319 " --> pdb=" O   LYS A 201 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   ILE A 203 " --> pdb=" O   LEU A 319 " (cutoff:3.500A)
      removed outlier: 8.059A  pdb=" N   GLY A 321 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 5.687A  pdb=" N   HIS A 205 " --> pdb=" O   GLY A 321 " (cutoff:3.500A)
      removed outlier: 8.478A  pdb=" N   ARG A 343 " --> pdb=" O   ILE A 202 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   PHE A 204 " --> pdb=" O   ARG A 343 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 395
      removed outlier: 6.628A  pdb=" N   GLU A 391 " --> pdb=" O   ILE A 420 " (cutoff:3.500A)
      removed outlier: 7.642A  pdb=" N   VAL A 422 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   ALA A 393 " --> pdb=" O   VAL A 422 " (cutoff:3.500A)
      removed outlier: 8.449A  pdb=" N   THR A 424 " --> pdb=" O   ALA A 393 " (cutoff:3.500A)
      removed outlier: 7.120A  pdb=" N   ILE A 395 " --> pdb=" O   THR A 424 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   ASP A 368 " --> pdb=" O   LYS A 419 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   LEU A 421 " --> pdb=" O   ASP A 368 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 444 through 445
    Processing sheet with id=AA4, first strand: chain 'A' and resid 509 through 510
    Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 252
      removed outlier: 4.357A  pdb=" N   ASP B 291 " --> pdb=" O   CYS B 230 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 351 through 353
      removed outlier: 3.574A  pdb=" N   VAL B 483 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   ASP B 368 " --> pdb=" O   LEU B 421 " (cutoff:3.500A)
      removed outlier: 8.593A  pdb=" N   ALA B 423 " --> pdb=" O   ASP B 368 " (cutoff:3.500A)
      removed outlier: 6.132A  pdb=" N   ILE B 370 " --> pdb=" O   ALA B 423 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 444 through 448

    497 hydrogen bonds defined for protein.
    1452 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.62

  Time building geometry restraints manager: 1.24 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: 3235
        1.34 -     1.46: 2133
        1.46 -     1.58: 4670
        1.58 -     1.70: 4
        1.70 -     1.82: 84
  Bond restraints: 10126
  Sorted by residual:
  bond pdb=" C1' ADP A 801 "
       pdb=" C2' ADP A 801 "
    ideal  model  delta    sigma   weight residual
    1.524  1.295  0.229 2.00e-02 2.50e+03 1.31e+02
  bond pdb=" C1' ADP A 801 "
       pdb=" O4' ADP A 801 "
    ideal  model  delta    sigma   weight residual
    1.426  1.622 -0.196 2.00e-02 2.50e+03 9.60e+01
  bond pdb=" C4  ADP A 801 "
       pdb=" C5  ADP A 801 "
    ideal  model  delta    sigma   weight residual
    1.490  1.346  0.144 2.00e-02 2.50e+03 5.18e+01
  bond pdb=" C4' ADP A 801 "
       pdb=" O4' ADP A 801 "
    ideal  model  delta    sigma   weight residual
    1.426  1.317  0.109 2.00e-02 2.50e+03 2.95e+01
  bond pdb=" C6  ADP A 801 "
       pdb=" N6  ADP A 801 "
    ideal  model  delta    sigma   weight residual
    1.355  1.456 -0.101 2.00e-02 2.50e+03 2.56e+01
  ... (remaining 10121 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.06: 13593
        3.06 -     6.11: 94
        6.11 -     9.17: 27
        9.17 -    12.22: 8
       12.22 -    15.28: 2
  Bond angle restraints: 13724
  Sorted by residual:
  angle pdb=" CA  MET A 330 "
        pdb=" CB  MET A 330 "
        pdb=" CG  MET A 330 "
      ideal   model   delta    sigma   weight residual
     114.10  125.32  -11.22 2.00e+00 2.50e-01 3.14e+01
  angle pdb=" N1  ADP A 801 "
        pdb=" C6  ADP A 801 "
        pdb=" N6  ADP A 801 "
      ideal   model   delta    sigma   weight residual
     120.00  104.72   15.28 3.00e+00 1.11e-01 2.59e+01
  angle pdb=" C5  ADP A 801 "
        pdb=" C6  ADP A 801 "
        pdb=" N6  ADP A 801 "
      ideal   model   delta    sigma   weight residual
     120.00  134.98  -14.98 3.00e+00 1.11e-01 2.49e+01
  angle pdb=" N   MET A 330 "
        pdb=" CA  MET A 330 "
        pdb=" CB  MET A 330 "
      ideal   model   delta    sigma   weight residual
     110.28  117.93   -7.65 1.55e+00 4.16e-01 2.43e+01
  angle pdb=" CA  TRP A 640 "
        pdb=" CB  TRP A 640 "
        pdb=" CG  TRP A 640 "
      ideal   model   delta    sigma   weight residual
     113.60  122.47   -8.87 1.90e+00 2.77e-01 2.18e+01
  ... (remaining 13719 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.31: 5643
       25.31 -    50.63: 455
       50.63 -    75.94: 54
       75.94 -   101.26: 8
      101.26 -   126.57: 2
  Dihedral angle restraints: 6162
    sinusoidal: 2535
      harmonic: 3627
  Sorted by residual:
  dihedral pdb=" O2A ADP A 801 "
           pdb=" O3A ADP A 801 "
           pdb=" PA  ADP A 801 "
           pdb=" PB  ADP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  173.43  126.57     1      2.00e+01 2.50e-03 3.83e+01
  dihedral pdb=" C5' ADP A 801 "
           pdb=" O5' ADP A 801 "
           pdb=" PA  ADP A 801 "
           pdb=" O2A ADP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   54.49 -114.49     1      2.00e+01 2.50e-03 3.39e+01
  dihedral pdb=" CA  CYS A 175 "
           pdb=" C   CYS A 175 "
           pdb=" N   LYS A 176 "
           pdb=" CA  LYS A 176 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.85   21.15     0      5.00e+00 4.00e-02 1.79e+01
  ... (remaining 6159 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1131
       0.041 -    0.082: 291
       0.082 -    0.123: 92
       0.123 -    0.164: 13
       0.164 -    0.205: 5
  Chirality restraints: 1532
  Sorted by residual:
  chirality pdb=" CA  MET B 330 "
            pdb=" N   MET B 330 "
            pdb=" C   MET B 330 "
            pdb=" CB  MET B 330 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CB  VAL A 329 "
