Starting phenix.real_space_refine
on Tue Mar  3 21:32:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wix_32539/03_2026/7wix_32539.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wix_32539/03_2026/7wix_32539.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wix_32539/03_2026/7wix_32539.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wix_32539/03_2026/7wix_32539.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wix_32539/03_2026/7wix_32539.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wix_32539/03_2026/7wix_32539.cif"
  }
  resolution = 3.53
  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=   0.043
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: 6
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     Mg      1      5.21       5
     S      14      5.16       5
     C    5521      2.51       5
     N    1557      2.21       5
     O    1573      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8670
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 571, 4344
          Classifications: {'peptide': 571}
          Link IDs: {'PTRANS': 25, 'TRANS': 545}
    Chain: "B"
      Number of atoms: 4271
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 576, 4271
          Classifications: {'peptide': 576}
          Link IDs: {'PTRANS': 25, 'TRANS': 550}
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.03, per 1000 atoms: 0.23
  Number of scatterers: 8670
  At special positions: 0
  Unit cell: (69.7, 98.4, 136.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      14     16.00
     P       4     15.00
     Mg      1     11.99
     O    1573      8.00
     N    1557      7.00
     C    5521      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: 0.74
  Conformation dependent library (CDL) restraints added in 321.9 milliseconds
  

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2102

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 5 sheets defined
      66.8% alpha, 3.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 286 through 288
      No H-bonds generated for 'chain 'A' and resid 286 through 288'
    Processing helix  chain 'A' and resid 289 through 322
      Proline residue:  A 310  - end of helix
    Processing helix  chain 'A' and resid 326 through 375
      removed outlier: 3.653A  pdb=" N   LEU A 330 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 386
      removed outlier: 4.055A  pdb=" N   PHE A 382 " --> pdb=" O   PRO A 378 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   THR A 383 " --> pdb=" O   LEU A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 430
      removed outlier: 4.875A  pdb=" N   VAL A 409 " --> pdb=" O   VAL A 405 " (cutoff:3.500A)
      Proline residue:  A 410  - end of helix
      Proline residue:  A 419  - end of helix
    Processing helix  chain 'A' and resid 432 through 454
      removed outlier: 4.268A  pdb=" N   GLY A 439 " --> pdb=" O   LEU A 435 " (cutoff:3.500A)
      Proline residue:  A 440  - end of helix
    Processing helix  chain 'A' and resid 455 through 479
      removed outlier: 3.986A  pdb=" N   VAL A 460 " --> pdb=" O   GLY A 456 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLY A 471 " --> pdb=" O   GLU A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 486
    Processing helix  chain 'A' and resid 487 through 489
      No H-bonds generated for 'chain 'A' and resid 487 through 489'
    Processing helix  chain 'A' and resid 490 through 509
    Processing helix  chain 'A' and resid 512 through 520
    Processing helix  chain 'A' and resid 523 through 541
      removed outlier: 3.637A  pdb=" N   PHE A 527 " --> pdb=" O   ARG A 523 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   THR A 541 " --> pdb=" O   LEU A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 548
    Processing helix  chain 'A' and resid 549 through 556
    Processing helix  chain 'A' and resid 558 through 573
      removed outlier: 3.636A  pdb=" N   LEU A 563 " --> pdb=" O   PHE A 559 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU A 564 " --> pdb=" O   GLY A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 588
    Processing helix  chain 'A' and resid 649 through 657
      removed outlier: 4.588A  pdb=" N   ALA A 653 " --> pdb=" O   LYS A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 677
    Processing helix  chain 'A' and resid 678 through 684
      removed outlier: 3.705A  pdb=" N   TYR A 683 " --> pdb=" O   ALA A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 699 through 705
    Processing helix  chain 'A' and resid 714 through 722
    Processing helix  chain 'A' and resid 725 through 732
    Processing helix  chain 'A' and resid 747 through 763
    Processing helix  chain 'A' and resid 772 through 777
      removed outlier: 3.705A  pdb=" N   PHE A 775 " --> pdb=" O   ALA A 772 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ALA A 776 " --> pdb=" O   THR A 773 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   ASP A 777 " --> pdb=" O   ALA A 774 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 772 through 777'
    Processing helix  chain 'A' and resid 781 through 792
    Processing helix  chain 'A' and resid 826 through 833
    Processing helix  chain 'A' and resid 836 through 843
