Starting phenix.real_space_refine
on Wed Jul 30 07:26:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zgp_60086/07_2025/8zgp_60086.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zgp_60086/07_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_60086/07_2025/8zgp_60086.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zgp_60086/07_2025/8zgp_60086.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zgp_60086/07_2025/8zgp_60086.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zgp_60086/07_2025/8zgp_60086.cif"
  }
  resolution = 1.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 15.76, per 1000 atoms: 1.30
  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: 3.08
  Conformation dependent library (CDL) restraints added in 3.0 seconds
  

  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: 1.36
  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: 4.13

  Time building geometry restraints manager: 3.57 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: 0.06
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:             3.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     40.680
  Find NCS groups from input model:        0.410
  Set up NCS constraints:                  0.050
  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:12.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   57.850
-------------------------------------------------------------------------------
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 : 6.29
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.22), 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
 TRP   0.016   0.002   TRP B 592 
 HIS   0.008   0.001   HIS B 635 
 PHE   0.030   0.002   PHE B 613 
 TYR   0.027   0.002   TYR A 328 
 ARG   0.005   0.001   ARG B 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11024 (  856)
  hydrogen bonds       : angle       6.01622 ( 2502)
  covalent geometry    : bond        0.00450 (12442)
  covalent geometry    : angle       0.71711 (17020)
  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  : 1.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 2
  residues processed: 147
  average time/residue: 1.3547
  time to fit residues: 215.8928
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  : 1.262 
-------------------------------------------------------------------------------
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 124 optimal weight:    0.5980
   chunk 112 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   chunk 59 optimal weight:    5.9990
   chunk 116 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 134 optimal weight:    2.9990
   overall best weight:    1.6584

-------------------------------------------------------------------------------
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 = 0.3460 r_free = 0.3460 target = 0.130593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.105889 restraints weight = 27867.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 1.14
r_work: 0.2817 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 3.61 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 = 0.50   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 = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8888
moved from start:          0.0496

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= 0.169
  Angle     :  0.645   8.135  17020  Z= 0.335
  Chirality :  0.043   0.150   1812
  Planarity :  0.005   0.041   2094
  Dihedral  :  7.817  89.623   1640
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 11.78 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.22), residues: 1482
  helix:  1.59 (0.16), residues: 1072
  sheet: -0.37 (1.01), residues: 20
  loop :  0.46 (0.35), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 342 
 HIS   0.008   0.001   HIS B 635 
 PHE   0.023   0.002   PHE B 639 
 TYR   0.021   0.002   TYR A 575 
 ARG   0.003   0.001   ARG B 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05847 (  856)
  hydrogen bonds       : angle       5.45371 ( 2502)
  covalent geometry    : bond        0.00362 (12442)
  covalent geometry    : angle       0.64488 (17020)
  Misc. bond           : bond        0.20521 (    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
  141 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 134
  time to evaluate  : 1.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7851 (mptt)
REVERT: A  498 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6829 (mt-10)
REVERT: A  665 ASP cc_start: 0.8261 (m-30) cc_final: 0.8058 (m-30)
REVERT: B  107 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7859 (mptt)
  outliers start: 7
  outliers final: 0
  residues processed: 140
  average time/residue: 1.7794
  time to fit residues: 269.9930
Evaluate side-chains
  134 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 131
  time to evaluate  : 1.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  498 GLU
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 145 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 69 optimal weight:    8.9990
   chunk 111 optimal weight:    0.8980
   chunk 119 optimal weight:    9.9990
   chunk 19 optimal weight:    0.8980
   chunk 89 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 144 optimal weight:    0.8980
   chunk 101 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3144 r_free = 0.3144 target = 0.107356 restraints weight = 26705.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 1.15
r_work: 0.2846 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2749 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2736
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2736 r_free = 0.2736    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2736 r_free = 0.2736    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2736
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8864
moved from start:          0.0709

