Starting phenix.real_space_refine
on Wed Mar  4 04:51:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xkj_22219/03_2026/6xkj_22219.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xkj_22219/03_2026/6xkj_22219.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xkj_22219/03_2026/6xkj_22219.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xkj_22219/03_2026/6xkj_22219.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xkj_22219/03_2026/6xkj_22219.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xkj_22219/03_2026/6xkj_22219.cif"
  }
  resolution = 3.54
  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: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    6832      2.51       5
     N    1968      2.21       5
     O    2224      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 208 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11056
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "C"
      Number of atoms: 691
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 691
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 1, 'TRANS': 83}
  Restraints were copied for chains:
    A, B, D, E, F, G, H, I, J, K, L, M, N, O, P
  Time building chain proxies: 1.14, per 1000 atoms: 0.10
  Number of scatterers: 11056
  At special positions: 0
  Unit cell: (87.3075, 87.3075, 120.567, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    2224      8.00
     N    1968      7.00
     C    6832      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.75
  Conformation dependent library (CDL) restraints added in 356.9 milliseconds
  

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2624

  Finding SS restraints...
    Secondary structure from input PDB file:
      112 helices and 0 sheets defined
      93.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'C' and resid 451 through 457
      removed outlier: 3.951A  pdb=" N   LYS C 455 " --> pdb=" O   ALA C 451 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 457 through 465
    Processing helix  chain 'C' and resid 468 through 478
    Processing helix  chain 'C' and resid 482 through 491
    Processing helix  chain 'C' and resid 494 through 510
      removed outlier: 3.748A  pdb=" N   LYS C 509 " --> pdb=" O   MET C 505 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLY C 510 " --> pdb=" O   VAL C 506 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 510 through 525
    Processing helix  chain 'C' and resid 525 through 534
    Processing helix  chain 'A' and resid 452 through 457
    Processing helix  chain 'A' and resid 457 through 465
    Processing helix  chain 'A' and resid 468 through 478
    Processing helix  chain 'A' and resid 482 through 491
    Processing helix  chain 'A' and resid 494 through 510
      removed outlier: 3.748A  pdb=" N   LYS A 509 " --> pdb=" O   MET A 505 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLY A 510 " --> pdb=" O   VAL A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 525
    Processing helix  chain 'A' and resid 525 through 534
    Processing helix  chain 'B' and resid 452 through 457
    Processing helix  chain 'B' and resid 457 through 465
    Processing helix  chain 'B' and resid 468 through 478
    Processing helix  chain 'B' and resid 482 through 491
    Processing helix  chain 'B' and resid 494 through 510
      removed outlier: 3.748A  pdb=" N   LYS B 509 " --> pdb=" O   MET B 505 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLY B 510 " --> pdb=" O   VAL B 506 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 525
    Processing helix  chain 'B' and resid 525 through 534
    Processing helix  chain 'D' and resid 452 through 457
    Processing helix  chain 'D' and resid 457 through 465
    Processing helix  chain 'D' and resid 468 through 478
    Processing helix  chain 'D' and resid 482 through 491
    Processing helix  chain 'D' and resid 494 through 510
      removed outlier: 3.747A  pdb=" N   LYS D 509 " --> pdb=" O   MET D 505 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLY D 510 " --> pdb=" O   VAL D 506 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 510 through 525
    Processing helix  chain 'D' and resid 525 through 534
    Processing helix  chain 'E' and resid 452 through 457
    Processing helix  chain 'E' and resid 457 through 465
    Processing helix  chain 'E' and resid 468 through 478
    Processing helix  chain 'E' and resid 482 through 491
    Processing helix  chain 'E' and resid 494 through 510
      removed outlier: 3.747A  pdb=" N   LYS E 509 " --> pdb=" O   MET E 505 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLY E 510 " --> pdb=" O   VAL E 506 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 510 through 525
    Processing helix  chain 'E' and resid 525 through 534
    Processing helix  chain 'F' and resid 452 through 457
    Processing helix  chain 'F' and resid 457 through 465
    Processing helix  chain 'F' and resid 468 through 478
    Processing helix  chain 'F' and resid 482 through 491
    Processing helix  chain 'F' and resid 494 through 510
      removed outlier: 3.747A  pdb=" N   LYS F 509 " --> pdb=" O   MET F 505 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLY F 510 " --> pdb=" O   VAL F 506 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 510 through 525
    Processing helix  chain 'F' and resid 525 through 534
    Processing helix  chain 'G' and resid 452 through 457
    Processing helix  chain 'G' and resid 457 through 465
    Processing helix  chain 'G' and resid 468 through 478
    Processing helix  chain 'G' and resid 482 through 491
    Processing helix  chain 'G' and resid 494 through 510