    Processing helix  chain 'B' and resid 13 through 45
      removed outlier: 3.869A  pdb=" N   LEU B  17 " --> pdb=" O   HIS B  13 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   THR B  35 " --> pdb=" O   ARG B  31 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   VAL B  36 " --> pdb=" O   ALA B  32 " (cutoff:3.500A)
      Proline residue:  B  40  - end of helix
    Processing helix  chain 'B' and resid 49 through 52
      removed outlier: 3.810A  pdb=" N   ARG B  52 " --> pdb=" O   ALA B  49 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 49 through 52'
    Processing helix  chain 'B' and resid 53 through 96
    Processing helix  chain 'B' and resid 101 through 105
    Processing helix  chain 'B' and resid 108 through 119
    Processing helix  chain 'B' and resid 120 through 150
      removed outlier: 3.575A  pdb=" N   LEU B 124 " --> pdb=" O   THR B 120 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   VAL B 129 " --> pdb=" O   VAL B 125 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU B 131 " --> pdb=" O   LEU B 127 " (cutoff:3.500A)
      Proline residue:  B 134  - end of helix
      Proline residue:  B 142  - end of helix
    Processing helix  chain 'B' and resid 153 through 193
      removed outlier: 4.264A  pdb=" N   ALA B 159 " --> pdb=" O   GLN B 155 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ALA B 160 " --> pdb=" O   LEU B 156 " (cutoff:3.500A)
      Proline residue:  B 165  - end of helix
    Processing helix  chain 'B' and resid 194 through 202
    Processing helix  chain 'B' and resid 202 through 209
    Processing helix  chain 'B' and resid 211 through 227
      removed outlier: 4.028A  pdb=" N   ALA B 215 " --> pdb=" O   ARG B 211 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   HIS B 227 " --> pdb=" O   LEU B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 238
    Processing helix  chain 'B' and resid 238 through 265
      removed outlier: 4.087A  pdb=" N   LEU B 242 " --> pdb=" O   ILE B 238 " (cutoff:3.500A)
      removed outlier: 5.557A  pdb=" N   PHE B 244 " --> pdb=" O   GLY B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 292
      Proline residue:  B 286  - end of helix
    Processing helix  chain 'B' and resid 293 through 312
      removed outlier: 3.707A  pdb=" N   ILE B 307 " --> pdb=" O   THR B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 381
      removed outlier: 4.056A  pdb=" N   LEU B 376 " --> pdb=" O   LYS B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 401 through 406
      removed outlier: 3.710A  pdb=" N   GLN B 406 " --> pdb=" O   ALA B 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 428
    Processing helix  chain 'B' and resid 435 through 446
    Processing helix  chain 'B' and resid 448 through 453
    Processing helix  chain 'B' and resid 472 through 486
      removed outlier: 3.678A  pdb=" N   VAL B 478 " --> pdb=" O   GLU B 474 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU B 485 " --> pdb=" O   ALA B 481 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LYS B 486 " --> pdb=" O   ARG B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 501 through 514
      removed outlier: 4.342A  pdb=" N   GLU B 505 " --> pdb=" O   ASP B 501 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 532
    Processing helix  chain 'B' and resid 550 through 556
      removed outlier: 3.991A  pdb=" N   THR B 556 " --> pdb=" O   SER B 552 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 572
      removed outlier: 3.618A  pdb=" N   ALA B 572 " --> pdb=" O   GLN B 568 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 610 through 611
      removed outlier: 3.629A  pdb=" N   ARG A 668 " --> pdb=" O   VAL A 611 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 616 through 617
    Processing sheet with id=AA3, first strand: chain 'A' and resid 768 through 770
      removed outlier: 7.372A  pdb=" N   LEU A 769 " --> pdb=" O   ILE A 800 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   THR A 639 " --> pdb=" O   VAL A 799 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   GLU A 823 " --> pdb=" O   VAL A 815 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 350 through 355
      removed outlier: 5.709A  pdb=" N   VAL B 337 " --> pdb=" O   GLY B 351 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   SER B 353 " --> pdb=" O   ASP B 335 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   ASP B 335 " --> pdb=" O   SER B 353 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   CYS B 355 " --> pdb=" O   GLU B 333 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   GLU B 333 " --> pdb=" O   CYS B 355 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   GLU B 333 " --> pdb=" O   LEU B 391 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ASP B 335 " --> pdb=" O   ARG B 389 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   ARG B 389 " --> pdb=" O   ASP B 335 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 490 through 494
      removed outlier: 3.536A  pdb=" N   ILE B 523 " --> pdb=" O   THR B 362 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   ALA B 363 " --> pdb=" O   LEU B 538 " (cutoff:3.500A)

    522 hydrogen bonds defined for protein.