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= 0.145
  Angle     :  0.594   8.810  17020  Z= 0.307
  Chirality :  0.041   0.143   1812
  Planarity :  0.004   0.040   2094
  Dihedral  :  7.646  87.892   1638
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 11.78 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.22), residues: 1482
  helix:  1.74 (0.16), residues: 1072
  sheet: -0.16 (1.01), residues: 20
  loop :  0.49 (0.36), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 342 
 HIS   0.005   0.001   HIS A  89 
 PHE   0.020   0.002   PHE A 639 
 TYR   0.016   0.002   TYR A 575 
 ARG   0.002   0.000   ARG A 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05317 (  856)
  hydrogen bonds       : angle       5.27106 ( 2502)
  covalent geometry    : bond        0.00307 (12442)
  covalent geometry    : angle       0.59360 (17020)
  Misc. bond           : bond        0.17362 (    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
  141 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 134
  time to evaluate  : 1.827 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7779 (mptt)
REVERT: A  498 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6789 (mt-10)
REVERT: B  107 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7780 (mptt)
  outliers start: 7
  outliers final: 0
  residues processed: 140
  average time/residue: 1.5931
  time to fit residues: 241.4453
Evaluate side-chains
  132 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 129
  time to evaluate  : 1.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  498 GLU
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 17 optimal weight:    4.9990
   chunk 24 optimal weight:    9.9990
   chunk 18 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0970
   chunk 39 optimal weight:    2.9990
   chunk 127 optimal weight:    2.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 86 optimal weight:    4.9990
   overall best weight:    1.0780

-------------------------------------------------------------------------------
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 = 0.3480 r_free = 0.3480 target = 0.132143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.107079 restraints weight = 23238.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 1.04
r_work: 0.2870 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2758
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2758 r_free = 0.2758    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2758 r_free = 0.2758    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2758
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8851
moved from start:          0.0777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.235  12446  Z= 0.144
  Angle     :  0.594   9.277  17020  Z= 0.306
  Chirality :  0.041   0.139   1812
  Planarity :  0.004   0.040   2094
  Dihedral  :  7.619  88.089   1638
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 11.78 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.22), residues: 1482
  helix:  1.78 (0.16), residues: 1074
  sheet: -0.13 (1.02), residues: 20
  loop :  0.45 (0.36), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 342 
 HIS   0.005   0.001   HIS B 635 
 PHE   0.019   0.002   PHE A 639 
 TYR   0.015   0.002   TYR A 575 
 ARG   0.007   0.001   ARG A 516 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05265 (  856)
  hydrogen bonds       : angle       5.24600 ( 2502)
  covalent geometry    : bond        0.00306 (12442)
  covalent geometry    : angle       0.59409 (17020)
  Misc. bond           : bond        0.17686 (    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: 7
    poor density    : 129
  time to evaluate  : 1.874 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7762 (mptt)
REVERT: B  107 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7767 (mptt)
  outliers start: 7
  outliers final: 0
  residues processed: 135
  average time/residue: 1.9148
  time to fit residues: 278.7044
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  : 1.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 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 29 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 103 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 45 optimal weight:    7.9990
   chunk 137 optimal weight:    0.9980
   chunk 140 optimal weight:    0.7980
   chunk 118 optimal weight:    2.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3489 r_free = 0.3489 target = 0.132867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.107623 restraints weight = 30563.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 1.25
r_work: 0.2856 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2761 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2748
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2748 r_free = 0.2748    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2748 r_free = 0.2748    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2748
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8851
moved from start:          0.0839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.228  12446  Z= 0.137
  Angle     :  0.581   9.386  17020  Z= 0.297
  Chirality :  0.040   0.136   1812
  Planarity :  0.004   0.039   2094
  Dihedral  :  7.539  87.546   1638
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 11.62 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.15 (0.22), residues: 1482
  helix:  1.84 (0.16), residues: 1074
  sheet: -0.22 (1.00), residues: 20
  loop :  0.51 (0.36), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 342 
 HIS   0.005   0.001   HIS B  89 
 PHE   0.019   0.001   PHE A 639 
 TYR   0.014   0.002   TYR B 575 
 ARG   0.003   0.000   ARG A 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05072 (  856)
  hydrogen bonds       : angle       5.17430 ( 2502)
  covalent geometry    : bond        0.00289 (12442)
  covalent geometry    : angle       0.58089 (17020)
  Misc. bond           : bond        0.17237 (    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
  137 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 133
  time to evaluate  : 1.313 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7743 (mptt)
REVERT: B  107 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7746 (mptt)
REVERT: B  497 PHE cc_start: 0.7838 (m-80) cc_final: 0.7632 (m-80)
REVERT: B  665 ASP cc_start: 0.8205 (m-30) cc_final: 0.7975 (m-30)
  outliers start: 4
  outliers final: 0
  residues processed: 137
  average time/residue: 1.6135
  time to fit residues: 237.3497
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  : 1.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 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 76 optimal weight:    7.9990
   chunk 137 optimal weight:    0.9980
   chunk 111 optimal weight:    7.9990
   chunk 126 optimal weight:    3.9990
   chunk 9 optimal weight:    7.9990
   chunk 136 optimal weight:    8.9990
   chunk 93 optimal weight:    6.9990
   chunk 16 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 135 optimal weight:    4.9990
   overall best weight:    2.0584