            pdb=" CA  VAL A 329 "
            pdb=" CG1 VAL A 329 "
            pdb=" CG2 VAL A 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CB  VAL B 144 "
            pdb=" CA  VAL B 144 "
            pdb=" CG1 VAL B 144 "
            pdb=" CG2 VAL B 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 8.97e-01
  ... (remaining 1529 not shown)

  Planarity restraints: 1764
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 640 "   -0.021 2.00e-02 2.50e+03   1.85e-02 8.60e+00
        pdb=" CG  TRP A 640 "    0.050 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 640 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 640 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 640 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 640 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 640 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 640 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 640 "   -0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 640 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 188 "    0.044 5.00e-02 4.00e+02   6.59e-02 6.95e+00
        pdb=" N   PRO B 189 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO B 189 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 189 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 617 "   -0.035 5.00e-02 4.00e+02   5.30e-02 4.50e+00
        pdb=" N   PRO A 618 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A 618 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 618 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1761 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 564
        2.72 -     3.27: 11122
        3.27 -     3.81: 18164
        3.81 -     4.36: 21341
        4.36 -     4.90: 33445
  Nonbonded interactions: 84636
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 347 "
            pdb=" O   ALA A 471 "
     model   vdw
     2.181 3.120
  nonbonded pdb=" O   LYS B 234 "
            pdb=" ND1 HIS B 238 "
     model   vdw
     2.200 3.120
  nonbonded pdb=" OG  SER A 398 "
            pdb=" OE1 GLU A 629 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   PHE A 161 "
            pdb=" ND1 HIS A 165 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" ND2 ASN A 210 "
            pdb=" OG1 THR A 349 "
     model   vdw
     2.238 3.120
  ... (remaining 84631 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 'A' and resid 87 through 688)
  selection = (chain 'B' and resid 87 through 688)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.400
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6936
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   0.229  10126  Z= 0.246
  Angle     :  0.764  15.278  13724  Z= 0.373
  Chirality :  0.042   0.205   1532
  Planarity :  0.005   0.066   1764
  Dihedral  : 17.432 126.571   3810
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 20.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  : 31.83 %
    Favored  : 67.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.24), residues: 1233
  helix:  0.69 (0.20), residues: 643
  sheet: -1.80 (0.46), residues: 121
  loop : -1.01 (0.30), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 644 
 TYR   0.030   0.002   TYR B 229 
 PHE   0.015   0.002   PHE B 159 
 TRP   0.050   0.002   TRP A 640 
 HIS   0.006   0.001   HIS B 511 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00502 /  0.25 (10126)
  covalent geometry    : angle       0.76447 /  0.37 (13724)
  hydrogen bonds       : bond        0.15017 /  9.52 (  497)
  hydrogen bonds       : angle       6.43227 /  4.54 ( 1452)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 125
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  626 MET cc_start: 0.8452 (mmm) cc_final: 0.7476 (mmp)
REVERT: A  648 MET cc_start: 0.8054 (mmm) cc_final: 0.7401 (mmm)
REVERT: B  198 MET cc_start: 0.4803 (ppp) cc_final: 0.4427 (ppp)
  outliers start: 2
  outliers final: 2
  residues processed: 127
  average time/residue: 0.0900
  time to fit residues: 16.9399
Evaluate side-chains
  123 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 121
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain B residue  520 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0370
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:   50.0000
   chunk 51 optimal weight:    9.9990
   chunk 117 optimal weight:    0.8980
   overall best weight:    1.7262

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 621 ASN
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 659 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.124742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.100190 restraints weight = 41028.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.102789 restraints weight = 27601.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.104473 restraints weight = 20699.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.105510 restraints weight = 16976.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.106250 restraints weight = 14884.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.4151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          0.0919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10126  Z= 0.144
  Angle     :  0.642   8.439  13724  Z= 0.322
  Chirality :  0.041   0.153   1532
  Planarity :  0.005   0.067   1764
  Dihedral  :  7.107 123.261   1357
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 16.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 26.61 %
    Favored  : 70.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.24), residues: 1233
  helix:  0.63 (0.20), residues: 656
  sheet: -2.07 (0.45), residues: 122
  loop : -0.90 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 644 
 TYR   0.018   0.001   TYR A 396 
