Starting phenix.real_space_refine
on Fri Jul  3 04:36:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zgp_60086/07_2026/8zgp_60086.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zgp_60086/07_2026/8zgp_60086.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zgp_60086/07_2026/8zgp_60086.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zgp_60086/07_2026/8zgp_60086.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zgp_60086/07_2026/8zgp_60086.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zgp_60086/07_2026/8zgp_60086.map"
  }
  resolution = 1.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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
     Ca      2      9.91       5
     Fe      6      7.16       5
     S      54      5.16       5
     C    7998      2.51       5
     N    1910      2.21       5
     O    2186      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12156
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5927
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 742, 5908
          Classifications: {'peptide': 742}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 712}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 742, 5908
          Classifications: {'peptide': 742}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 712}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 6077
    Chain: "A"
      Number of atoms: 88
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 86
          Ad-hoc single atom residues: {' FE': 1, ' CA': 1}
          Unusual residues: {'HEM': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 63
          Classifications: {'water': 63}
          Link IDs: {None: 62}
    Chain: "B"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 63
          Classifications: {'water': 63}
          Link IDs: {None: 62}
  Restraints were copied for chains:
    B
  Time building chain proxies: 6.20, per 1000 atoms: 0.51
  Number of scatterers: 12156
  At special positions: 0
  Unit cell: (109.04, 106.032, 103.776, 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)
     Fe      6     26.01
     Ca      2     19.99
     S      54     16.00
     O    2186      8.00
     N    1910      7.00
     C    7998      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 823.9 milliseconds
  

