Starting phenix.real_space_refine
on Sat Aug 23 12:45:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zgp_60086/08_2025/8zgp_60086.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zgp_60086/08_2025/8zgp_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zgp_60086/08_2025/8zgp_60086.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zgp_60086/08_2025/8zgp_60086.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zgp_60086/08_2025/8zgp_60086.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zgp_60086/08_2025/8zgp_60086.cif"
  }
  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-2.0-5787/lib/python3.9/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, 88
          Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    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: 6.79, per 1000 atoms: 0.56
  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: 1.19
  Conformation dependent library (CDL) restraints added in 955.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.46
  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: 2.09

  Time building geometry restraints manager: 1.55 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 2.260
  nonbonded pdb="FE    FE B 803 "
            pdb=" O   HOH B 905 "
     model   vdw
     2.066 2.260
  nonbonded pdb=" ND1 HIS B 490 "
            pdb="FE    FE B 803 "
     model   vdw
     2.078 2.340
  nonbonded pdb=" ND1 HIS A 490 "
            pdb="FE    FE A 803 "
     model   vdw
     2.079 2.340
  nonbonded pdb=" NE2 HIS B 542 "
            pdb="FE    FE B 803 "
     model   vdw
     2.146 2.340
  ... (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:             4.390
  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:          0.230
  Check model and map are aligned:         0.020
  Set scattering table:                    0.050
  Process input model:                     17.520
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  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:6.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
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 aren 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
  covalent geometry    : bond        0.00450 (12442)
  covalent geometry    : angle       0.71711 (17020)
  hydrogen bonds       : bond        0.11024 (  856)
  hydrogen bonds       : angle       6.01622 ( 2502)
  Misc. bond           : bond        0.20888 (    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  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 2
  residues processed: 147
  average time/residue: 0.6560
  time to fit residues: 104.3755
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  : 0.367 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3507 r_free = 0.3507 target = 0.134419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.108229 restraints weight = 25436.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 1.23
r_work: 0.2892 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2788
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2788
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8818
moved from start:          0.0714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.231  12446  Z= 0.132
  Angle     :  0.574   8.286  17020  Z= 0.296
  Chirality :  0.040   0.138   1812
  Planarity :  0.004   0.038   2094
  Dihedral  :  7.588  88.411   1640
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 11.87 %
    Favored  : 87.40 %
  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 aren not related in a simple way.
  whole:  2.05 (0.22), residues: 1482
  helix:  1.74 (0.16), residues: 1074
  sheet: -0.71 (0.92), residues: 20
  loop :  0.59 (0.36), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 707 
 TYR   0.014   0.002   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 A  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (12442)
  covalent geometry    : angle       0.57403 (17020)
  hydrogen bonds       : bond        0.04982 (  856)
  hydrogen bonds       : angle       5.15050 ( 2502)
  Misc. bond           : bond        0.16929 (    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
  144 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 137
  time to evaluate  : 0.482 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7792 (mptt)
REVERT: A  362 LYS cc_start: 0.7607 (pttm) cc_final: 0.7361 (ptpp)
REVERT: B  107 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7791 (mptt)
REVERT: B  362 LYS cc_start: 0.7620 (pttm) cc_final: 0.7378 (ptpp)
  outliers start: 7
  outliers final: 0
  residues processed: 143
  average time/residue: 0.6764
  time to fit residues: 103.9285
Evaluate side-chains
  132 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 130
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 140 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 132 optimal weight:    2.9990
   chunk 126 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 129 optimal weight:    0.9980
   chunk 7 optimal weight:    7.9990
   chunk 19 optimal weight:    7.9990
   chunk 45 optimal weight:    9.9990
   overall best weight:    2.7986

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3440 r_free = 0.3440 target = 0.129021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.102862 restraints weight = 26963.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 1.11
r_work: 0.2799 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2702 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2691
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2691 r_free = 0.2691    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 = 0.2691 r_free = 0.2691    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2691
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8899
moved from start:          0.0651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.279  12446  Z= 0.216
  Angle     :  0.704   8.184  17020  Z= 0.367
  Chirality :  0.045   0.158   1812
  Planarity :  0.005   0.042   2094
  Dihedral  :  7.926  89.526   1638
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 11.46 %
    Favored  : 88.05 %
  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 aren not related in a simple way.