 PHE   0.015   0.002   PHE A 478 
 TRP   0.037   0.002   TRP A 640 
 HIS   0.004   0.001   HIS B 238 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.14 (10126)
  covalent geometry    : angle       0.64218 /  0.32 (13724)
  hydrogen bonds       : bond        0.04128 /  2.66 (  497)
  hydrogen bonds       : angle       5.34467 /  3.84 ( 1452)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 126
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 MET cc_start: 0.8883 (mmp) cc_final: 0.8649 (mmp)
REVERT: A  454 ARG cc_start: 0.7018 (tpt90) cc_final: 0.6742 (tpt90)
REVERT: A  626 MET cc_start: 0.8472 (mmm) cc_final: 0.7627 (mmp)
REVERT: B  253 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7100 (tt)
REVERT: B  254 VAL cc_start: 0.7152 (t) cc_final: 0.6862 (p)
REVERT: B  291 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.6733 (p0)
REVERT: B  292 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6739 (pm20)
REVERT: B  575 CYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7066 (t)
  outliers start: 36
  outliers final: 17
  residues processed: 150
  average time/residue: 0.0944
  time to fit residues: 20.5807
Evaluate side-chains
  139 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  221 TYR
Chi-restraints excluded: chain A residue  255 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  295 MET
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  523 HIS
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  292 GLU
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  520 PHE
Chi-restraints excluded: chain B residue  531 ASN
Chi-restraints excluded: chain B residue  575 CYS
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  603 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 74 optimal weight:    0.0980
   chunk 66 optimal weight:    7.9990
   chunk 101 optimal weight:    9.9990
   chunk 77 optimal weight:    2.9990
   chunk 56 optimal weight:    7.9990
   chunk 67 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 107 optimal weight:   10.0000
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 210 ASN
** B 168 GLN ** 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 = 0.4477 r_free = 0.4477 target = 0.126109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.101553 restraints weight = 40526.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.104147 restraints weight = 27257.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.105839 restraints weight = 20472.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.107023 restraints weight = 16701.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.107842 restraints weight = 14489.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.4180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6899
moved from start:          0.1185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10126  Z= 0.124
  Angle     :  0.641   8.665  13724  Z= 0.315
  Chirality :  0.041   0.201   1532
  Planarity :  0.005   0.070   1764
  Dihedral  :  7.030 119.754   1355
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 15.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 25.60 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.24), residues: 1233
  helix:  0.61 (0.20), residues: 663
  sheet: -2.15 (0.45), residues: 123
  loop : -0.92 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 644 
 TYR   0.016   0.001   TYR A 396 
 PHE   0.014   0.002   PHE B 241 
 TRP   0.039   0.002   TRP A 640 
 HIS   0.004   0.001   HIS B 238 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.12 (10126)
  covalent geometry    : angle       0.64072 /  0.32 (13724)
  hydrogen bonds       : bond        0.03798 /  2.47 (  497)
  hydrogen bonds       : angle       5.14529 /  3.71 ( 1452)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 125
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 MET cc_start: 0.8971 (mmp) cc_final: 0.8676 (mmp)
REVERT: A  454 ARG cc_start: 0.6952 (tpt90) cc_final: 0.6518 (tpt90)
REVERT: A  626 MET cc_start: 0.8401 (mmm) cc_final: 0.7604 (mmp)
REVERT: A  648 MET cc_start: 0.8016 (mmm) cc_final: 0.7226 (mmm)
REVERT: B  179 LEU cc_start: 0.8130 (mm) cc_final: 0.7644 (mm)
REVERT: B  253 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7136 (tt)
REVERT: B  254 VAL cc_start: 0.7158 (t) cc_final: 0.6882 (p)
REVERT: B  291 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.6871 (p0)
REVERT: B  292 GLU cc_start: 0.6863 (pm20) cc_final: 0.6623 (pm20)
REVERT: B  374 SER cc_start: 0.7035 (OUTLIER) cc_final: 0.6164 (t)
REVERT: B  519 MET cc_start: 0.9389 (pmm) cc_final: 0.9126 (pmm)
REVERT: B  551 MET cc_start: 0.7719 (pmm) cc_final: 0.7303 (pmm)
REVERT: B  646 MET cc_start: 0.8239 (pmm) cc_final: 0.8032 (pmm)
  outliers start: 40
  outliers final: 19
  residues processed: 154
  average time/residue: 0.0830
  time to fit residues: 19.1116
Evaluate side-chains
  140 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  221 TYR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  356 HIS
Chi-restraints excluded: chain A residue  374 SER
Chi-restraints excluded: chain A residue  523 HIS
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain B residue  200 ARG
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  520 PHE
Chi-restraints excluded: chain B residue  531 ASN
Chi-restraints excluded: chain B residue  587 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 111 optimal weight:    7.9990
   chunk 88 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 39 optimal weight:   20.0000
   chunk 115 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 74 optimal weight:    0.3980
   chunk 18 optimal weight:   20.0000