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2724

  Finding SS restraints...
    Secondary structure from input PDB file:
      80 helices and 4 sheets defined
      81.3% alpha, 1.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 3
      No H-bonds generated for 'chain 'A' and resid 1 through 3'
    Processing helix  chain 'A' and resid 4 through 33
    Processing helix  chain 'A' and resid 51 through 65
    Processing helix  chain 'A' and resid 66 through 69
    Processing helix  chain 'A' and resid 82 through 104
    Processing helix  chain 'A' and resid 107 through 111
      removed outlier: 3.574A  pdb=" N   VAL A 111 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 129
    Processing helix  chain 'A' and resid 142 through 161
      Proline residue:  A 154  - end of helix
    Processing helix  chain 'A' and resid 163 through 165
      No H-bonds generated for 'chain 'A' and resid 163 through 165'
    Processing helix  chain 'A' and resid 166 through 173
    Processing helix  chain 'A' and resid 182 through 202
    Processing helix  chain 'A' and resid 218 through 222
    Processing helix  chain 'A' and resid 226 through 255
    Processing helix  chain 'A' and resid 266 through 271
      removed outlier: 3.854A  pdb=" N   VAL A 271 " --> pdb=" O   PRO A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 279
    Processing helix  chain 'A' and resid 280 through 307
      removed outlier: 3.541A  pdb=" N   VAL A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 326
      removed outlier: 4.271A  pdb=" N   TRP A 325 " --> pdb=" O   GLU A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 359
      Proline residue:  A 356  - end of helix
    Processing helix  chain 'A' and resid 366 through 394
    Processing helix  chain 'A' and resid 398 through 400
      No H-bonds generated for 'chain 'A' and resid 398 through 400'
    Processing helix  chain 'A' and resid 401 through 406
    Processing helix  chain 'A' and resid 416 through 436
    Processing helix  chain 'A' and resid 438 through 444
    Processing helix  chain 'A' and resid 449 through 465
    Processing helix  chain 'A' and resid 466 through 471
    Processing helix  chain 'A' and resid 477 through 512
      removed outlier: 3.735A  pdb=" N   VAL A 493 " --> pdb=" O   VAL A 489 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   PHE A 496 " --> pdb=" O   TRP A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 539
      removed outlier: 3.543A  pdb=" N   GLY A 534 " --> pdb=" O   ILE A 530 " (cutoff:3.500A)
      Proline residue:  A 537  - end of helix
    Processing helix  chain 'A' and resid 540 through 543
    Processing helix  chain 'A' and resid 549 through 568
      removed outlier: 3.623A  pdb=" N   LEU A 562 " --> pdb=" O   CYS A 558 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLU A 563 " --> pdb=" O   PHE A 559 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   VAL A 564 " --> pdb=" O   SER A 560 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   VAL A 565 " --> pdb=" O   ALA A 561 " (cutoff:3.500A)
      Proline residue:  A 566  - end of helix
    Processing helix  chain 'A' and resid 570 through 581
      removed outlier: 4.154A  pdb=" N   GLN A 581 " --> pdb=" O   HIS A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 586 through 589
    Processing helix  chain 'A' and resid 590 through 606
    Processing helix  chain 'A' and resid 608 through 614
    Processing helix  chain 'A' and resid 617 through 625
      removed outlier: 4.300A  pdb=" N   TYR A 623 " --> pdb=" O   ILE A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 658
      removed outlier: 3.937A  pdb=" N   ALA A 631 " --> pdb=" O   LEU A 627 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   PHE A 644 " --> pdb=" O   GLY A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 664 through 686
    Processing helix  chain 'A' and resid 686 through 701
    Processing helix  chain 'A' and resid 702 through 707
    Processing helix  chain 'A' and resid 708 through 713
    Processing helix  chain 'A' and resid 714 through 747
      removed outlier: 4.208A  pdb=" N   THR A 725 " --> pdb=" O   ARG A 721 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   ALA A 726 " --> pdb=" O   TRP A 722 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   ALA A 727 " --> pdb=" O   VAL A 723 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1 through 3
      No H-bonds generated for 'chain 'B' and resid 1 through 3'
    Processing helix  chain 'B' and resid 4 through 33
    Processing helix  chain 'B' and resid 51 through 65
    Processing helix  chain 'B' and resid 66 through 69
    Processing helix  chain 'B' and resid 82 through 104
    Processing helix  chain 'B' and resid 107 through 111
      removed outlier: 3.575A  pdb=" N   VAL B 111 " --> pdb=" O   PHE B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 129
    Processing helix  chain 'B' and resid 142 through 161
      Proline residue:  B 154  - end of helix
    Processing helix  chain 'B' and resid 163 through 165
      No H-bonds generated for 'chain 'B' and resid 163 through 165'
    Processing helix  chain 'B' and resid 166 through 173
    Processing helix  chain 'B' and resid 182 through 202
    Processing helix  chain 'B' and resid 218 through 222
    Processing helix  chain 'B' and resid 226 through 255
    Processing helix  chain 'B' and resid 266 through 271
      removed outlier: 3.854A  pdb=" N   VAL B 271 " --> pdb=" O   PRO B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 279
    Processing helix  chain 'B' and resid 280 through 307
      removed outlier: 3.540A  pdb=" N   VAL B 306 " --> pdb=" O   ALA B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 326
      removed outlier: 4.271A  pdb=" N   TRP B 325 " --> pdb=" O   GLU B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 359
      Proline residue:  B 356  - end of helix
    Processing helix  chain 'B' and resid 366 through 394
    Processing helix  chain 'B' and resid 398 through 400
      No H-bonds generated for 'chain 'B' and resid 398 through 400'
    Processing helix  chain 'B' and resid 401 through 406
    Processing helix  chain 'B' and resid 416 through 436
    Processing helix  chain 'B' and resid 438 through 444
    Processing helix  chain 'B' and resid 449 through 465
    Processing helix  chain 'B' and resid 466 through 471
    Processing helix  chain 'B' and resid 477 through 512
      removed outlier: 3.735A  pdb=" N   VAL B 493 " --> pdb=" O   VAL B 489 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   PHE B 496 " --> pdb=" O   TRP B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 516 through 539
      removed outlier: 3.543A  pdb=" N   GLY B 534 " --> pdb=" O   ILE B 530 " (cutoff:3.500A)
      Proline residue:  B 537  - end of helix
    Processing helix  chain 'B' and resid 540 through 543
    Processing helix  chain 'B' and resid 549 through 568
      removed outlier: 3.624A  pdb=" N   LEU B 562 " --> pdb=" O   CYS B 558 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLU B 563 " --> pdb=" O   PHE B 559 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   VAL B 564 " --> pdb=" O   SER B 560 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   VAL B 565 " --> pdb=" O   ALA B 561 " (cutoff:3.500A)
      Proline residue:  B 566  - end of helix
    Processing helix  chain 'B' and resid 570 through 581
      removed outlier: 4.154A  pdb=" N   GLN B 581 " --> pdb=" O   HIS B 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 586 through 589
    Processing helix  chain 'B' and resid 590 through 606
    Processing helix  chain 'B' and resid 608 through 614
    Processing helix  chain 'B' and resid 617 through 625
      removed outlier: 4.300A  pdb=" N   TYR B 623 " --> pdb=" O   ILE B 619 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 627 through 658
      removed outlier: 3.937A  pdb=" N   ALA B 631 " --> pdb=" O   LEU B 627 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   PHE B 644 " --> pdb=" O   GLY B 640 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 664 through 686
    Processing helix  chain 'B' and resid 686 through 701
    Processing helix  chain 'B' and resid 702 through 707
    Processing helix  chain 'B' and resid 708 through 713
    Processing helix  chain 'B' and resid 714 through 747
      removed outlier: 4.208A  pdb=" N   THR B 725 " --> pdb=" O   ARG B 721 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   ALA B 726 " --> pdb=" O   TRP B 722 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   ALA B 727 " --> pdb=" O   VAL B 723 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50
      removed outlier: 6.725A  pdb=" N   VAL A  40 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 50
      removed outlier: 6.725A  pdb=" N   VAL B  40 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 71 through 72

    856 hydrogen bonds defined for protein.
    2502 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.14