-------------------------------------------------------------------------------
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 = 0.3452 r_free = 0.3452 target = 0.129915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.107164 restraints weight = 27382.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 0.91
r_work: 0.2846 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2739 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2725
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2725
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8879
moved from start:          0.0715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.277  12446  Z= 0.182
  Angle     :  0.658   8.772  17020  Z= 0.338
  Chirality :  0.043   0.152   1812
  Planarity :  0.005   0.040   2094
  Dihedral  :  7.815  89.863   1638
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.22), residues: 1482
  helix:  1.65 (0.16), residues: 1072
  sheet:  0.13 (1.11), residues: 20
  loop :  0.44 (0.36), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 342 
 HIS   0.011   0.002   HIS A 635 
 PHE   0.024   0.002   PHE A 639 
 TYR   0.021   0.002   TYR A 575 
 ARG   0.005   0.001   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05999 (  856)
  hydrogen bonds       : angle       5.47421 ( 2502)
  covalent geometry    : bond        0.00392 (12442)
  covalent geometry    : angle       0.65751 (17020)
  Misc. bond           : bond        0.20586 (    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
  136 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 131
  time to evaluate  : 1.284 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7787 (mptt)
REVERT: B  107 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7783 (mptt)
  outliers start: 5
  outliers final: 2
  residues processed: 135
  average time/residue: 1.4438
  time to fit residues: 210.9847
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  : 1.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  723 VAL
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  723 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 83 optimal weight:    8.9990
   chunk 93 optimal weight:    6.9990
   chunk 127 optimal weight:    1.9990
   chunk 140 optimal weight:    0.7980
   chunk 146 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 37 optimal weight:    8.9990
   chunk 138 optimal weight:    9.9990
   chunk 143 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
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 = 0.3453 r_free = 0.3453 target = 0.130050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.105312 restraints weight = 26677.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 1.14
r_work: 0.2810 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2711 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2696
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2696 r_free = 0.2696    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2696 r_free = 0.2696    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2696
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8896
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   0.260  12446  Z= 0.177
  Angle     :  0.646   8.476  17020  Z= 0.332
  Chirality :  0.043   0.150   1812
  Planarity :  0.005   0.041   2094
  Dihedral  :  7.837  89.279   1638
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 10.97 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.22), residues: 1482
  helix:  1.65 (0.15), residues: 1072
  sheet:  0.14 (1.14), residues: 20
  loop :  0.43 (0.36), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 342 
 HIS   0.009   0.002   HIS A 635 
 PHE   0.024   0.002   PHE A 639 
 TYR   0.020   0.002   TYR B 575 
 ARG   0.004   0.001   ARG A 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05882 (  856)
  hydrogen bonds       : angle       5.46525 ( 2502)
  covalent geometry    : bond        0.00381 (12442)
  covalent geometry    : angle       0.64647 (17020)
  Misc. bond           : bond        0.19632 (    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
  136 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 129
  time to evaluate  : 1.468 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7796 (mptt)
REVERT: B  107 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7795 (mptt)
  outliers start: 7
  outliers final: 2
  residues processed: 135
  average time/residue: 1.7607
  time to fit residues: 258.0758
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  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  723 VAL
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  723 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 129 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 41 optimal weight:    0.9990
   chunk 128 optimal weight:    0.6980
   chunk 143 optimal weight:    4.9990
   chunk 93 optimal weight:    5.9990
   chunk 133 optimal weight:    0.5980
   chunk 107 optimal weight:    7.9990
   overall best weight:    1.0586