   chunk 80 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   overall best weight:    1.9784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.124086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.099187 restraints weight = 41340.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.101674 restraints weight = 28057.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.103247 restraints weight = 21282.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.104416 restraints weight = 17584.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.105128 restraints weight = 15325.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
moved from start:          0.1447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10126  Z= 0.143
  Angle     :  0.641  11.243  13724  Z= 0.316
  Chirality :  0.041   0.159   1532
  Planarity :  0.005   0.069   1764
  Dihedral  :  7.039 117.397   1355
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 16.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 25.23 %
    Favored  : 69.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.24), residues: 1233
  helix:  0.61 (0.20), residues: 664
  sheet: -1.96 (0.48), residues: 112
  loop : -0.99 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 307 
 TYR   0.017   0.001   TYR A 396 
 PHE   0.015   0.002   PHE B 159 
 TRP   0.037   0.002   TRP A 640 
 HIS   0.003   0.001   HIS B 121 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.14 (10126)
  covalent geometry    : angle       0.64078 /  0.32 (13724)
  hydrogen bonds       : bond        0.03684 /  2.39 (  497)
  hydrogen bonds       : angle       5.15423 /  3.72 ( 1452)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 121
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  454 ARG cc_start: 0.7008 (tpt90) cc_final: 0.6526 (tpt90)
REVERT: A  626 MET cc_start: 0.8404 (mmm) cc_final: 0.7597 (mmp)
REVERT: B  179 LEU cc_start: 0.8093 (mm) cc_final: 0.7572 (mm)
REVERT: B  254 VAL cc_start: 0.7296 (t) cc_final: 0.6981 (p)
REVERT: B  291 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7061 (p0)
REVERT: B  292 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6725 (pm20)
REVERT: B  409 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8416 (mmtm)
REVERT: B  575 CYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7045 (t)
  outliers start: 55
  outliers final: 30
  residues processed: 161
  average time/residue: 0.0893
  time to fit residues: 21.2317
Evaluate side-chains
  149 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 115
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  221 TYR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  374 SER
Chi-restraints excluded: chain A residue  523 HIS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain B residue  200 ARG
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  292 GLU
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain B residue  377 ASP
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  409 LYS
Chi-restraints excluded: chain B residue  520 PHE
Chi-restraints excluded: chain B residue  531 ASN
Chi-restraints excluded: chain B residue  549 CYS
Chi-restraints excluded: chain B residue  575 CYS
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  603 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 38 optimal weight:   20.0000
   chunk 65 optimal weight:    9.9990
   chunk 119 optimal weight:    7.9990
   chunk 87 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 107 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   chunk 22 optimal weight:    0.2980
   chunk 78 optimal weight:    2.9990
   chunk 120 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    2.4588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.122681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.097898 restraints weight = 39934.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.100384 restraints weight = 27772.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.101891 restraints weight = 21081.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.103097 restraints weight = 17423.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.103756 restraints weight = 15095.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7017
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10126  Z= 0.162
  Angle     :  0.672  11.663  13724  Z= 0.332
  Chirality :  0.042   0.293   1532
  Planarity :  0.005   0.068   1764
  Dihedral  :  7.090 116.732   1355
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 17.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 27.06 %
    Favored  : 68.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.24), residues: 1233
  helix:  0.55 (0.20), residues: 664
  sheet: -1.90 (0.49), residues: 111
  loop : -1.09 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 307 
 TYR   0.017   0.002   TYR A 396 
 PHE   0.028   0.002   PHE A 478 
 TRP   0.037   0.002   TRP A 640 
 HIS   0.004   0.001   HIS B 238 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00370 /  0.16 (10126)
  covalent geometry    : angle       0.67205 /  0.33 (13724)
  hydrogen bonds       : bond        0.03739 /  2.41 (  497)
  hydrogen bonds       : angle       5.24136 /  3.81 ( 1452)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 114
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 ASP cc_start: 0.8697 (m-30) cc_final: 0.7700 (p0)
REVERT: A  339 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6985 (mp0)
REVERT: A  454 ARG cc_start: 0.6973 (tpt90) cc_final: 0.6599 (tpt90)
REVERT: A  626 MET cc_start: 0.8418 (mmm) cc_final: 0.7822 (mmm)
REVERT: B  170 PHE cc_start: 0.8027 (m-80) cc_final: 0.7451 (m-80)
REVERT: B  179 LEU cc_start: 0.8186 (mm) cc_final: 0.7692 (mm)
REVERT: B  254 VAL cc_start: 0.7143 (t) cc_final: 0.6807 (p)
REVERT: B  291 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7084 (p0)
REVERT: B  292 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6755 (pm20)