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.22 -     1.39: 5253
        1.39 -     1.56: 7075
        1.56 -     1.73: 0
        1.73 -     1.91: 98
        1.91 -     2.08: 16
  Bond restraints: 12442
  Sorted by residual:
  bond pdb=" N   ARG B 122 "
       pdb=" CA BARG B 122 "
    ideal  model  delta    sigma   weight residual
    1.459  1.555 -0.096 1.19e-02 7.06e+03 6.51e+01
  bond pdb=" N   ARG A 122 "
       pdb=" CA BARG A 122 "
    ideal  model  delta    sigma   weight residual
    1.459  1.555 -0.096 1.19e-02 7.06e+03 6.49e+01
  bond pdb=" C   ARG B 122 "
       pdb=" CA BARG B 122 "
    ideal  model  delta    sigma   weight residual
    1.524  1.471  0.052 1.27e-02 6.20e+03 1.70e+01
  bond pdb=" C   ARG A 122 "
       pdb=" CA BARG A 122 "
    ideal  model  delta    sigma   weight residual
    1.524  1.472  0.052 1.27e-02 6.20e+03 1.67e+01
  bond pdb=" CE1 HIS B 335 "
       pdb=" NE2 HIS B 335 "
    ideal  model  delta    sigma   weight residual
    1.321  1.362 -0.041 1.00e-02 1.00e+04 1.66e+01
  ... (remaining 12437 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 16524
        1.86 -     3.73: 418
        3.73 -     5.59: 64
        5.59 -     7.45: 10
        7.45 -     9.32: 4
  Bond angle restraints: 17020
  Sorted by residual:
  angle pdb=" C   ILE A 685 "
        pdb=" N   SER A 686 "
        pdb=" CA  SER A 686 "
      ideal   model   delta    sigma   weight residual
     122.17  115.84    6.33 1.54e+00 4.22e-01 1.69e+01
  angle pdb=" C   ILE B 685 "
        pdb=" N   SER B 686 "
        pdb=" CA  SER B 686 "
      ideal   model   delta    sigma   weight residual
     122.17  115.86    6.31 1.54e+00 4.22e-01 1.68e+01
  angle pdb=" CB  MET A 481 "
        pdb=" CG  MET A 481 "
        pdb=" SD  MET A 481 "
      ideal   model   delta    sigma   weight residual
     112.70  122.02   -9.32 3.00e+00 1.11e-01 9.65e+00
  angle pdb=" CB  MET B 481 "
        pdb=" CG  MET B 481 "
        pdb=" SD  MET B 481 "
      ideal   model   delta    sigma   weight residual
     112.70  122.02   -9.32 3.00e+00 1.11e-01 9.65e+00
  angle pdb=" CA  TRP A 342 "
        pdb=" CB  TRP A 342 "
        pdb=" CG  TRP A 342 "
      ideal   model   delta    sigma   weight residual
     113.60  119.48   -5.88 1.90e+00 2.77e-01 9.58e+00
  ... (remaining 17015 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 6150
       17.87 -    35.74: 574
       35.74 -    53.61: 128
       53.61 -    71.48: 52
       71.48 -    89.35: 28
  Dihedral angle restraints: 6932
    sinusoidal: 2648
      harmonic: 4284
  Sorted by residual:
  dihedral pdb=" CA  PHE A 465 "
           pdb=" C   PHE A 465 "
           pdb=" N   TYR A 466 "
           pdb=" CA  TYR A 466 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.25   18.75     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  PHE B 465 "
           pdb=" C   PHE B 465 "
           pdb=" N   TYR B 466 "
           pdb=" CA  TYR B 466 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.26   18.74     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  GLU A 307 "
           pdb=" C   GLU A 307 "
           pdb=" N   GLY A 308 "
           pdb=" CA  GLY A 308 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.72  -18.28     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 6929 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1099
       0.036 -    0.071: 507
       0.071 -    0.107: 162
       0.107 -    0.142: 34
       0.142 -    0.178: 10
  Chirality restraints: 1812
  Sorted by residual:
  chirality pdb=" CA BARG A 122 "
            pdb=" N   ARG A 122 "
            pdb=" C   ARG A 122 "
            pdb=" CB BARG A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.90e-01
  chirality pdb=" CA  ILE A 336 "
            pdb=" N   ILE A 336 "
            pdb=" C   ILE A 336 "
            pdb=" CB  ILE A 336 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.90e-01
  chirality pdb=" CA  ILE B 336 "
            pdb=" N   ILE B 336 "
            pdb=" C   ILE B 336 "
            pdb=" CB  ILE B 336 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.80e-01
  ... (remaining 1809 not shown)