      removed outlier: 3.747A  pdb=" N   LYS G 509 " --> pdb=" O   MET G 505 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLY G 510 " --> pdb=" O   VAL G 506 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 510 through 525
    Processing helix  chain 'G' and resid 525 through 534
    Processing helix  chain 'H' and resid 452 through 457
    Processing helix  chain 'H' and resid 457 through 465
    Processing helix  chain 'H' and resid 468 through 478
    Processing helix  chain 'H' and resid 482 through 491
    Processing helix  chain 'H' and resid 494 through 510
      removed outlier: 3.747A  pdb=" N   LYS H 509 " --> pdb=" O   MET H 505 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLY H 510 " --> pdb=" O   VAL H 506 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 510 through 525
    Processing helix  chain 'H' and resid 525 through 534
    Processing helix  chain 'I' and resid 452 through 457
    Processing helix  chain 'I' and resid 457 through 465
    Processing helix  chain 'I' and resid 468 through 478
    Processing helix  chain 'I' and resid 482 through 491
    Processing helix  chain 'I' and resid 494 through 510
      removed outlier: 3.747A  pdb=" N   LYS I 509 " --> pdb=" O   MET I 505 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLY I 510 " --> pdb=" O   VAL I 506 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 510 through 525
    Processing helix  chain 'I' and resid 525 through 534
    Processing helix  chain 'J' and resid 452 through 457
    Processing helix  chain 'J' and resid 457 through 465
    Processing helix  chain 'J' and resid 468 through 478
    Processing helix  chain 'J' and resid 482 through 491
    Processing helix  chain 'J' and resid 494 through 510
      removed outlier: 3.748A  pdb=" N   LYS J 509 " --> pdb=" O   MET J 505 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLY J 510 " --> pdb=" O   VAL J 506 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 510 through 525
    Processing helix  chain 'J' and resid 525 through 534
    Processing helix  chain 'K' and resid 452 through 457
    Processing helix  chain 'K' and resid 457 through 465
    Processing helix  chain 'K' and resid 468 through 478
    Processing helix  chain 'K' and resid 482 through 491
    Processing helix  chain 'K' and resid 494 through 510
      removed outlier: 3.747A  pdb=" N   LYS K 509 " --> pdb=" O   MET K 505 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLY K 510 " --> pdb=" O   VAL K 506 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 510 through 525
    Processing helix  chain 'K' and resid 525 through 534
    Processing helix  chain 'L' and resid 452 through 457
    Processing helix  chain 'L' and resid 457 through 465
    Processing helix  chain 'L' and resid 468 through 478
    Processing helix  chain 'L' and resid 482 through 491
    Processing helix  chain 'L' and resid 494 through 510
      removed outlier: 3.748A  pdb=" N   LYS L 509 " --> pdb=" O   MET L 505 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLY L 510 " --> pdb=" O   VAL L 506 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 510 through 525
    Processing helix  chain 'L' and resid 525 through 534
    Processing helix  chain 'M' and resid 452 through 457
    Processing helix  chain 'M' and resid 457 through 465
    Processing helix  chain 'M' and resid 468 through 478
    Processing helix  chain 'M' and resid 482 through 491
    Processing helix  chain 'M' and resid 494 through 510
      removed outlier: 3.747A  pdb=" N   LYS M 509 " --> pdb=" O   MET M 505 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLY M 510 " --> pdb=" O   VAL M 506 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 510 through 525
    Processing helix  chain 'M' and resid 525 through 534
    Processing helix  chain 'N' and resid 452 through 457
    Processing helix  chain 'N' and resid 457 through 465
    Processing helix  chain 'N' and resid 468 through 478
    Processing helix  chain 'N' and resid 482 through 491
    Processing helix  chain 'N' and resid 494 through 510
      removed outlier: 3.747A  pdb=" N   LYS N 509 " --> pdb=" O   MET N 505 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLY N 510 " --> pdb=" O   VAL N 506 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 510 through 525
    Processing helix  chain 'N' and resid 525 through 534
    Processing helix  chain 'O' and resid 452 through 457
    Processing helix  chain 'O' and resid 457 through 465
    Processing helix  chain 'O' and resid 468 through 478
    Processing helix  chain 'O' and resid 482 through 491
    Processing helix  chain 'O' and resid 494 through 510
      removed outlier: 3.747A  pdb=" N   LYS O 509 " --> pdb=" O   MET O 505 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLY O 510 " --> pdb=" O   VAL O 506 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 510 through 525
    Processing helix  chain 'O' and resid 525 through 534
    Processing helix  chain 'P' and resid 452 through 457
    Processing helix  chain 'P' and resid 457 through 465
    Processing helix  chain 'P' and resid 468 through 478
    Processing helix  chain 'P' and resid 482 through 491
    Processing helix  chain 'P' and resid 494 through 510
      removed outlier: 3.747A  pdb=" N   LYS P 509 " --> pdb=" O   MET P 505 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLY P 510 " --> pdb=" O   VAL P 506 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 510 through 525
    Processing helix  chain 'P' and resid 525 through 534

    784 hydrogen bonds defined for protein.