    1545 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: 1.48

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1407
        1.31 -     1.43: 2266
        1.43 -     1.56: 5134
        1.56 -     1.68: 6
        1.68 -     1.81: 23
  Bond restraints: 8836
  Sorted by residual:
  bond pdb=" C4  ADP B 601 "
       pdb=" C5  ADP B 601 "
    ideal  model  delta    sigma   weight residual
    1.490  1.381  0.109 2.00e-02 2.50e+03 2.95e+01
  bond pdb=" C4  ADP A 901 "
       pdb=" C5  ADP A 901 "
    ideal  model  delta    sigma   weight residual
    1.490  1.381  0.109 2.00e-02 2.50e+03 2.95e+01
  bond pdb=" C   VAL A 611 "
       pdb=" O   VAL A 611 "
    ideal  model  delta    sigma   weight residual
    1.236  1.186  0.050 9.90e-03 1.02e+04 2.59e+01
  bond pdb=" C5  ADP A 901 "
       pdb=" C6  ADP A 901 "
    ideal  model  delta    sigma   weight residual
    1.490  1.408  0.082 2.00e-02 2.50e+03 1.68e+01
  bond pdb=" C5  ADP B 601 "
       pdb=" C6  ADP B 601 "
    ideal  model  delta    sigma   weight residual
    1.490  1.409  0.081 2.00e-02 2.50e+03 1.64e+01
  ... (remaining 8831 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 11738
        2.42 -     4.85: 293
        4.85 -     7.27: 36
        7.27 -     9.70: 9
        9.70 -    12.12: 5
  Bond angle restraints: 12081
  Sorted by residual:
  angle pdb=" N   PRO A 607 "
        pdb=" CA  PRO A 607 "
        pdb=" C   PRO A 607 "
      ideal   model   delta    sigma   weight residual
     112.47  101.44   11.03 2.06e+00 2.36e-01 2.87e+01
  angle pdb=" O   ALA B 229 "
        pdb=" C   ALA B 229 "
        pdb=" N   THR B 230 "
      ideal   model   delta    sigma   weight residual
     121.47  125.36   -3.89 7.50e-01 1.78e+00 2.69e+01
  angle pdb=" C   ALA B 229 "
        pdb=" CA  ALA B 229 "
        pdb=" CB  ALA B 229 "
      ideal   model   delta    sigma   weight residual
     117.07  110.29    6.78 1.44e+00 4.82e-01 2.22e+01
  angle pdb=" CA  ALA B 229 "
        pdb=" C   ALA B 229 "
        pdb=" N   THR B 230 "
      ideal   model   delta    sigma   weight residual
     120.47  115.63    4.84 1.03e+00 9.43e-01 2.21e+01
  angle pdb=" N   THR A 522 "
        pdb=" CA  THR A 522 "
        pdb=" C   THR A 522 "
      ideal   model   delta    sigma   weight residual
     114.75  108.95    5.80 1.26e+00 6.30e-01 2.12e+01
  ... (remaining 12076 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.86: 5033
       28.86 -    57.73: 166
       57.73 -    86.59: 20
       86.59 -   115.46: 1
      115.46 -   144.32: 3
  Dihedral angle restraints: 5223
    sinusoidal: 1962
      harmonic: 3261
  Sorted by residual:
  dihedral pdb=" O1B ADP A 901 "
           pdb=" O3A ADP A 901 "
           pdb=" PB  ADP A 901 "
           pdb=" PA  ADP A 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   84.32 -144.32     1      2.00e+01 2.50e-03 4.35e+01
  dihedral pdb=" O2A ADP B 601 "
           pdb=" O3A ADP B 601 "
           pdb=" PA  ADP B 601 "
           pdb=" PB  ADP B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   69.06 -129.06     1      2.00e+01 2.50e-03 3.91e+01
  dihedral pdb=" O2A ADP A 901 "
           pdb=" O3A ADP A 901 "
           pdb=" PA  ADP A 901 "
           pdb=" PB  ADP A 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   66.48 -126.48     1      2.00e+01 2.50e-03 3.83e+01
  ... (remaining 5220 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1306
       0.068 -    0.136: 148
       0.136 -    0.203: 12
       0.203 -    0.271: 2
       0.271 -    0.339: 2
  Chirality restraints: 1470
  Sorted by residual:
  chirality pdb=" CA  HIS B 227 "
            pdb=" N   HIS B 227 "
            pdb=" C   HIS B 227 "
            pdb=" CB  HIS B 227 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.87e+00
  chirality pdb=" CA  THR B 230 "
            pdb=" N   THR B 230 "
            pdb=" C   THR B 230 "
            pdb=" CB  THR B 230 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.19    0.33 2.00e-01 2.50e+01 2.80e+00
  chirality pdb=" CB  THR B 230 "
            pdb=" CA  THR B 230 "
            pdb=" OG1 THR B 230 "
            pdb=" CG2 THR B 230 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.29    0.26 2.00e-01 2.50e+01 1.67e+00
  ... (remaining 1467 not shown)

  Planarity restraints: 1538
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  97 "   -0.066 5.00e-02 4.00e+02   1.00e-01 1.60e+01
        pdb=" N   PRO B  98 "    0.173 5.00e-02 4.00e+02
        pdb=" CA  PRO B  98 "   -0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO B  98 "   -0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 605 "    0.018 2.00e-02 2.50e+03   3.70e-02 1.37e+01
        pdb=" C   GLU A 605 "   -0.064 2.00e-02 2.50e+03
        pdb=" O   GLU A 605 "    0.024 2.00e-02 2.50e+03
        pdb=" N   ALA A 606 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 836 "   -0.015 2.00e-02 2.50e+03   3.02e-02 9.12e+00
        pdb=" C   ARG A 836 "    0.052 2.00e-02 2.50e+03
        pdb=" O   ARG A 836 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   TYR A 837 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1535 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 106
        2.63 -     3.20: 8317
        3.20 -     3.77: 13404
        3.77 -     4.33: 16835
        4.33 -     4.90: 28731
  Nonbonded interactions: 67393
  Sorted by model distance:
  nonbonded pdb=" O1B ADP B 601 "
            pdb="MG    MG B 602 "
     model   vdw
     2.063 2.170
  nonbonded pdb=" OE2 GLU A 681 "
            pdb=" NH2 ARG A 685 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" O   GLU A 605 "
            pdb=" CG2 THR A 609 "
     model   vdw
     2.261 3.460