  Planarity restraints: 2094
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 132 "    0.230 9.50e-02 1.11e+02   1.03e-01 6.52e+00
        pdb=" NE  ARG B 132 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 132 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 132 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 132 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 132 "    0.229 9.50e-02 1.11e+02   1.03e-01 6.47e+00
        pdb=" NE  ARG A 132 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 132 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 132 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 132 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 487 "   -0.010 2.00e-02 2.50e+03   1.98e-02 3.92e+00
        pdb=" C   TRP A 487 "    0.034 2.00e-02 2.50e+03
        pdb=" O   TRP A 487 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   VAL A 488 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 2091 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 168
        2.63 -     3.20: 11809
        3.20 -     3.77: 21861
        3.77 -     4.33: 30936
        4.33 -     4.90: 48525
  Nonbonded interactions: 113299
  Sorted by model distance:
  nonbonded pdb="FE    FE A 803 "
            pdb=" O   HOH A 905 "
     model   vdw
     2.066 3.000
  nonbonded pdb="FE    FE B 803 "
            pdb=" O   HOH B 905 "
     model   vdw
     2.066 3.000
  nonbonded pdb=" ND1 HIS B 490 "
            pdb="FE    FE B 803 "
     model   vdw
     2.078 3.080
  nonbonded pdb=" ND1 HIS A 490 "
            pdb="FE    FE A 803 "
     model   vdw
     2.079 3.080
  nonbonded pdb=" NE2 HIS B 542 "
            pdb="FE    FE B 803 "
     model   vdw
     2.146 3.080
  ... (remaining 113294 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     16.150
  Find NCS groups from input model:        0.120
  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:             0.010
  Load rotamer database and sin/cos tables:6.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.295  12446  Z= 0.267
  Angle     :  0.717   9.319  17020  Z= 0.414
  Chirality :  0.046   0.178   1812
  Planarity :  0.006   0.103   2094
  Dihedral  : 16.716  89.352   4208
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 11.54 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.72 (0.22), residues: 1482
  helix:  1.47 (0.16), residues: 1060
  sheet:  None (None), residues: 0
  loop :  0.52 (0.33), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 128 
 TYR   0.027   0.002   TYR A 328 
 PHE   0.030   0.002   PHE B 613 
 TRP   0.016   0.002   TRP B 592 
 HIS   0.008   0.001   HIS B 635 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00450 /  0.27 (12442)
  covalent geometry    : angle       0.71711 /  0.41 (17020)
  hydrogen bonds       : bond        0.11024 /  6.93 (  856)
  hydrogen bonds       : angle       6.01622 /  4.43 ( 2502)
  Misc. bond           : bond        0.20888 / 10.20 (    4)

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

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

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 140
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 2
  residues processed: 147
  average time/residue: 0.5593
  time to fit residues: 89.0750
Evaluate side-chains
  131 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 129
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  723 VAL
Chi-restraints excluded: chain B residue  723 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    0.5980
   chunk 77 optimal weight:    0.0170
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.5818

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 511 ASN
B 511 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.135179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.110881 restraints weight = 23245.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 1.05
r_work: 0.2914 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2823 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2809
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2809 r_free = 0.2809    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2809 r_free = 0.2809    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.2809
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8907
moved from start:          0.0678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.227  12446  Z= 0.134
  Angle     :  0.579   8.402  17020  Z= 0.300
  Chirality :  0.040   0.141   1812
  Planarity :  0.004   0.039   2094
  Dihedral  :  7.400  82.059   1640
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 12.03 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.02 (0.22), residues: 1482
  helix:  1.73 (0.16), residues: 1074
  sheet: -0.69 (0.93), residues: 20
  loop :  0.56 (0.35), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 707 
 TYR   0.014   0.002   TYR A 575 
 PHE   0.020   0.001   PHE B 639 
 TRP   0.022   0.002   TRP B 342 
 HIS   0.005   0.001   HIS A  89 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.13 (12442)
  covalent geometry    : angle       0.57948 /  0.30 (17020)
  hydrogen bonds       : bond        0.05052 /  3.35 (  856)
  hydrogen bonds       : angle       5.19013 /  3.82 ( 2502)
  Misc. bond           : bond        0.16371 /  8.38 (    4)