    2352 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.62

  Time building geometry restraints manager: 1.04 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3623
        1.33 -     1.45: 910
        1.45 -     1.57: 6523
        1.57 -     1.68: 16
        1.68 -     1.80: 64
  Bond restraints: 11136
  Sorted by residual:
  bond pdb=" CA  GLN M 534 "
       pdb=" CB  GLN M 534 "
    ideal  model  delta    sigma   weight residual
    1.530  1.571 -0.041 1.69e-02 3.50e+03 5.95e+00
  bond pdb=" CA  GLN J 534 "
       pdb=" CB  GLN J 534 "
    ideal  model  delta    sigma   weight residual
    1.530  1.571 -0.041 1.69e-02 3.50e+03 5.95e+00
  bond pdb=" CA  GLN P 534 "
       pdb=" CB  GLN P 534 "
    ideal  model  delta    sigma   weight residual
    1.530  1.571 -0.041 1.69e-02 3.50e+03 5.88e+00
  bond pdb=" CA  GLN I 534 "
       pdb=" CB  GLN I 534 "
    ideal  model  delta    sigma   weight residual
    1.530  1.571 -0.041 1.69e-02 3.50e+03 5.87e+00
  bond pdb=" CA  GLN E 534 "
       pdb=" CB  GLN E 534 "
    ideal  model  delta    sigma   weight residual
    1.530  1.571 -0.041 1.69e-02 3.50e+03 5.82e+00
  ... (remaining 11131 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.10: 13092
        1.10 -     2.21: 1438
        2.21 -     3.31: 239
        3.31 -     4.41: 94
        4.41 -     5.52: 49
  Bond angle restraints: 14912
  Sorted by residual:
  angle pdb=" C   LEU I 461 "
        pdb=" N   GLN I 462 "
        pdb=" CA  GLN I 462 "
      ideal   model   delta    sigma   weight residual
     120.31  115.88    4.43 1.52e+00 4.33e-01 8.48e+00
  angle pdb=" C   LEU K 461 "
        pdb=" N   GLN K 462 "
        pdb=" CA  GLN K 462 "
      ideal   model   delta    sigma   weight residual
     120.31  115.93    4.38 1.52e+00 4.33e-01 8.29e+00
  angle pdb=" C   LEU A 461 "
        pdb=" N   GLN A 462 "
        pdb=" CA  GLN A 462 "
      ideal   model   delta    sigma   weight residual
     120.31  115.94    4.37 1.52e+00 4.33e-01 8.28e+00
  angle pdb=" C   LEU G 461 "
        pdb=" N   GLN G 462 "
        pdb=" CA  GLN G 462 "
      ideal   model   delta    sigma   weight residual
     120.31  115.94    4.37 1.52e+00 4.33e-01 8.27e+00
  angle pdb=" C   LEU D 461 "
        pdb=" N   GLN D 462 "
        pdb=" CA  GLN D 462 "
      ideal   model   delta    sigma   weight residual
     120.31  115.94    4.37 1.52e+00 4.33e-01 8.26e+00
  ... (remaining 14907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.19: 6032
       14.19 -    28.38: 672
       28.38 -    42.58: 304
       42.58 -    56.77: 32
       56.77 -    70.96: 32
  Dihedral angle restraints: 7072
    sinusoidal: 3072
      harmonic: 4000
  Sorted by residual:
  dihedral pdb=" CA  ASP H 474 "
           pdb=" CB  ASP H 474 "
           pdb=" CG  ASP H 474 "
           pdb=" OD1 ASP H 474 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -80.29   50.29     1      2.00e+01 2.50e-03 8.67e+00
  dihedral pdb=" CA  ASP K 474 "
           pdb=" CB  ASP K 474 "
           pdb=" CG  ASP K 474 "
           pdb=" OD1 ASP K 474 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -80.25   50.25     1      2.00e+01 2.50e-03 8.65e+00
  dihedral pdb=" CA  ASP B 474 "
           pdb=" CB  ASP B 474 "
           pdb=" CG  ASP B 474 "
           pdb=" OD1 ASP B 474 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -80.24   50.24     1      2.00e+01 2.50e-03 8.65e+00
  ... (remaining 7069 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 678