REVERT: B  409 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8405 (mmtm)
REVERT: B  519 MET cc_start: 0.9327 (pmm) cc_final: 0.9016 (pmm)
REVERT: B  575 CYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7144 (t)
  outliers start: 50
  outliers final: 35
  residues processed: 154
  average time/residue: 0.0823
  time to fit residues: 18.8888
Evaluate side-chains
  152 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 112
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  221 TYR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  277 GLU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  339 GLU
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  356 HIS
Chi-restraints excluded: chain A residue  374 SER
Chi-restraints excluded: chain A residue  523 HIS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain B residue  200 ARG
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  292 GLU
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain B residue  377 ASP
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  409 LYS
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  520 PHE
Chi-restraints excluded: chain B residue  531 ASN
Chi-restraints excluded: chain B residue  549 CYS
Chi-restraints excluded: chain B residue  575 CYS
Chi-restraints excluded: chain B residue  580 ASN
Chi-restraints excluded: chain B residue  581 LYS
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  603 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 74 optimal weight:    0.0050
   chunk 62 optimal weight:    6.9990
   chunk 98 optimal weight:   20.0000
   chunk 117 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 105 optimal weight:   20.0000
   chunk 75 optimal weight:    8.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    3.4002

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.120163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.094822 restraints weight = 41757.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.097252 restraints weight = 29128.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.098809 restraints weight = 22270.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.099987 restraints weight = 18403.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.100610 restraints weight = 16122.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10126  Z= 0.202
  Angle     :  0.720  11.357  13724  Z= 0.361
  Chirality :  0.043   0.218   1532
  Planarity :  0.005   0.065   1764
  Dihedral  :  7.280 117.067   1355
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 22.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 27.06 %
    Favored  : 67.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.74 (0.24), residues: 1233
  helix:  0.35 (0.20), residues: 664
  sheet: -1.98 (0.49), residues: 111
  loop : -1.22 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 307 
 TYR   0.019   0.002   TYR A 396 
 PHE   0.020   0.002   PHE A 556 
 TRP   0.042   0.003   TRP A 640 
 HIS   0.004   0.001   HIS B 121 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00450 /  0.20 (10126)
  covalent geometry    : angle       0.71990 /  0.36 (13724)
  hydrogen bonds       : bond        0.03992 /  2.59 (  497)
  hydrogen bonds       : angle       5.42687 /  3.96 ( 1452)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 119
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 ASP cc_start: 0.8807 (m-30) cc_final: 0.7920 (p0)
REVERT: A  339 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7132 (mp0)
REVERT: A  454 ARG cc_start: 0.7147 (tpt90) cc_final: 0.6791 (tpt90)
REVERT: A  626 MET cc_start: 0.8471 (mmm) cc_final: 0.7864 (mmm)
REVERT: B  170 PHE cc_start: 0.8077 (m-80) cc_final: 0.7717 (m-80)
REVERT: B  194 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6733 (p0)
REVERT: B  291 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7297 (p0)
REVERT: B  292 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6958 (pm20)
REVERT: B  409 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8446 (mmtm)
REVERT: B  482 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6202 (mp0)
REVERT: B  575 CYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7327 (t)
  outliers start: 54
  outliers final: 36
  residues processed: 164
  average time/residue: 0.0905
  time to fit residues: 21.7080
Evaluate side-chains
  155 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 112
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  191 TRP
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  221 TYR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  339 GLU
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  356 HIS
Chi-restraints excluded: chain A residue  374 SER
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain B residue  194 ASP
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  292 GLU
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain B residue  377 ASP
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  409 LYS
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  482 GLU
Chi-restraints excluded: chain B residue  520 PHE
Chi-restraints excluded: chain B residue  531 ASN
Chi-restraints excluded: chain B residue  549 CYS
Chi-restraints excluded: chain B residue  575 CYS
Chi-restraints excluded: chain B residue  580 ASN
Chi-restraints excluded: chain B residue  581 LYS
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  604 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 93 optimal weight:    5.9990
   chunk 113 optimal weight:    0.8980
   chunk 103 optimal weight:    1.9990
   chunk 109 optimal weight:    0.6980
   chunk 121 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.6980
   chunk 89 optimal weight:    5.9990