  nonbonded pdb=" O   GLU B 465 "
            pdb=" OG  SER B 468 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   ASP A 680 "
            pdb=" OG1 THR A 684 "
     model   vdw
     2.279 3.040
  ... (remaining 67388 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             4.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.200
  Find NCS groups from input model:        0.050
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
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   0.109   8836  Z= 0.266
  Angle     :  0.925  12.123  12081  Z= 0.550
  Chirality :  0.045   0.339   1470
  Planarity :  0.005   0.100   1538
  Dihedral  : 14.856 144.323   3121
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 10.15 %
    Favored  : 89.50 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  6.70 %
    Favored  : 92.73 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.81 (0.22), residues: 1143
  helix: -0.61 (0.18), residues: 711
  sheet: -2.68 (0.61), residues: 62
  loop : -4.20 (0.25), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 753 
 TYR   0.008   0.001   TYR A 736 
 PHE   0.024   0.001   PHE B 334 
 TRP   0.008   0.001   TRP B  56 
 HIS   0.010   0.001   HIS B 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 8836)
  covalent geometry    : angle       0.92523 (12081)
  hydrogen bonds       : bond        0.12779 (  522)
  hydrogen bonds       : angle       5.55414 ( 1545)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  691 GLN cc_start: 0.7183 (mm-40) cc_final: 0.6797 (mm-40)
  outliers start: 5
  outliers final: 5
  residues processed: 103
  average time/residue: 0.1140
  time to fit residues: 15.6316
Evaluate side-chains
  61 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  232 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.4980
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0370
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.6462

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

Flipped N/Q/H residues before XYZ refinement:
A 461 GLN
A 582 HIS
A 752 GLN
B 204 GLN
B 420 HIS
B 504 ASN
B 569 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.079788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.068068 restraints weight = 23663.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.070127 restraints weight = 12759.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.071600 restraints weight = 8527.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.072589 restraints weight = 6400.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.073304 restraints weight = 5214.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.1306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8836  Z= 0.140
  Angle     :  0.708   8.680  12081  Z= 0.345
  Chirality :  0.042   0.162   1470
  Planarity :  0.005   0.093   1538
  Dihedral  :  9.349 155.422   1279
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.57 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 13.07 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.00 %
    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: -1.07 (0.25), residues: 1143
  helix:  0.76 (0.20), residues: 722
  sheet: -1.72 (0.65), residues: 59
  loop : -3.71 (0.28), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 207 
 TYR   0.010   0.001   TYR A 444 
 PHE   0.022   0.001   PHE B 334 
 TRP   0.008   0.001   TRP A 841 
 HIS   0.004   0.001   HIS A 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8836)
  covalent geometry    : angle       0.70752 (12081)
  hydrogen bonds       : bond        0.04646 (  522)
  hydrogen bonds       : angle       4.56913 ( 1545)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 74
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
  outliers start: 27
  outliers final: 14
  residues processed: 92
  average time/residue: 0.0832
  time to fit residues: 11.1497
Evaluate side-chains
  76 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  654 THR
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  232 ARG
Chi-restraints excluded: chain B residue  322 THR
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0030
   chunk 7 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   chunk 83 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 67 optimal weight:    0.4980
   chunk 14 optimal weight:    4.9990
   chunk 92 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
A 582 HIS
B 569 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.080359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.068549 restraints weight = 23605.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.070670 restraints weight = 12739.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.072128 restraints weight = 8483.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.073108 restraints weight = 6383.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.073781 restraints weight = 5223.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.1633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8836  Z= 0.126
  Angle     :  0.674  10.442  12081  Z= 0.326
  Chirality :  0.041   0.162   1470
  Planarity :  0.005   0.090   1538
  Dihedral  :  9.012 159.128   1278
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.31 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 14.55 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.00 %
    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 (0.26), residues: 1143
  helix:  1.26 (0.20), residues: 715
  sheet: -1.76 (0.62), residues: 74
  loop : -3.31 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 560 
 TYR   0.008   0.001   TYR A 837 
 PHE   0.020   0.001   PHE B 334 
 TRP   0.008   0.001   TRP A 841 