-------------------------------------------------------------------------------
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 = 0.3478 r_free = 0.3478 target = 0.131984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.106790 restraints weight = 29178.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 1.14
r_work: 0.2847 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2749 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2749
-------------------------------------------------------------------------------
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 = 0.35   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 = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2737
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8864
moved from start:          0.0850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.235  12446  Z= 0.143
  Angle     :  0.598  10.299  17020  Z= 0.305
  Chirality :  0.041   0.138   1812
  Planarity :  0.004   0.040   2094
  Dihedral  :  7.681  87.938   1638
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.22), residues: 1482
  helix:  1.80 (0.16), residues: 1074
  sheet:  0.05 (1.10), residues: 20
  loop :  0.48 (0.36), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 342 
 HIS   0.006   0.001   HIS B  89 
 PHE   0.020   0.001   PHE B 639 
 TYR   0.015   0.002   TYR B 575 
 ARG   0.004   0.000   ARG A 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05248 (  856)
  hydrogen bonds       : angle       5.25623 ( 2502)
  covalent geometry    : bond        0.00304 (12442)
  covalent geometry    : angle       0.59771 (17020)
  Misc. bond           : bond        0.18290 (    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
  134 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 129
  time to evaluate  : 1.903 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7777 (mptt)
REVERT: B  107 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7772 (mptt)
  outliers start: 5
  outliers final: 2
  residues processed: 133
  average time/residue: 1.9681
  time to fit residues: 282.7592
Evaluate side-chains
  131 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 127
  time to evaluate  : 3.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  723 VAL
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 19 optimal weight:    5.9990
   chunk 105 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 6 optimal weight:   10.0000
   chunk 64 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3493 r_free = 0.3493 target = 0.133194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.108523 restraints weight = 26385.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 1.16
r_work: 0.2867 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2770 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2758
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2758 r_free = 0.2758    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2758 r_free = 0.2758    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2758
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8848
moved from start:          0.0950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.228  12446  Z= 0.133
  Angle     :  0.580  10.497  17020  Z= 0.295
  Chirality :  0.040   0.137   1812
  Planarity :  0.004   0.039   2094
  Dihedral  :  7.566  87.231   1638
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.22), residues: 1482
  helix:  1.87 (0.16), residues: 1074
  sheet: -0.15 (1.04), residues: 20
  loop :  0.53 (0.36), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 342 
 HIS   0.005   0.001   HIS B  89 
 PHE   0.018   0.001   PHE B 639 
 TYR   0.013   0.001   TYR B 575 
 ARG   0.004   0.000   ARG A 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04988 (  856)
  hydrogen bonds       : angle       5.15397 ( 2502)
  covalent geometry    : bond        0.00283 (12442)
  covalent geometry    : angle       0.58029 (17020)
  Misc. bond           : bond        0.17868 (    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
  135 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 130
  time to evaluate  : 1.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7779 (mptt)
REVERT: A  448 ASP cc_start: 0.7620 (t70) cc_final: 0.7323 (t0)
REVERT: A  497 PHE cc_start: 0.7878 (m-80) cc_final: 0.7675 (m-80)
REVERT: B  107 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7775 (mptt)
  outliers start: 5
  outliers final: 2
  residues processed: 135
  average time/residue: 1.9119
  time to fit residues: 279.4115
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  : 1.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  723 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 115 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 54 optimal weight:   10.0000
   chunk 122 optimal weight:    0.8980
   chunk 83 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   chunk 127 optimal weight:    0.9980
   chunk 90 optimal weight:    0.7980
   chunk 105 optimal weight:    6.9990
   chunk 139 optimal weight:    0.7980
   chunk 133 optimal weight:    3.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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
B 662 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.132988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.108326 restraints weight = 24997.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 1.11
r_work: 0.2870 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2760
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2760 r_free = 0.2760    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2760 r_free = 0.2760    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2760
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8847
moved from start:          0.0952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.226  12446  Z= 0.137
  Angle     :  0.586  10.586  17020  Z= 0.299
  Chirality :  0.040   0.138   1812
  Planarity :  0.004   0.040   2094
  Dihedral  :  7.537  87.709   1638
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 5.03
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.22), residues: 1482
  helix:  1.86 (0.16), residues: 1074
  sheet: -0.17 (1.04), residues: 20
  loop :  0.53 (0.36), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 342 
 HIS   0.005   0.001   HIS B  89 
 PHE   0.018   0.001   PHE B 639 
 TYR   0.013   0.001   TYR B 575 
 ARG   0.004   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05057 (  856)
  hydrogen bonds       : angle       5.16616 ( 2502)
  covalent geometry    : bond        0.00291 (12442)
  covalent geometry    : angle       0.58645 (17020)
  Misc. bond           : bond        0.17376 (    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: 4
    poor density    : 126
  time to evaluate  : 1.407 
Fit side-chains
REVERT: A  107 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7727 (mptt)
REVERT: A  448 ASP cc_start: 0.7605 (t70) cc_final: 0.7357 (t0)
REVERT: B  107 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7724 (mptt)
REVERT: B  448 ASP cc_start: 0.7601 (t70) cc_final: 0.7344 (t0)
REVERT: B  497 PHE cc_start: 0.7863 (m-80) cc_final: 0.7642 (m-80)
  outliers start: 4
  outliers final: 2
  residues processed: 130
  average time/residue: 1.4617
  time to fit residues: 205.1577
Evaluate side-chains
  131 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 127
  time to evaluate  : 1.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  723 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 90 optimal weight:    0.0060
   chunk 30 optimal weight:    9.9990
   chunk 100 optimal weight:    9.9990
   chunk 28 optimal weight:    3.9990
   chunk 83 optimal weight:    9.9990
   chunk 95 optimal weight:    2.9990
   chunk 124 optimal weight:    0.9990
   chunk 136 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 80 optimal weight:    4.9990
   chunk 126 optimal weight:    8.9990
   overall best weight:    2.2004