       0.027 -    0.053: 577
       0.053 -    0.080: 280
       0.080 -    0.106: 113
       0.106 -    0.133: 32
  Chirality restraints: 1680
  Sorted by residual:
  chirality pdb=" CA  GLU I 479 "
            pdb=" N   GLU I 479 "
            pdb=" C   GLU I 479 "
            pdb=" CB  GLU I 479 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.40e-01
  chirality pdb=" CA  GLU D 479 "
            pdb=" N   GLU D 479 "
            pdb=" C   GLU D 479 "
            pdb=" CB  GLU D 479 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.40e-01
  chirality pdb=" CA  GLU N 479 "
            pdb=" N   GLU N 479 "
            pdb=" C   GLU N 479 "
            pdb=" CB  GLU N 479 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.39e-01
  ... (remaining 1677 not shown)

  Planarity restraints: 1984
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN L 534 "   -0.006 2.00e-02 2.50e+03   1.29e-02 1.65e+00
        pdb=" C   GLN L 534 "    0.022 2.00e-02 2.50e+03
        pdb=" O   GLN L 534 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   GLN L 535 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN H 534 "   -0.006 2.00e-02 2.50e+03   1.29e-02 1.65e+00
        pdb=" C   GLN H 534 "    0.022 2.00e-02 2.50e+03
        pdb=" O   GLN H 534 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   GLN H 535 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B 534 "    0.006 2.00e-02 2.50e+03   1.28e-02 1.65e+00
        pdb=" C   GLN B 534 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   GLN B 534 "    0.008 2.00e-02 2.50e+03
        pdb=" N   GLN B 535 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1981 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2424
        2.78 -     3.31: 11712
        3.31 -     3.84: 18266
        3.84 -     4.37: 21191
        4.37 -     4.90: 37554
  Nonbonded interactions: 91147
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU E 483 "
            pdb=" NE2 GLN F 496 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" OE2 GLU F 483 "
            pdb=" NE2 GLN G 496 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" OE2 GLU A 483 "
            pdb=" NE2 GLN B 496 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" NE  ARG K 459 "
            pdb=" OD2 ASP N 477 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" OE2 GLU O 483 "
            pdb=" NE2 GLN P 496 "
     model   vdw
     2.277 3.120
  ... (remaining 91142 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 'C'
  selection = chain 'A'
  selection = chain 'B'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'P'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             25.410
  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:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.690
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
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      :  0.009   0.041  11136  Z= 0.396
  Angle     :  0.826   5.518  14912  Z= 0.485
  Chirality :  0.047   0.133   1680
  Planarity :  0.003   0.013   1984
  Dihedral  : 14.922  70.960   4448
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.23), residues: 1328
  helix:  0.60 (0.15), residues: 1184
  sheet:  None (None), residues: 0
  loop : -0.81 (0.49), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.002   ARG N 459 
 TYR   0.017   0.005   TYR A 531 
 PHE   0.007   0.002   PHE C 453 
 HIS   0.002   0.001   HIS L 458 

Details of bonding type rmsd