 HIS   0.003   0.001   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8836)
  covalent geometry    : angle       0.67368 (12081)
  hydrogen bonds       : bond        0.04314 (  522)
  hydrogen bonds       : angle       4.33118 ( 1545)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 70
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
REVERT: A  750 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6796 (mt-10)
  outliers start: 32
  outliers final: 19
  residues processed: 93
  average time/residue: 0.0791
  time to fit residues: 10.7618
Evaluate side-chains
  79 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 60
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  591 GLU
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  637 THR
Chi-restraints excluded: chain A residue  654 THR
Chi-restraints excluded: chain A residue  769 LEU
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  232 ARG
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  322 THR
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 16 optimal weight:    0.1980
   chunk 37 optimal weight:    0.8980
   chunk 96 optimal weight:    0.8980
   chunk 79 optimal weight:    0.0000
   chunk 61 optimal weight:    0.6980
   chunk 94 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0470
   chunk 100 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 69 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.3082

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.082338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.070446 restraints weight = 23815.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.072613 restraints weight = 12748.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.074113 restraints weight = 8462.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.075097 restraints weight = 6345.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.075840 restraints weight = 5174.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8836  Z= 0.119
  Angle     :  0.651   9.840  12081  Z= 0.313
  Chirality :  0.041   0.160   1470
  Planarity :  0.005   0.086   1538
  Dihedral  :  8.651 166.712   1275
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.49 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 15.91 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.00 %
    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: -0.06 (0.26), residues: 1143
  helix:  1.46 (0.20), residues: 717
  sheet: -1.18 (0.66), residues: 69
  loop : -3.08 (0.30), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 385 
 TYR   0.015   0.001   TYR A 403 
 PHE   0.014   0.001   PHE B 334 
 TRP   0.009   0.001   TRP A 841 
 HIS   0.002   0.001   HIS B 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 8836)
  covalent geometry    : angle       0.65128 (12081)
  hydrogen bonds       : bond        0.03889 (  522)
  hydrogen bonds       : angle       4.10374 ( 1545)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 74
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: A  750 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6704 (mt-10)
  outliers start: 33
  outliers final: 26
  residues processed: 99
  average time/residue: 0.0728
  time to fit residues: 10.6241
Evaluate side-chains
  89 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 63
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  591 GLU
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  632 THR
Chi-restraints excluded: chain A residue  637 THR
Chi-restraints excluded: chain A residue  654 THR
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  769 LEU
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  232 ARG
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  322 THR
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  569 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 106 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 66 optimal weight:    0.0070
   chunk 1 optimal weight:    0.9980
   chunk 78 optimal weight:    0.7980
   chunk 99 optimal weight:    0.4980
   chunk 50 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 79 optimal weight:    0.1980
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
A 703 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.082213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.070451 restraints weight = 23428.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.072625 restraints weight = 12613.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.074084 restraints weight = 8372.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.075034 restraints weight = 6288.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.075800 restraints weight = 5162.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8836  Z= 0.119
  Angle     :  0.649   7.774  12081  Z= 0.312
  Chirality :  0.041   0.160   1470
  Planarity :  0.005   0.084   1538
  Dihedral  :  8.634 175.714   1274
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.22 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 17.61 %
    Favored  : 78.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.00 %
    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:  0.15 (0.26), residues: 1143
  helix:  1.59 (0.20), residues: 716
  sheet: -1.16 (0.64), residues: 74
  loop : -2.89 (0.30), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 751 
 TYR   0.007   0.001   TYR A 736 
 PHE   0.014   0.001   PHE B 334 
 TRP   0.009   0.001   TRP A 841 
 HIS   0.003   0.000   HIS B 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 8836)
  covalent geometry    : angle       0.64869 (12081)
  hydrogen bonds       : bond        0.03813 (  522)