  whole:  1.75 (0.22), residues: 1482
  helix:  1.52 (0.16), residues: 1072
  sheet:  0.02 (1.09), residues: 20
  loop :  0.42 (0.36), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 516 
 TYR   0.024   0.003   TYR A 575 
 PHE   0.028   0.002   PHE B 613 
 TRP   0.018   0.003   TRP A 342 
 HIS   0.014   0.002   HIS A 635 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 (12442)
  covalent geometry    : angle       0.70403 (17020)
  hydrogen bonds       : bond        0.06526 (  856)
  hydrogen bonds       : angle       5.64135 ( 2502)
  Misc. bond           : bond        0.20790 (    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
  135 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 131
  time to evaluate  : 0.411 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7784 (mptt)
REVERT: B  107 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7794 (mptt)
REVERT: B  362 LYS cc_start: 0.7632 (pttm) cc_final: 0.7411 (ptpp)
  outliers start: 4
  outliers final: 2
  residues processed: 135
  average time/residue: 0.7096
  time to fit residues: 103.2114
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  : 0.460 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 99 optimal weight:    8.9990
   chunk 44 optimal weight:   10.0000
   chunk 141 optimal weight:    9.9990
   chunk 93 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 130 optimal weight:    8.9990
   chunk 128 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.3470 r_free = 0.3470 target = 0.131386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.108940 restraints weight = 27255.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 0.91
r_work: 0.2878 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2759
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2759
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8852
moved from start:          0.0772

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= 0.152
  Angle     :  0.608   8.208  17020  Z= 0.313
  Chirality :  0.041   0.144   1812
  Planarity :  0.004   0.041   2094
  Dihedral  :  7.749  88.421   1638
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 11.21 %
    Favored  : 88.05 %
  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 aren not related in a simple way.
  whole:  1.97 (0.22), residues: 1482
  helix:  1.70 (0.16), residues: 1072
  sheet: -0.08 (1.06), residues: 20
  loop :  0.48 (0.36), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 516 
 TYR   0.016   0.002   TYR A 575 
 PHE   0.020   0.002   PHE B 639 
 TRP   0.023   0.002   TRP A 342 
 HIS   0.006   0.001   HIS A  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (12442)
  covalent geometry    : angle       0.60759 (17020)
  hydrogen bonds       : bond        0.05447 (  856)
  hydrogen bonds       : angle       5.32703 ( 2502)
  Misc. bond           : bond        0.18992 (    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
  138 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 131
  time to evaluate  : 0.472 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7801 (mptt)
REVERT: B  107 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7800 (mptt)
REVERT: B  362 LYS cc_start: 0.7611 (pttm) cc_final: 0.7396 (ptpp)
REVERT: B  516 ARG cc_start: 0.7749 (mtm180) cc_final: 0.7522 (mtp-110)
  outliers start: 7
  outliers final: 2
  residues processed: 137
  average time/residue: 0.7282
  time to fit residues: 107.4952
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  : 0.491 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 111 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 105 optimal weight:    9.9990
   chunk 55 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 127 optimal weight:    0.8980
   chunk 120 optimal weight:    0.0980
   chunk 116 optimal weight:    0.7980
   chunk 66 optimal weight:    0.3980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3503 r_free = 0.3503 target = 0.134086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.109743 restraints weight = 30136.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.21
r_work: 0.2881 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2785 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2785
-------------------------------------------------------------------------------
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 = 0.37   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 = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2770
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8836
moved from start:          0.0948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.219  12446  Z= 0.127
  Angle     :  0.558   7.713  17020  Z= 0.286
  Chirality :  0.040   0.133   1812
  Planarity :  0.004   0.039   2094
  Dihedral  :  7.543  86.855   1638
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 10.97 %
    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 aren not related in a simple way.