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

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

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 135
  time to evaluate  : 0.483 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7771 (mptt)
REVERT: A  362 LYS cc_start: 0.7614 (pttm) cc_final: 0.7376 (ptpp)
REVERT: B  107 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7777 (mptt)
REVERT: B  362 LYS cc_start: 0.7628 (pttm) cc_final: 0.7391 (ptpp)
  outliers start: 7
  outliers final: 0
  residues processed: 141
  average time/residue: 0.6353
  time to fit residues: 96.5091
Evaluate side-chains
  133 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 131
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain B residue  107 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 50 optimal weight:   10.0000
   chunk 140 optimal weight:    0.8980
   chunk 0 optimal weight:   20.0000
   chunk 132 optimal weight:    2.9990
   chunk 126 optimal weight:    0.9980
   chunk 1 optimal weight:    7.9990
   chunk 129 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   chunk 45 optimal weight:    9.9990
   overall best weight:    2.5786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 511 ASN
B 511 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.129852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.104788 restraints weight = 26588.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 1.14
r_work: 0.2806 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2706 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2694
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2694 r_free = 0.2694    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2694 r_free = 0.2694    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.2694
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8981
moved from start:          0.0660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.286  12446  Z= 0.209
  Angle     :  0.689   8.189  17020  Z= 0.359
  Chirality :  0.044   0.157   1812
  Planarity :  0.005   0.041   2094
  Dihedral  :  7.717  83.353   1638
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 11.70 %
    Favored  : 87.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.22), residues: 1482
  helix:  1.55 (0.16), residues: 1072
  sheet: -0.07 (1.08), residues: 20
  loop :  0.41 (0.36), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 516 
 TYR   0.024   0.003   TYR A 575 
 PHE   0.027   0.002   PHE A 613 
 TRP   0.017   0.003   TRP A 342 
 HIS   0.013   0.002   HIS A 635 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00450 /  0.21 (12442)
  covalent geometry    : angle       0.68918 /  0.36 (17020)
  hydrogen bonds       : bond        0.06370 /  4.20 (  856)
  hydrogen bonds       : angle       5.59571 /  4.11 ( 2502)
  Misc. bond           : bond        0.20749 / 10.62 (    4)

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

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

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 131
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7796 (mptt)
REVERT: B  107 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7798 (mptt)
REVERT: B  362 LYS cc_start: 0.7639 (pttm) cc_final: 0.7416 (ptpp)
  outliers start: 6
  outliers final: 2
  residues processed: 137
  average time/residue: 0.5787
  time to fit residues: 85.5248
Evaluate side-chains
  132 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 128
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue  107 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 115 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 99 optimal weight:    8.9990
   chunk 44 optimal weight:   10.0000
   chunk 141 optimal weight:    9.9990
   chunk 93 optimal weight:    0.9980
   chunk 91 optimal weight:    1.9990
   chunk 130 optimal weight:    8.9990
   chunk 128 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    1.7986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 511 ASN
B 511 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.131004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.105800 restraints weight = 26224.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 1.11
r_work: 0.2831 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2732 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2719
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2719 r_free = 0.2719    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2719 r_free = 0.2719    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2719
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8970
moved from start:          0.0752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.262  12446  Z= 0.174
  Angle     :  0.637   8.083  17020  Z= 0.331
  Chirality :  0.042   0.151   1812
  Planarity :  0.005   0.053   2094
  Dihedral  :  7.654  82.973   1638
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 11.78 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.22), residues: 1482
  helix:  1.61 (0.16), residues: 1072
  sheet:  0.03 (1.11), residues: 20
  loop :  0.42 (0.36), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 516 
 TYR   0.020   0.002   TYR A 575 
 PHE   0.023   0.002   PHE B 639 
 TRP   0.022   0.002   TRP A 342 
 HIS   0.008   0.001   HIS B 635 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00377 /  0.17 (12442)
  covalent geometry    : angle       0.63709 /  0.33 (17020)
  hydrogen bonds       : bond        0.05825 /  3.85 (  856)
  hydrogen bonds       : angle       5.45720 /  4.01 ( 2502)
  Misc. bond           : bond        0.19031 /  9.74 (    4)

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

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

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 130
  time to evaluate  : 0.474 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7804 (mptt)
REVERT: B  107 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7808 (mptt)
REVERT: B  362 LYS cc_start: 0.7646 (pttm) cc_final: 0.7428 (ptpp)
  outliers start: 6
  outliers final: 2
  residues processed: 135
  average time/residue: 0.6251
  time to fit residues: 91.1687
Evaluate side-chains
  133 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 129
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue  107 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 117 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   chunk 111 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 105 optimal weight:   10.0000
   chunk 55 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 127 optimal weight:    1.9990
   chunk 120 optimal weight:    0.0980
   chunk 116 optimal weight:    0.7980
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 511 ASN
B 511 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.134660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.109810 restraints weight = 28554.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.11
r_work: 0.2895 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2804 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2792
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2792 r_free = 0.2792    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2792 r_free = 0.2792    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2792
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8915
moved from start:          0.0940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.227  12446  Z= 0.133
  Angle     :  0.566   7.707  17020  Z= 0.291
  Chirality :  0.040   0.137   1812
  Planarity :  0.004   0.039   2094
  Dihedral  :  7.418  81.731   1638
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 11.29 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.14 (0.22), residues: 1482
  helix:  1.82 (0.16), residues: 1076
  sheet: -0.07 (1.05), residues: 20
  loop :  0.54 (0.36), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 332 
 TYR   0.012   0.001   TYR A 575 
 PHE   0.019   0.001   PHE B 639 
 TRP   0.024   0.002   TRP B 342 
 HIS   0.005   0.001   HIS B  89 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.13 (12442)
  covalent geometry    : angle       0.56613 /  0.29 (17020)
  hydrogen bonds       : bond        0.04921 /  3.27 (  856)
  hydrogen bonds       : angle       5.16316 /  3.81 ( 2502)
  Misc. bond           : bond        0.16720 /  8.55 (    4)