  hydrogen bonds       : angle       4.01514 ( 1545)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 69
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A  750 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6730 (mt-10)
REVERT: B  236 MET cc_start: 0.7398 (tmm) cc_final: 0.6991 (mmt)
  outliers start: 36
  outliers final: 23
  residues processed: 96
  average time/residue: 0.0707
  time to fit residues: 10.7023
Evaluate side-chains
  87 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 64
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  591 GLU
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  632 THR
Chi-restraints excluded: chain A residue  637 THR
Chi-restraints excluded: chain A residue  654 THR
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  769 LEU
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  322 THR
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   chunk 27 optimal weight:    0.6980
   chunk 90 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 85 optimal weight:    0.7980
   chunk 99 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
B 383 HIS
B 438 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.079664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.067809 restraints weight = 23534.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.069941 restraints weight = 12741.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.071372 restraints weight = 8520.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.072362 restraints weight = 6472.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.073013 restraints weight = 5276.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8836  Z= 0.153
  Angle     :  0.683  16.115  12081  Z= 0.329
  Chirality :  0.042   0.160   1470
  Planarity :  0.005   0.087   1538
  Dihedral  :  8.345 169.092   1270
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.10 %
    Favored  : 90.81 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 18.64 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.00 %
    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:  0.25 (0.26), residues: 1143
  helix:  1.65 (0.20), residues: 716
  sheet: -1.14 (0.64), residues: 74
  loop : -2.79 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 385 
 TYR   0.017   0.002   TYR A 403 
 PHE   0.020   0.001   PHE B 334 
 TRP   0.006   0.001   TRP A 841 
 HIS   0.005   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8836)
  covalent geometry    : angle       0.68272 (12081)
  hydrogen bonds       : bond        0.04267 (  522)
  hydrogen bonds       : angle       4.09432 ( 1545)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 67
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A  750 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6866 (mt-10)
REVERT: B  231 MET cc_start: 0.7269 (mpp) cc_final: 0.7002 (ptp)
REVERT: B  236 MET cc_start: 0.7519 (tmm) cc_final: 0.7012 (mmt)
  outliers start: 31
  outliers final: 28
  residues processed: 89
  average time/residue: 0.0662
  time to fit residues: 9.0750
Evaluate side-chains
  90 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 62
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  591 GLU
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  632 THR
Chi-restraints excluded: chain A residue  637 THR
Chi-restraints excluded: chain A residue  654 THR
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  769 LEU
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  182 ASP
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  322 THR
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  569 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   chunk 88 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   chunk 98 optimal weight:    0.0570
   chunk 23 optimal weight:    0.9980
   chunk 110 optimal weight:    0.9980
   chunk 96 optimal weight:    4.9990
   overall best weight:    0.7898

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.080606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.068768 restraints weight = 23753.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.070945 restraints weight = 12753.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.072417 restraints weight = 8466.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.073369 restraints weight = 6352.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.074160 restraints weight = 5195.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8836  Z= 0.128
  Angle     :  0.669  14.536  12081  Z= 0.319
  Chirality :  0.041   0.159   1470
  Planarity :  0.005   0.086   1538
  Dihedral  :  7.867 149.854   1270
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.92 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 19.43 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.00 %
    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:  0.36 (0.27), residues: 1143
  helix:  1.71 (0.20), residues: 716
  sheet: -1.09 (0.64), residues: 74
  loop : -2.70 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 385 
 TYR   0.008   0.001   TYR A 425 
 PHE   0.016   0.001   PHE B 334 
 TRP   0.008   0.001   TRP A 841 
 HIS   0.006   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8836)
  covalent geometry    : angle       0.66869 (12081)
  hydrogen bonds       : bond        0.04016 (  522)
  hydrogen bonds       : angle       4.02484 ( 1545)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 63
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A  392 LYS cc_start: 0.9071 (tmtt) cc_final: 0.8516 (tmmt)
REVERT: A  396 ASP cc_start: 0.7774 (m-30) cc_final: 0.7449 (m-30)
REVERT: A  397 ASP cc_start: 0.7657 (m-30) cc_final: 0.7347 (m-30)