  whole:  2.19 (0.22), residues: 1482
  helix:  1.86 (0.16), residues: 1076
  sheet: -0.23 (0.99), residues: 20
  loop :  0.56 (0.36), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 517 
 TYR   0.011   0.001   TYR A 575 
 PHE   0.017   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
  covalent geometry    : bond        0.00267 (12442)
  covalent geometry    : angle       0.55843 (17020)
  hydrogen bonds       : bond        0.04804 (  856)
  hydrogen bonds       : angle       5.09733 ( 2502)
  Misc. bond           : bond        0.17416 (    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  : 0.431 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7793 (mptt)
REVERT: A  448 ASP cc_start: 0.7568 (t70) cc_final: 0.7243 (t0)
REVERT: A  497 PHE cc_start: 0.7845 (m-10) cc_final: 0.7641 (m-80)
REVERT: A  665 ASP cc_start: 0.8206 (m-30) cc_final: 0.7970 (m-30)
REVERT: B  107 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7749 (mptt)
REVERT: B  362 LYS cc_start: 0.7647 (pttm) cc_final: 0.7428 (ptpp)
REVERT: B  448 ASP cc_start: 0.7588 (t70) cc_final: 0.7260 (t0)
REVERT: B  516 ARG cc_start: 0.7826 (mtm180) cc_final: 0.7569 (mtp180)
REVERT: B  665 ASP cc_start: 0.8221 (m-30) cc_final: 0.7980 (m-30)
  outliers start: 8
  outliers final: 2
  residues processed: 140
  average time/residue: 0.6257
  time to fit residues: 94.5990
Evaluate side-chains
  134 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 130
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 147 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 101 optimal weight:    4.9990
   chunk 141 optimal weight:    9.9990
   chunk 136 optimal weight:    5.9990
   chunk 128 optimal weight:    9.9990
   chunk 67 optimal weight:   10.0000
   chunk 4 optimal weight:    7.9990
   chunk 81 optimal weight:    5.9990
   overall best weight:    3.3186

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3434 r_free = 0.3434 target = 0.128506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.105780 restraints weight = 26209.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 0.90
r_work: 0.2823 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2702
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2702
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8898
moved from start:          0.0788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.291  12446  Z= 0.237
  Angle     :  0.729   8.944  17020  Z= 0.377
  Chirality :  0.046   0.164   1812
  Planarity :  0.005   0.046   2094
  Dihedral  :  7.994  88.978   1638
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 11.29 %
    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 aren not related in a simple way.
  whole:  1.71 (0.22), residues: 1482
  helix:  1.49 (0.15), residues: 1072
  sheet:  0.11 (1.13), residues: 20
  loop :  0.39 (0.36), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 516 
 TYR   0.026   0.003   TYR B 575 
 PHE   0.028   0.003   PHE A 639 
 TRP   0.017   0.003   TRP A 342 
 HIS   0.016   0.002   HIS B 635 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 (12442)
  covalent geometry    : angle       0.72888 (17020)
  hydrogen bonds       : bond        0.06694 (  856)
  hydrogen bonds       : angle       5.70203 ( 2502)
  Misc. bond           : bond        0.21676 (    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
  134 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 129
  time to evaluate  : 0.338 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7806 (mptt)
REVERT: A  516 ARG cc_start: 0.7896 (mtm180) cc_final: 0.7667 (mtp-110)
REVERT: B  107 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7809 (mptt)
REVERT: B  362 LYS cc_start: 0.7654 (pttm) cc_final: 0.7442 (ptpp)
  outliers start: 5
  outliers final: 2
  residues processed: 133
  average time/residue: 0.6381
  time to fit residues: 91.2080
Evaluate side-chains
  128 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 124
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 87 optimal weight:    4.9990
   chunk 129 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 4 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   chunk 107 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 120 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3465 r_free = 0.3465 target = 0.131013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.106534 restraints weight = 27015.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 1.13
r_work: 0.2829 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2731 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2718
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2718
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8879
moved from start:          0.0831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.255  12446  Z= 0.154
  Angle     :  0.615   8.732  17020  Z= 0.315
  Chirality :  0.041   0.144   1812
  Planarity :  0.004   0.056   2094
  Dihedral  :  7.821  88.849   1638
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  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 aren not related in a simple way.