  covalent geometry    : bond        0.00893 (11136)
  covalent geometry    : angle       0.82638 (14912)
  hydrogen bonds       : bond        0.14200 (  784)
  hydrogen bonds       : angle       6.10481 ( 2352)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  540 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 540
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  478 ASN cc_start: 0.8752 (m110) cc_final: 0.8335 (m110)
REVERT: A  515 ASP cc_start: 0.7947 (t0) cc_final: 0.7714 (t0)
REVERT: B  473 ASP cc_start: 0.7987 (m-30) cc_final: 0.7424 (m-30)
REVERT: B  474 ASP cc_start: 0.7932 (t70) cc_final: 0.7606 (t0)
REVERT: B  477 ASP cc_start: 0.7817 (m-30) cc_final: 0.7522 (m-30)
REVERT: B  530 SER cc_start: 0.8602 (t) cc_final: 0.8400 (m)
REVERT: D  473 ASP cc_start: 0.7444 (m-30) cc_final: 0.7048 (m-30)
REVERT: D  474 ASP cc_start: 0.8161 (t70) cc_final: 0.7857 (t70)
REVERT: D  478 ASN cc_start: 0.8636 (m110) cc_final: 0.8370 (m110)
REVERT: D  530 SER cc_start: 0.9027 (t) cc_final: 0.8743 (p)
REVERT: E  462 GLN cc_start: 0.8035 (pt0) cc_final: 0.7380 (pt0)
REVERT: E  469 LYS cc_start: 0.8641 (mmtm) cc_final: 0.8257 (mmmm)
REVERT: E  473 ASP cc_start: 0.7772 (m-30) cc_final: 0.7264 (m-30)
REVERT: E  477 ASP cc_start: 0.7975 (m-30) cc_final: 0.7744 (m-30)
REVERT: E  525 ASP cc_start: 0.8228 (t0) cc_final: 0.7838 (t0)
REVERT: E  530 SER cc_start: 0.8908 (t) cc_final: 0.8562 (m)
REVERT: F  477 ASP cc_start: 0.7921 (m-30) cc_final: 0.7682 (m-30)
REVERT: G  462 GLN cc_start: 0.8302 (pt0) cc_final: 0.8101 (pt0)
REVERT: I  462 GLN cc_start: 0.8388 (pt0) cc_final: 0.7760 (pt0)
REVERT: I  491 GLN cc_start: 0.8636 (pp30) cc_final: 0.8047 (pp30)
REVERT: I  495 ARG cc_start: 0.8744 (ptm-80) cc_final: 0.8272 (ttp-110)
REVERT: I  530 SER cc_start: 0.9039 (t) cc_final: 0.8776 (m)
REVERT: J  473 ASP cc_start: 0.7764 (m-30) cc_final: 0.7334 (m-30)
REVERT: J  479 GLU cc_start: 0.7914 (mp0) cc_final: 0.7561 (mp0)
REVERT: K  477 ASP cc_start: 0.7961 (m-30) cc_final: 0.7682 (m-30)
REVERT: K  486 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8170 (tttm)
REVERT: K  495 ARG cc_start: 0.8302 (ptm-80) cc_final: 0.8085 (ttp-110)
REVERT: K  508 LYS cc_start: 0.8309 (mttp) cc_final: 0.8098 (mtpt)
REVERT: K  530 SER cc_start: 0.9155 (t) cc_final: 0.8904 (p)
REVERT: L  490 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7926 (mm-30)
REVERT: L  530 SER cc_start: 0.9009 (t) cc_final: 0.8653 (p)
REVERT: M  530 SER cc_start: 0.8980 (t) cc_final: 0.8719 (m)
REVERT: N  469 LYS cc_start: 0.8632 (mmtm) cc_final: 0.8328 (mmmm)
REVERT: N  473 ASP cc_start: 0.7689 (m-30) cc_final: 0.6765 (m-30)
REVERT: N  477 ASP cc_start: 0.8019 (m-30) cc_final: 0.7807 (m-30)
REVERT: O  477 ASP cc_start: 0.8034 (m-30) cc_final: 0.7760 (m-30)
REVERT: O  485 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7589 (mt-10)
REVERT: P  485 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8091 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 540
  average time/residue: 0.1289
  time to fit residues: 91.9837
Evaluate side-chains
  479 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 479
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9980
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C 484 ASN
A 484 ASN
G 458 HIS
** G 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 458 HIS
K 476 GLN
M 458 HIS