-------------------------------------------------------------------------------
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 = 0.3451 r_free = 0.3451 target = 0.129856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.105006 restraints weight = 25876.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3105 rms_B_bonded: 1.13
r_work: 0.2809 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2712 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2698
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2698 r_free = 0.2698    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2698 r_free = 0.2698    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2698
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8893
moved from start:          0.0799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.276  12446  Z= 0.189
  Angle     :  0.671  10.524  17020  Z= 0.344
  Chirality :  0.043   0.155   1812
  Planarity :  0.005   0.041   2094
  Dihedral  :  7.829  89.933   1638
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 11.37 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.22), residues: 1482
  helix:  1.67 (0.16), residues: 1072
  sheet:  0.08 (1.13), residues: 20
  loop :  0.44 (0.36), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 342 
 HIS   0.011   0.002   HIS A 635 
 PHE   0.025   0.002   PHE B 639 
 TYR   0.021   0.002   TYR B 575 
 ARG   0.004   0.001   ARG B 721 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06067 (  856)
  hydrogen bonds       : angle       5.50648 ( 2502)
  covalent geometry    : bond        0.00409 (12442)
  covalent geometry    : angle       0.67069 (17020)
  Misc. bond           : bond        0.20473 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 15968.67 seconds
wall clock time: 283 minutes 11.51 seconds (16991.51 seconds total)