  whole:  1.97 (0.22), residues: 1482
  helix:  1.70 (0.16), residues: 1072
  sheet: -0.04 (1.10), residues: 20
  loop :  0.44 (0.36), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 516 
 TYR   0.017   0.002   TYR A 575 
 PHE   0.021   0.002   PHE B 639 
 TRP   0.023   0.002   TRP B 342 
 HIS   0.006   0.001   HIS A 635 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (12442)
  covalent geometry    : angle       0.61460 (17020)
  hydrogen bonds       : bond        0.05519 (  856)
  hydrogen bonds       : angle       5.36586 ( 2502)
  Misc. bond           : bond        0.19501 (    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
  135 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 130
  time to evaluate  : 0.464 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7780 (mptt)
REVERT: A  448 ASP cc_start: 0.7575 (t70) cc_final: 0.7244 (t0)
REVERT: A  516 ARG cc_start: 0.7977 (mtm180) cc_final: 0.7740 (mtp-110)
REVERT: B  107 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7794 (mptt)
REVERT: B  362 LYS cc_start: 0.7665 (pttm) cc_final: 0.7449 (ptpp)
  outliers start: 5
  outliers final: 2
  residues processed: 135
  average time/residue: 0.7373
  time to fit residues: 107.0118
Evaluate side-chains
  129 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 125
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 98 optimal weight:    5.9990
   chunk 123 optimal weight:    2.9990
   chunk 93 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0570
   chunk 1 optimal weight:    1.9990
   chunk 144 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 137 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.9704

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3483 r_free = 0.3483 target = 0.132473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.108132 restraints weight = 27057.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 1.12
r_work: 0.2857 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2761 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2746
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2746 r_free = 0.2746    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2746 r_free = 0.2746    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2746
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8855
moved from start:          0.0936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.233  12446  Z= 0.139
  Angle     :  0.591  10.292  17020  Z= 0.301
  Chirality :  0.041   0.140   1812
  Planarity :  0.004   0.040   2094
  Dihedral  :  7.660  87.641   1638
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 11.13 %
    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 aren not related in a simple way.