REVERT: A  511 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9052 (pp)
REVERT: A  750 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6846 (mt-10)
REVERT: B  231 MET cc_start: 0.7144 (mpp) cc_final: 0.6865 (ptp)
REVERT: B  236 MET cc_start: 0.7467 (tmm) cc_final: 0.7013 (mmt)
  outliers start: 36
  outliers final: 27
  residues processed: 89
  average time/residue: 0.0701
  time to fit residues: 9.6007
Evaluate side-chains
  89 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 61
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  591 GLU
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  632 THR
Chi-restraints excluded: chain A residue  637 THR
Chi-restraints excluded: chain A residue  654 THR
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  769 LEU
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  182 ASP
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  322 THR
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  337 VAL
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  569 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 110 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 74 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 86 optimal weight:    4.9990
   chunk 80 optimal weight:    0.1980
   chunk 29 optimal weight:    5.9990
   overall best weight:    0.7182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.081100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.069281 restraints weight = 23546.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.071428 restraints weight = 12683.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.072914 restraints weight = 8438.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.073950 restraints weight = 6331.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.074658 restraints weight = 5136.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8836  Z= 0.126
  Angle     :  0.667  14.742  12081  Z= 0.319
  Chirality :  0.041   0.162   1470
  Planarity :  0.005   0.085   1538
  Dihedral  :  7.301 133.374   1270
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.14 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 19.32 %
    Favored  : 76.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.00 %
    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:  0.44 (0.27), residues: 1143
  helix:  1.76 (0.20), residues: 716
  sheet: -1.04 (0.64), residues: 74
  loop : -2.65 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 385 
 TYR   0.014   0.001   TYR A 444 
 PHE   0.014   0.001   PHE B 334 
 TRP   0.008   0.001   TRP A 841 
 HIS   0.005   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 8836)
  covalent geometry    : angle       0.66657 (12081)
  hydrogen bonds       : bond        0.03935 (  522)
  hydrogen bonds       : angle       3.97511 ( 1545)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 62
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: A  511 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9043 (pp)
REVERT: A  750 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6753 (mt-10)
REVERT: B  231 MET cc_start: 0.7095 (mpp) cc_final: 0.6844 (ptp)
REVERT: B  236 MET cc_start: 0.7426 (tmm) cc_final: 0.6934 (mmt)
  outliers start: 33
  outliers final: 25
  residues processed: 86
  average time/residue: 0.0700
  time to fit residues: 9.3033
Evaluate side-chains
  87 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 61
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  591 GLU
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  632 THR
Chi-restraints excluded: chain A residue  637 THR
Chi-restraints excluded: chain A residue  654 THR
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  769 LEU
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  182 ASP
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  322 THR
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  540 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 35 optimal weight:    0.0570
   chunk 73 optimal weight:    0.0970
   chunk 10 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 103 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.5496

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.081992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.070278 restraints weight = 23512.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.072488 restraints weight = 12592.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.073959 restraints weight = 8319.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.074909 restraints weight = 6232.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.075641 restraints weight = 5089.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8836  Z= 0.120
  Angle     :  0.668  14.000  12081  Z= 0.317
  Chirality :  0.041   0.176   1470
  Planarity :  0.005   0.084   1538
  Dihedral  :  6.925 132.081   1270
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.05 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 19.43 %
    Favored  : 76.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.00 %
    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:  0.49 (0.27), residues: 1143
  helix:  1.79 (0.20), residues: 718
  sheet: -1.02 (0.64), residues: 74
  loop : -2.61 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 385 
 TYR   0.006   0.001   TYR A 736 
 PHE   0.011   0.001   PHE B 334 
 TRP   0.008   0.001   TRP A 841 
 HIS   0.004   0.000   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 8836)
  covalent geometry    : angle       0.66778 (12081)
  hydrogen bonds       : bond        0.03785 (  522)
  hydrogen bonds       : angle       3.91363 ( 1545)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 68