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

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

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 132
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7782 (mptt)
REVERT: A  448 ASP cc_start: 0.7579 (t70) cc_final: 0.7252 (t0)
REVERT: A  516 ARG cc_start: 0.7652 (mtm180) cc_final: 0.7376 (mtp-110)
REVERT: A  665 ASP cc_start: 0.8193 (m-30) cc_final: 0.7975 (m-30)
REVERT: B  107 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7783 (mptt)
REVERT: B  362 LYS cc_start: 0.7645 (pttm) cc_final: 0.7431 (ptpp)
REVERT: B  448 ASP cc_start: 0.7573 (t70) cc_final: 0.7230 (t0)
REVERT: B  516 ARG cc_start: 0.7655 (mtm180) cc_final: 0.7377 (mtp-110)
REVERT: B  665 ASP cc_start: 0.8203 (m-30) cc_final: 0.7984 (m-30)
  outliers start: 8
  outliers final: 2
  residues processed: 139
  average time/residue: 0.6239
  time to fit residues: 93.7244
Evaluate side-chains
  126 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 122
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue  107 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 147 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0770
   chunk 101 optimal weight:    2.9990
   chunk 141 optimal weight:    9.9990
   chunk 136 optimal weight:    0.9990
   chunk 128 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   chunk 4 optimal weight:    7.9990
   chunk 81 optimal weight:    7.9990
   overall best weight:    1.4144

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 511 ASN
B 511 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.132086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.106350 restraints weight = 25549.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 1.08
r_work: 0.2858 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2750
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2750
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8947
moved from start:          0.0820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.254  12446  Z= 0.159
  Angle     :  0.613   8.782  17020  Z= 0.315
  Chirality :  0.041   0.143   1812
  Planarity :  0.004   0.040   2094
  Dihedral  :  7.517  82.854   1638
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 11.05 %
    Favored  : 88.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.22), residues: 1482
  helix:  1.77 (0.16), residues: 1074
  sheet: -0.06 (1.07), residues: 20
  loop :  0.50 (0.36), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 517 
 TYR   0.017   0.002   TYR A 575 
 PHE   0.020   0.002   PHE B 639 
 TRP   0.020   0.002   TRP A 342 
 HIS   0.008   0.001   HIS A 635 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00343 /  0.16 (12442)
  covalent geometry    : angle       0.61257 /  0.32 (17020)
  hydrogen bonds       : bond        0.05538 /  3.67 (  856)
  hydrogen bonds       : angle       5.33031 /  3.92 ( 2502)
  Misc. bond           : bond        0.18507 /  9.47 (    4)

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

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

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 124
  time to evaluate  : 0.465 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7767 (mptt)
REVERT: A  448 ASP cc_start: 0.7551 (t70) cc_final: 0.7223 (t0)
REVERT: A  516 ARG cc_start: 0.7747 (mtm180) cc_final: 0.7431 (mtp180)
REVERT: B  107 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7767 (mptt)
REVERT: B  362 LYS cc_start: 0.7637 (pttm) cc_final: 0.7418 (ptpp)
REVERT: B  448 ASP cc_start: 0.7557 (t70) cc_final: 0.7227 (t0)
REVERT: B  516 ARG cc_start: 0.7742 (mtm180) cc_final: 0.7422 (mtp180)
  outliers start: 8
  outliers final: 2
  residues processed: 131
  average time/residue: 0.6629
  time to fit residues: 93.8101
Evaluate side-chains
  125 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 121
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue  107 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 109 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 129 optimal weight:    6.9990
   chunk 6 optimal weight:    0.5980
   chunk 4 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 107 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 120 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 511 ASN
B 511 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.133431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.107935 restraints weight = 26064.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 1.10
r_work: 0.2876 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2783 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2770
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2770 r_free = 0.2770    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2770 r_free = 0.2770    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2770
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8935
moved from start:          0.0903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.237  12446  Z= 0.143
  Angle     :  0.586   9.235  17020  Z= 0.301
  Chirality :  0.041   0.138   1812
  Planarity :  0.004   0.040   2094
  Dihedral  :  7.423  83.152   1638
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 11.05 %
    Favored  : 88.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.22), residues: 1482
  helix:  1.82 (0.16), residues: 1074
  sheet: -0.12 (1.05), residues: 20
  loop :  0.53 (0.36), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 517 
 TYR   0.014   0.002   TYR A 575 
 PHE   0.020   0.001   PHE B 639 
 TRP   0.023   0.002   TRP A 342 
 HIS   0.005   0.001   HIS B  89 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.14 (12442)
  covalent geometry    : angle       0.58607 /  0.30 (17020)
  hydrogen bonds       : bond        0.05168 /  3.43 (  856)
  hydrogen bonds       : angle       5.21812 /  3.84 ( 2502)
  Misc. bond           : bond        0.17349 /  8.87 (    4)