  whole:  2.11 (0.22), residues: 1482
  helix:  1.81 (0.16), residues: 1074
  sheet: -0.12 (1.07), residues: 20
  loop :  0.48 (0.36), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 517 
 TYR   0.014   0.002   TYR A 575 
 PHE   0.019   0.001   PHE B 639 
 TRP   0.024   0.002   TRP B 342 
 HIS   0.006   0.001   HIS A  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (12442)
  covalent geometry    : angle       0.59088 (17020)
  hydrogen bonds       : bond        0.05133 (  856)
  hydrogen bonds       : angle       5.21937 ( 2502)
  Misc. bond           : bond        0.18155 (    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
  133 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 128
  time to evaluate  : 0.472 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7763 (mptt)
REVERT: A  448 ASP cc_start: 0.7566 (t70) cc_final: 0.7250 (t0)
REVERT: A  516 ARG cc_start: 0.7866 (mtm180) cc_final: 0.7641 (mtp-110)
REVERT: A  665 ASP cc_start: 0.8209 (m-30) cc_final: 0.7999 (m-30)
REVERT: B  107 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7769 (mptt)
REVERT: B  362 LYS cc_start: 0.7653 (pttm) cc_final: 0.7437 (ptpp)
REVERT: B  448 ASP cc_start: 0.7563 (t70) cc_final: 0.7231 (t0)
REVERT: B  497 PHE cc_start: 0.7880 (m-80) cc_final: 0.7678 (m-80)
REVERT: B  516 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7551 (mtp-110)
REVERT: B  665 ASP cc_start: 0.8218 (m-30) cc_final: 0.8003 (m-30)
  outliers start: 5
  outliers final: 2
  residues processed: 133
  average time/residue: 0.7467
  time to fit residues: 106.7829
Evaluate side-chains
  128 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 124
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 30 optimal weight:    9.9990
   chunk 85 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   chunk 106 optimal weight:    2.9990
   chunk 6 optimal weight:    0.4980
   chunk 26 optimal weight:    3.9990
   chunk 107 optimal weight:    0.4980
   chunk 123 optimal weight:    0.8980
   chunk 51 optimal weight:   20.0000
   chunk 15 optimal weight:    3.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3479 r_free = 0.3479 target = 0.132115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.107760 restraints weight = 27399.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 1.12
r_work: 0.2849 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2751 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2737
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2737 r_free = 0.2737    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2737 r_free = 0.2737    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2737
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8864
moved from start:          0.0939

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= 0.144
  Angle     :  0.603  10.507  17020  Z= 0.307
  Chirality :  0.041   0.140   1812
  Planarity :  0.004   0.041   2094
  Dihedral  :  7.641  88.200   1638
  Min Nonbonded Distance : 2.074

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 aren not related in a simple way.
  whole:  2.11 (0.22), residues: 1482
  helix:  1.81 (0.16), residues: 1074
  sheet: -0.10 (1.06), residues: 20
  loop :  0.49 (0.36), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 517 
 TYR   0.015   0.002   TYR A 575 
 PHE   0.019   0.002   PHE B 639 
 TRP   0.023   0.002   TRP B 342 
 HIS   0.005   0.001   HIS B 635 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (12442)
  covalent geometry    : angle       0.60252 (17020)
  hydrogen bonds       : bond        0.05261 (  856)
  hydrogen bonds       : angle       5.24576 ( 2502)
  Misc. bond           : bond        0.18190 (    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
  130 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 126
  time to evaluate  : 0.562 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7762 (mptt)
REVERT: A  448 ASP cc_start: 0.7577 (t70) cc_final: 0.7266 (t0)
REVERT: A  497 PHE cc_start: 0.7873 (m-80) cc_final: 0.7666 (m-80)
REVERT: A  516 ARG cc_start: 0.7894 (mtm180) cc_final: 0.7664 (mtp-110)
REVERT: A  665 ASP cc_start: 0.8210 (m-30) cc_final: 0.7994 (m-30)
REVERT: B  107 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7765 (mptt)
REVERT: B  362 LYS cc_start: 0.7652 (pttm) cc_final: 0.7437 (ptpp)
REVERT: B  448 ASP cc_start: 0.7568 (t70) cc_final: 0.7244 (t0)
REVERT: B  497 PHE cc_start: 0.7890 (m-80) cc_final: 0.7681 (m-80)
REVERT: B  516 ARG cc_start: 0.7864 (mtm-85) cc_final: 0.7536 (mtp-110)
REVERT: B  665 ASP cc_start: 0.8216 (m-30) cc_final: 0.7993 (m-30)
  outliers start: 4
  outliers final: 2
  residues processed: 130
  average time/residue: 0.7003
  time to fit residues: 98.2383
Evaluate side-chains
  128 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 124
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 91 optimal weight:    0.9980
   chunk 79 optimal weight:    7.9990
   chunk 89 optimal weight:    1.9990
   chunk 51 optimal weight:   20.0000
   chunk 38 optimal weight:    6.9990
   chunk 93 optimal weight:    1.9990
   chunk 127 optimal weight:    1.9990
   chunk 121 optimal weight:   10.0000
   chunk 140 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 511 ASN
A 662 GLN
B 511 ASN
B 662 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.132319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.106256 restraints weight = 30276.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 1.21
r_work: 0.2850 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2754 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2744
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2744 r_free = 0.2744    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2744 r_free = 0.2744    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2744
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8855
moved from start:          0.0946

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= 0.144
  Angle     :  0.602  10.596  17020  Z= 0.306
  Chirality :  0.041   0.140   1812
  Planarity :  0.004   0.041   2094
  Dihedral  :  7.611  87.977   1638
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 11.13 %
    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 aren not related in a simple way.