   chunk 52 optimal weight:    0.3980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.123594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.099547 restraints weight = 39780.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.101935 restraints weight = 27566.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.103636 restraints weight = 20711.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.104828 restraints weight = 16738.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.105552 restraints weight = 14450.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6953
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  10126  Z= 0.132
  Angle     :  0.708  10.561  13724  Z= 0.347
  Chirality :  0.043   0.187   1532
  Planarity :  0.005   0.071   1764
  Dihedral  :  7.134 115.295   1355
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 17.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 29.36 %
    Favored  : 67.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.24), residues: 1233
  helix:  0.44 (0.20), residues: 663
  sheet: -2.03 (0.47), residues: 112
  loop : -1.17 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 347 
 TYR   0.015   0.001   TYR A 396 
 PHE   0.032   0.002   PHE A 539 
 TRP   0.042   0.002   TRP A 640 
 HIS   0.004   0.001   HIS A 165 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.13 (10126)
  covalent geometry    : angle       0.70821 /  0.35 (13724)
  hydrogen bonds       : bond        0.03673 /  2.39 (  497)
  hydrogen bonds       : angle       5.16883 /  3.77 ( 1452)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 122
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 ASP cc_start: 0.8676 (m-30) cc_final: 0.7790 (p0)
REVERT: A  441 TYR cc_start: 0.8365 (t80) cc_final: 0.7581 (t80)
REVERT: A  454 ARG cc_start: 0.7119 (tpt90) cc_final: 0.6749 (tpt90)
REVERT: A  626 MET cc_start: 0.8421 (mmm) cc_final: 0.7643 (mmp)
REVERT: B  179 LEU cc_start: 0.8268 (mm) cc_final: 0.7803 (mm)
REVERT: B  254 VAL cc_start: 0.7163 (t) cc_final: 0.6868 (p)
REVERT: B  291 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7033 (p0)
REVERT: B  292 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6765 (pm20)
REVERT: B  482 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.6106 (mp0)
REVERT: B  575 CYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7138 (t)
  outliers start: 38
  outliers final: 25
  residues processed: 153
  average time/residue: 0.0854
  time to fit residues: 19.5355
Evaluate side-chains
  143 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 114
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  221 TYR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  356 HIS
Chi-restraints excluded: chain A residue  374 SER
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  522 TYR
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  292 GLU
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  482 GLU
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  520 PHE
Chi-restraints excluded: chain B residue  575 CYS
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  604 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 38 optimal weight:    9.9990
   chunk 90 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0370
   chunk 56 optimal weight:    0.9990
   chunk 100 optimal weight:    6.9990
   chunk 77 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 4 optimal weight:   10.0000
   overall best weight:    1.3464

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 356 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.123472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.099295 restraints weight = 39378.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.101679 restraints weight = 27814.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.103322 restraints weight = 21055.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.104396 restraints weight = 17229.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.105153 restraints weight = 15030.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.4136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6970
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10126  Z= 0.137
  Angle     :  0.706  11.451  13724  Z= 0.345
  Chirality :  0.043   0.357   1532
  Planarity :  0.005   0.072   1764
  Dihedral  :  7.086 113.562   1355
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 17.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 30.00 %
    Favored  : 66.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.60 (0.24), residues: 1233
  helix:  0.47 (0.20), residues: 663
  sheet: -2.04 (0.47), residues: 111
  loop : -1.13 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 569 
 TYR   0.016   0.001   TYR A 396 
 PHE   0.027   0.002   PHE A 539 
 TRP   0.041   0.002   TRP A 640 
 HIS   0.004   0.001   HIS A 165 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.14 (10126)
  covalent geometry    : angle       0.70604 /  0.34 (13724)
  hydrogen bonds       : bond        0.03595 /  2.34 (  497)
  hydrogen bonds       : angle       5.15550 /  3.77 ( 1452)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 121
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 ASP cc_start: 0.8697 (m-30) cc_final: 0.7784 (p0)
REVERT: A  441 TYR cc_start: 0.8307 (t80) cc_final: 0.7789 (t80)
REVERT: A  454 ARG cc_start: 0.7117 (tpt90) cc_final: 0.6734 (tpt90)
REVERT: A  626 MET cc_start: 0.8406 (mmm) cc_final: 0.7841 (mmm)
REVERT: B  170 PHE cc_start: 0.7899 (m-80) cc_final: 0.7389 (m-80)
REVERT: B  179 LEU cc_start: 0.8159 (mm) cc_final: 0.7676 (mm)
REVERT: B  254 VAL cc_start: 0.7139 (t) cc_final: 0.6811 (p)
REVERT: B  291 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7123 (p0)
REVERT: B  292 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6755 (pm20)