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

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

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 121
  time to evaluate  : 0.468 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7774 (mptt)
REVERT: A  448 ASP cc_start: 0.7571 (t70) cc_final: 0.7250 (t0)
REVERT: A  516 ARG cc_start: 0.7788 (mtm180) cc_final: 0.7470 (mtp180)
REVERT: B  107 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7776 (mptt)
REVERT: B  362 LYS cc_start: 0.7642 (pttm) cc_final: 0.7427 (ptpp)
REVERT: B  448 ASP cc_start: 0.7553 (t70) cc_final: 0.7233 (t0)
REVERT: B  516 ARG cc_start: 0.7768 (mtm180) cc_final: 0.7471 (mtp180)
  outliers start: 5
  outliers final: 2
  residues processed: 126
  average time/residue: 0.6935
  time to fit residues: 94.1211
Evaluate side-chains
  125 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 121
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue  107 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 98 optimal weight:    5.9990
   chunk 123 optimal weight:    2.9990
   chunk 93 optimal weight:    7.9990
   chunk 33 optimal weight:    0.1980
   chunk 1 optimal weight:    0.0870
   chunk 144 optimal weight:    2.9990
   chunk 34 optimal weight:   10.0000
   chunk 137 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   overall best weight:    1.4564

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 511 ASN
B 511 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.132048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.107014 restraints weight = 25879.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 1.08
r_work: 0.2852 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2756 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2742
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2742 r_free = 0.2742    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2742 r_free = 0.2742    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2742
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8956
moved from start:          0.0840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.250  12446  Z= 0.160
  Angle     :  0.615   9.520  17020  Z= 0.316
  Chirality :  0.042   0.144   1812
  Planarity :  0.004   0.040   2094
  Dihedral  :  7.504  82.920   1638
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 11.21 %
    Favored  : 88.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.22), residues: 1482
  helix:  1.76 (0.16), residues: 1074
  sheet:  0.01 (1.09), residues: 20
  loop :  0.50 (0.36), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 517 
 TYR   0.017   0.002   TYR A 575 
 PHE   0.021   0.002   PHE B 639 
 TRP   0.020   0.002   TRP A 342 
 HIS   0.008   0.001   HIS B 635 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.16 (12442)
  covalent geometry    : angle       0.61514 /  0.32 (17020)
  hydrogen bonds       : bond        0.05540 /  3.67 (  856)
  hydrogen bonds       : angle       5.33355 /  3.92 ( 2502)
  Misc. bond           : bond        0.18257 /  9.34 (    4)

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

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

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 124
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7770 (mptt)
REVERT: A  448 ASP cc_start: 0.7581 (t70) cc_final: 0.7260 (t0)
REVERT: A  516 ARG cc_start: 0.7826 (mtm180) cc_final: 0.7489 (mtp-110)
REVERT: B  107 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7768 (mptt)
REVERT: B  362 LYS cc_start: 0.7638 (pttm) cc_final: 0.7423 (ptpp)
REVERT: B  448 ASP cc_start: 0.7570 (t70) cc_final: 0.7250 (t0)
REVERT: B  516 ARG cc_start: 0.7834 (mtm180) cc_final: 0.7493 (mtp-110)
  outliers start: 5
  outliers final: 2
  residues processed: 128
  average time/residue: 0.6860
  time to fit residues: 94.7655
Evaluate side-chains
  125 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 121
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue  107 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 30 optimal weight:    9.9990
   chunk 85 optimal weight:    0.9990
   chunk 34 optimal weight:    9.9990
   chunk 106 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 26 optimal weight:    0.4980
   chunk 107 optimal weight:    0.2980
   chunk 123 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 511 ASN
B 511 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.134653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.109805 restraints weight = 26595.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 1.11
r_work: 0.2893 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2800 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2787
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2787 r_free = 0.2787    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2787 r_free = 0.2787    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2787
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8920
moved from start:          0.0984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.230  12446  Z= 0.133
  Angle     :  0.572   9.812  17020  Z= 0.293
  Chirality :  0.040   0.136   1812
  Planarity :  0.004   0.039   2094
  Dihedral  :  7.333  82.991   1638
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 11.13 %
    Favored  : 88.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.21 (0.22), residues: 1482
  helix:  1.87 (0.16), residues: 1076
  sheet: -0.19 (1.04), residues: 20
  loop :  0.58 (0.36), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 517 
 TYR   0.012   0.001   TYR A 575 
 PHE   0.019   0.001   PHE A 639 
 TRP   0.023   0.002   TRP A 342 
 HIS   0.005   0.001   HIS B  89 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.13 (12442)
  covalent geometry    : angle       0.57193 /  0.29 (17020)
  hydrogen bonds       : bond        0.04932 /  3.28 (  856)
  hydrogen bonds       : angle       5.13814 /  3.79 ( 2502)
  Misc. bond           : bond        0.16948 /  8.67 (    4)