  whole:  2.12 (0.22), residues: 1482
  helix:  1.81 (0.16), residues: 1074
  sheet: -0.11 (1.07), residues: 20
  loop :  0.51 (0.36), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 517 
 TYR   0.015   0.002   TYR A 575 
 PHE   0.020   0.002   PHE B 455 
 TRP   0.023   0.002   TRP B 342 
 HIS   0.005   0.001   HIS B 635 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (12442)
  covalent geometry    : angle       0.60250 (17020)
  hydrogen bonds       : bond        0.05228 (  856)
  hydrogen bonds       : angle       5.23932 ( 2502)
  Misc. bond           : bond        0.18081 (    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
  130 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 125
  time to evaluate  : 0.362 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7751 (mptt)
REVERT: A  448 ASP cc_start: 0.7558 (t70) cc_final: 0.7230 (t0)
REVERT: A  516 ARG cc_start: 0.7860 (mtm180) cc_final: 0.7616 (mtp-110)
REVERT: A  665 ASP cc_start: 0.8190 (m-30) cc_final: 0.7975 (m-30)
REVERT: B  107 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7735 (mptt)
REVERT: B  362 LYS cc_start: 0.7640 (pttm) cc_final: 0.7426 (ptpp)
REVERT: B  448 ASP cc_start: 0.7529 (t70) cc_final: 0.7204 (t0)
REVERT: B  516 ARG cc_start: 0.7756 (mtm-85) cc_final: 0.7418 (mtp-110)
REVERT: B  665 ASP cc_start: 0.8200 (m-30) cc_final: 0.7977 (m-30)
  outliers start: 5
  outliers final: 2
  residues processed: 129
  average time/residue: 0.6481
  time to fit residues: 89.8071
Evaluate side-chains
  129 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 125
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 116 optimal weight:    4.9990
   chunk 140 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 34 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 90 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   chunk 67 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 511 ASN
A 662 GLN
B 511 ASN
B 662 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.130231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.105429 restraints weight = 25397.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 1.13
r_work: 0.2816 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2705
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8886
moved from start:          0.0844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.274  12446  Z= 0.177
  Angle     :  0.655  10.598  17020  Z= 0.335
  Chirality :  0.043   0.152   1812
  Planarity :  0.005   0.041   2094
  Dihedral  :  7.794  89.586   1638
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 11.13 %
    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 aren not related in a simple way.
  whole:  1.94 (0.22), residues: 1482
  helix:  1.68 (0.16), residues: 1072
  sheet:  0.09 (1.14), residues: 20
  loop :  0.45 (0.36), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 517 
 TYR   0.020   0.002   TYR B 575 
 PHE   0.023   0.002   PHE B 639 
 TRP   0.017   0.002   TRP B 342 
 HIS   0.010   0.002   HIS A 635 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (12442)
  covalent geometry    : angle       0.65511 (17020)
  hydrogen bonds       : bond        0.05884 (  856)
  hydrogen bonds       : angle       5.45729 ( 2502)
  Misc. bond           : bond        0.20411 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6623.92 seconds
wall clock time: 113 minutes 10.33 seconds (6790.33 seconds total)