REVERT: B  482 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6375 (mp0)
REVERT: B  519 MET cc_start: 0.9426 (pmm) cc_final: 0.9071 (pmm)
REVERT: B  575 CYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7162 (t)
  outliers start: 38
  outliers final: 28
  residues processed: 149
  average time/residue: 0.0881
  time to fit residues: 19.4715
Evaluate side-chains
  152 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 120
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  221 TYR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  334 TYR
Chi-restraints excluded: chain A residue  356 HIS
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  522 TYR
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain B residue  161 PHE
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  292 GLU
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  358 LEU
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain B residue  377 ASP
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  482 GLU
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  520 PHE
Chi-restraints excluded: chain B residue  575 CYS
Chi-restraints excluded: chain B residue  581 LYS
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  604 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 103 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9990
   chunk 113 optimal weight:    3.9990
   chunk 115 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   chunk 110 optimal weight:    0.7980
   chunk 8 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    1.7588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.123166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.098749 restraints weight = 39001.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.101053 restraints weight = 27280.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.102664 restraints weight = 21076.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.103520 restraints weight = 17493.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.104365 restraints weight = 15674.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.4123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7002
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10126  Z= 0.147
  Angle     :  0.716  11.307  13724  Z= 0.351
  Chirality :  0.043   0.307   1532
  Planarity :  0.005   0.071   1764
  Dihedral  :  7.111 113.175   1355
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 18.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 29.63 %
    Favored  : 66.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.62 (0.24), residues: 1233
  helix:  0.44 (0.20), residues: 663
  sheet: -2.01 (0.47), residues: 111
  loop : -1.14 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 569 
 TYR   0.010   0.001   TYR B 396 
 PHE   0.043   0.002   PHE B 127 
 TRP   0.046   0.002   TRP A 640 
 HIS   0.005   0.001   HIS A 165 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.15 (10126)
  covalent geometry    : angle       0.71611 /  0.35 (13724)
  hydrogen bonds       : bond        0.03655 /  2.40 (  497)
  hydrogen bonds       : angle       5.17826 /  3.79 ( 1452)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 122
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 ASP cc_start: 0.8715 (m-30) cc_final: 0.7830 (p0)
REVERT: A  377 ASP cc_start: 0.8740 (t70) cc_final: 0.8271 (t70)
REVERT: A  454 ARG cc_start: 0.7174 (tpt90) cc_final: 0.6797 (tpt90)
REVERT: A  626 MET cc_start: 0.8501 (mmm) cc_final: 0.7748 (mmp)
REVERT: B  170 PHE cc_start: 0.7913 (m-80) cc_final: 0.7418 (m-80)
REVERT: B  179 LEU cc_start: 0.8170 (mm) cc_final: 0.7670 (mm)
REVERT: B  254 VAL cc_start: 0.7156 (t) cc_final: 0.6846 (p)
REVERT: B  291 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7198 (p0)
REVERT: B  292 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6802 (pm20)
REVERT: B  482 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6600 (mp0)
REVERT: B  519 MET cc_start: 0.9463 (pmm) cc_final: 0.9115 (pmm)
REVERT: B  575 CYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7195 (t)
  outliers start: 40
  outliers final: 30
  residues processed: 150
  average time/residue: 0.0884
  time to fit residues: 19.7222
Evaluate side-chains
  151 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 117
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 TRP
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  221 TYR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  334 TYR
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  356 HIS
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  522 TYR
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain B residue  161 PHE
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  292 GLU
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain B residue  377 ASP
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  482 GLU
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  520 PHE
Chi-restraints excluded: chain B residue  531 ASN
Chi-restraints excluded: chain B residue  575 CYS
Chi-restraints excluded: chain B residue  581 LYS
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  604 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 33 optimal weight:    6.9990
   chunk 109 optimal weight:    9.9990
   chunk 0 optimal weight:   30.0000
   chunk 121 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 53 optimal weight:   10.0000
   chunk 70 optimal weight:    9.9990
   chunk 57 optimal weight:    0.9990
   chunk 101 optimal weight:    5.9990
   overall best weight:    1.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 580 ASN
** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 GLN ** 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 = 0.4429 r_free = 0.4429 target = 0.122666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.098421 restraints weight = 39363.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.100698 restraints weight = 27740.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.102274 restraints weight = 21423.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.103314 restraints weight = 17801.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.103819 restraints weight = 15653.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7013
moved from start:          0.2376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10126  Z= 0.152
  Angle     :  0.736  11.841  13724  Z= 0.361
  Chirality :  0.044   0.313   1532
  Planarity :  0.005   0.071   1764
  Dihedral  :  7.145 113.138   1355
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 18.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 30.00 %
    Favored  : 66.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.24), residues: 1233
  helix:  0.42 (0.20), residues: 663
  sheet: -2.00 (0.47), residues: 111
  loop : -1.15 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 569 
 TYR   0.011   0.001   TYR B 396 
 PHE   0.031   0.002   PHE B 127 
 TRP   0.049   0.002   TRP A 640 
 HIS   0.005   0.001   HIS A 165 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.15 (10126)
  covalent geometry    : angle       0.73633 /  0.36 (13724)
  hydrogen bonds       : bond        0.03671 /  2.41 (  497)
  hydrogen bonds       : angle       5.18070 /  3.80 ( 1452)

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

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

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2466 Ramachandran restraints generated.
    1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 119
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 ASP cc_start: 0.8751 (m-30) cc_final: 0.7881 (p0)
REVERT: A  377 ASP cc_start: 0.8778 (t70) cc_final: 0.8324 (t70)
REVERT: A  454 ARG cc_start: 0.7190 (tpt90) cc_final: 0.6819 (tpt90)
REVERT: A  626 MET cc_start: 0.8464 (mmm) cc_final: 0.7695 (mmp)
REVERT: B  179 LEU cc_start: 0.8136 (mm) cc_final: 0.7624 (mm)
REVERT: B  254 VAL cc_start: 0.7200 (t) cc_final: 0.6875 (p)
REVERT: B  291 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7215 (p0)
REVERT: B  292 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6829 (pm20)
REVERT: B  482 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6710 (mp0)
REVERT: B  519 MET cc_start: 0.9458 (pmm) cc_final: 0.9122 (pmm)
REVERT: B  575 CYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7194 (t)
  outliers start: 34
  outliers final: 30
  residues processed: 142
  average time/residue: 0.0844
  time to fit residues: 17.9303
Evaluate side-chains
  151 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 117
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 TRP
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  221 TYR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  334 TYR
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  356 HIS
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  522 TYR
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  611 TYR
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain B residue  161 PHE
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  292 GLU
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain B residue  377 ASP
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  482 GLU
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  520 PHE
Chi-restraints excluded: chain B residue  531 ASN
Chi-restraints excluded: chain B residue  575 CYS
Chi-restraints excluded: chain B residue  581 LYS
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  604 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 122 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 105 optimal weight:   10.0000
   chunk 100 optimal weight:   10.0000
   chunk 0 optimal weight:   30.0000
   chunk 83 optimal weight:    4.9990
   chunk 110 optimal weight:    0.9980
   chunk 109 optimal weight:    1.9990
   chunk 115 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.123366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.099068 restraints weight = 39993.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.101325 restraints weight = 27718.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.102954 restraints weight = 21412.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.104004 restraints weight = 17768.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.104514 restraints weight = 15601.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.4127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6991
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10126  Z= 0.145
  Angle     :  0.731  12.060  13724  Z= 0.358
  Chirality :  0.044   0.311   1532
  Planarity :  0.005   0.072   1764
  Dihedral  :  7.146 112.784   1355
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 18.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 30.18 %
    Favored  : 66.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.24), residues: 1233
  helix:  0.43 (0.20), residues: 662
  sheet: -1.92 (0.46), residues: 117
  loop : -1.14 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 569 
 TYR   0.010   0.001   TYR B 396 
 PHE   0.024   0.002   PHE A 539 
 TRP   0.047   0.003   TRP A 640 
 HIS   0.004   0.001   HIS A 165 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.15 (10126)
  covalent geometry    : angle       0.73098 /  0.36 (13724)
  hydrogen bonds       : bond        0.03652 /  2.39 (  497)
  hydrogen bonds       : angle       5.14702 /  3.78 ( 1452)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1898.84 seconds
wall clock time: 33 minutes 50.29 seconds (2030.29 seconds total)