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

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

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 121
  time to evaluate  : 0.505 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7787 (mptt)
REVERT: A  448 ASP cc_start: 0.7573 (t70) cc_final: 0.7259 (t0)
REVERT: A  516 ARG cc_start: 0.7832 (mtm180) cc_final: 0.7495 (mtp-110)
REVERT: A  665 ASP cc_start: 0.8190 (m-30) cc_final: 0.7961 (m-30)
REVERT: B  107 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7791 (mptt)
REVERT: B  362 LYS cc_start: 0.7653 (pttm) cc_final: 0.7437 (ptpp)
REVERT: B  448 ASP cc_start: 0.7574 (t70) cc_final: 0.7262 (t0)
REVERT: B  516 ARG cc_start: 0.7814 (mtm180) cc_final: 0.7500 (mtp-110)
REVERT: B  665 ASP cc_start: 0.8205 (m-30) cc_final: 0.7969 (m-30)
  outliers start: 6
  outliers final: 2
  residues processed: 127
  average time/residue: 0.7046
  time to fit residues: 96.6219
Evaluate side-chains
  124 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 120
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue  107 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 91 optimal weight:    1.9990
   chunk 79 optimal weight:    6.9990
   chunk 89 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0070
   chunk 38 optimal weight:    0.8980
   chunk 93 optimal weight:    1.9990
   chunk 127 optimal weight:    1.9990
   chunk 121 optimal weight:   10.0000
   chunk 140 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.1602

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 511 ASN
A 662 GLN
B 511 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.133169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.110640 restraints weight = 29197.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 0.90
r_work: 0.2901 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2801 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2789
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8932
moved from start:          0.0931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.238  12446  Z= 0.148
  Angle     :  0.597   9.755  17020  Z= 0.306
  Chirality :  0.041   0.139   1812
  Planarity :  0.004   0.040   2094
  Dihedral  :  7.399  82.846   1638
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 11.13 %
    Favored  : 88.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.15 (0.22), residues: 1482
  helix:  1.83 (0.16), residues: 1074
  sheet: -0.16 (1.05), residues: 20
  loop :  0.54 (0.36), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 517 
 TYR   0.015   0.002   TYR A 575 
 PHE   0.020   0.002   PHE A 639 
 TRP   0.021   0.002   TRP B 342 
 HIS   0.006   0.001   HIS B 635 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.15 (12442)
  covalent geometry    : angle       0.59671 /  0.31 (17020)
  hydrogen bonds       : bond        0.05276 /  3.50 (  856)
  hydrogen bonds       : angle       5.24118 /  3.86 ( 2502)
  Misc. bond           : bond        0.17410 /  8.91 (    4)

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

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

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 120
  time to evaluate  : 0.593 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7745 (mptt)
REVERT: A  448 ASP cc_start: 0.7555 (t70) cc_final: 0.7227 (t0)
REVERT: A  516 ARG cc_start: 0.7824 (mtm180) cc_final: 0.7486 (mtp-110)
REVERT: B  107 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7748 (mptt)
REVERT: B  362 LYS cc_start: 0.7638 (pttm) cc_final: 0.7426 (ptpp)
REVERT: B  448 ASP cc_start: 0.7561 (t70) cc_final: 0.7232 (t0)
REVERT: B  516 ARG cc_start: 0.7825 (mtm180) cc_final: 0.7486 (mtp-110)
  outliers start: 4
  outliers final: 2
  residues processed: 124
  average time/residue: 0.7037
  time to fit residues: 94.2382
Evaluate side-chains
  125 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 121
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue  107 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 88 optimal weight:    9.9990
   chunk 116 optimal weight:    4.9990
   chunk 140 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   chunk 34 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 90 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 511 ASN
A 662 GLN
B 511 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.131457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.106822 restraints weight = 24665.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 1.05
r_work: 0.2844 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2746 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2732
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2732 r_free = 0.2732    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2732 r_free = 0.2732    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2732
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8964
moved from start:          0.0827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.267  12446  Z= 0.172
  Angle     :  0.638   9.573  17020  Z= 0.328
  Chirality :  0.042   0.152   1812
  Planarity :  0.004   0.041   2094
  Dihedral  :  7.553  83.022   1638
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 11.21 %
    Favored  : 88.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.02 (0.22), residues: 1482
  helix:  1.73 (0.16), residues: 1072
  sheet:  0.05 (1.13), residues: 20
  loop :  0.48 (0.36), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 517 
 TYR   0.019   0.002   TYR A 575 
 PHE   0.022   0.002   PHE B 639 
 TRP   0.017   0.002   TRP B 342 
 HIS   0.009   0.002   HIS A 635 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00373 /  0.17 (12442)
  covalent geometry    : angle       0.63802 /  0.33 (17020)
  hydrogen bonds       : bond        0.05755 /  3.81 (  856)
  hydrogen bonds       : angle       5.40645 /  3.97 ( 2502)
  Misc. bond           : bond        0.19517 /  9.99 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6341.91 seconds
wall clock time: 108 minutes 26.12 seconds (6506.12 seconds total)