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
REVERT: A  397 ASP cc_start: 0.7682 (m-30) cc_final: 0.7428 (m-30)
REVERT: A  511 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9047 (pp)
REVERT: A  750 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6760 (mt-10)
REVERT: B  231 MET cc_start: 0.7108 (mpp) cc_final: 0.6864 (ptp)
REVERT: B  236 MET cc_start: 0.7448 (tmm) cc_final: 0.6931 (mmt)
  outliers start: 34
  outliers final: 26
  residues processed: 91
  average time/residue: 0.0789
  time to fit residues: 10.7592
Evaluate side-chains
  93 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 66
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  591 GLU
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  632 THR
Chi-restraints excluded: chain A residue  637 THR
Chi-restraints excluded: chain A residue  654 THR
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  769 LEU
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  182 ASP
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  322 THR
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  540 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 87 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 100 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 80 optimal weight:    0.9990
   chunk 95 optimal weight:    0.0870
   chunk 97 optimal weight:    3.9990
   overall best weight:    0.5558

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.082055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.070342 restraints weight = 23426.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.072516 restraints weight = 12556.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.073997 restraints weight = 8330.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.074950 restraints weight = 6229.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.075711 restraints weight = 5082.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8836  Z= 0.119
  Angle     :  0.671  11.571  12081  Z= 0.318
  Chirality :  0.041   0.174   1470
  Planarity :  0.005   0.084   1538
  Dihedral  :  6.739 131.748   1270
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.14 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 20.23 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.00 %
    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:  0.54 (0.26), residues: 1143
  helix:  1.78 (0.20), residues: 721
  sheet: -0.63 (0.67), residues: 67
  loop : -2.57 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 385 
 TYR   0.013   0.001   TYR A 403 
 PHE   0.012   0.001   PHE B 334 
 TRP   0.008   0.001   TRP A 841 
 HIS   0.003   0.000   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8836)
  covalent geometry    : angle       0.67097 (12081)
  hydrogen bonds       : bond        0.03738 (  522)
  hydrogen bonds       : angle       3.86914 ( 1545)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 68
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A  511 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9041 (pp)
REVERT: A  750 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6748 (mt-10)
REVERT: B  231 MET cc_start: 0.7038 (mpp) cc_final: 0.6800 (ptp)
REVERT: B  236 MET cc_start: 0.7452 (tmm) cc_final: 0.6911 (mmt)
  outliers start: 29
  outliers final: 26
  residues processed: 90
  average time/residue: 0.0802
  time to fit residues: 10.5545
Evaluate side-chains
  90 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 63
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  591 GLU
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  632 THR
Chi-restraints excluded: chain A residue  637 THR
Chi-restraints excluded: chain A residue  654 THR
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  769 LEU
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  182 ASP
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  322 THR
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  569 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 86 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.9584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.078811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.066500 restraints weight = 24132.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.068814 restraints weight = 11953.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.070346 restraints weight = 7604.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.071474 restraints weight = 5616.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.072198 restraints weight = 4480.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8836  Z= 0.136
  Angle     :  0.692  12.403  12081  Z= 0.330
  Chirality :  0.042   0.164   1470
  Planarity :  0.005   0.084   1538
  Dihedral  :  6.701 132.911   1270
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.49 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 20.34 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.00 %
    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:  0.56 (0.27), residues: 1143
  helix:  1.82 (0.20), residues: 718
  sheet: -0.62 (0.68), residues: 67
  loop : -2.60 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 385 
 TYR   0.011   0.001   TYR A 444 
 PHE   0.023   0.001   PHE B 334 
 TRP   0.006   0.001   TRP A 841 
 HIS   0.003   0.000   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 8836)
  covalent geometry    : angle       0.69165 (12081)
  hydrogen bonds       : bond        0.03933 (  522)
  hydrogen bonds       : angle       3.90721 ( 1545)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1283.61 seconds
wall clock time: 22 minutes 47.08 seconds (1367.08 seconds total)