O 535 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.098917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.089980 restraints weight = 17263.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.093159 restraints weight = 8504.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.095129 restraints weight = 4691.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.096394 restraints weight = 2778.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.097220 restraints weight = 1720.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11136  Z= 0.130
  Angle     :  0.527   7.115  14912  Z= 0.290
  Chirality :  0.035   0.120   1680
  Planarity :  0.003   0.029   1984
  Dihedral  :  3.358  12.398   1472
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  :  8.60 %
    Favored  : 89.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.24), residues: 1328
  helix:  1.17 (0.15), residues: 1216
  sheet:  None (None), residues: 0
  loop : -1.14 (0.47), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F 533 
 TYR   0.008   0.001   TYR H 527 
 PHE   0.007   0.001   PHE C 453 
 HIS   0.003   0.001   HIS D 458 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (11136)
  covalent geometry    : angle       0.52667 (14912)
  hydrogen bonds       : bond        0.04064 (  784)
  hydrogen bonds       : angle       4.64137 ( 2352)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  539 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 513
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
REVERT: C  473 ASP cc_start: 0.7428 (t0) cc_final: 0.7058 (t0)
REVERT: C  477 ASP cc_start: 0.7859 (m-30) cc_final: 0.7642 (m-30)
REVERT: C  525 ASP cc_start: 0.7767 (t0) cc_final: 0.7472 (t0)
REVERT: B  473 ASP cc_start: 0.7963 (m-30) cc_final: 0.7341 (m-30)
REVERT: B  474 ASP cc_start: 0.7786 (t70) cc_final: 0.7442 (t0)
REVERT: B  477 ASP cc_start: 0.7679 (m-30) cc_final: 0.7330 (m-30)
REVERT: B  525 ASP cc_start: 0.7971 (t0) cc_final: 0.7754 (t0)
REVERT: D  473 ASP cc_start: 0.7286 (m-30) cc_final: 0.7033 (m-30)
REVERT: D  474 ASP cc_start: 0.7986 (t70) cc_final: 0.7405 (t70)
REVERT: D  478 ASN cc_start: 0.8552 (m110) cc_final: 0.8179 (m-40)
REVERT: D  499 ASN cc_start: 0.8852 (m-40) cc_final: 0.8582 (m110)
REVERT: D  523 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7836 (mp0)
REVERT: D  525 ASP cc_start: 0.7841 (t0) cc_final: 0.7640 (t0)
REVERT: D  530 SER cc_start: 0.9022 (t) cc_final: 0.8758 (p)
REVERT: E  469 LYS cc_start: 0.8551 (mmtm) cc_final: 0.8251 (mmmm)
REVERT: E  473 ASP cc_start: 0.7939 (m-30) cc_final: 0.7130 (m-30)
REVERT: E  477 ASP cc_start: 0.8195 (m-30) cc_final: 0.7881 (m-30)
REVERT: E  530 SER cc_start: 0.8900 (t) cc_final: 0.8530 (m)
REVERT: F  477 ASP cc_start: 0.7972 (m-30) cc_final: 0.7688 (m-30)
REVERT: G  473 ASP cc_start: 0.8091 (m-30) cc_final: 0.7530 (m-30)
REVERT: G  477 ASP cc_start: 0.7781 (m-30) cc_final: 0.7556 (m-30)
REVERT: G  486 LYS cc_start: 0.8927 (ttpp) cc_final: 0.8310 (ttpp)
REVERT: G  500 GLU cc_start: 0.8061 (tp30) cc_final: 0.7747 (tp30)
REVERT: G  519 ARG cc_start: 0.7615 (ttp-110) cc_final: 0.7150 (ptp-110)
REVERT: G  525 ASP cc_start: 0.7970 (t0) cc_final: 0.7663 (t0)
REVERT: I  491 GLN cc_start: 0.8618 (pp30) cc_final: 0.8172 (pp30)
REVERT: I  523 GLU cc_start: 0.7907 (pp20) cc_final: 0.7649 (pt0)
REVERT: I  530 SER cc_start: 0.9024 (t) cc_final: 0.8771 (m)
REVERT: J  477 ASP cc_start: 0.7866 (m-30) cc_final: 0.7500 (m-30)
REVERT: J  478 ASN cc_start: 0.8855 (m-40) cc_final: 0.8620 (m-40)
REVERT: J  479 GLU cc_start: 0.7802 (mp0) cc_final: 0.7537 (mp0)
REVERT: J  486 LYS cc_start: 0.8671 (ttpp) cc_final: 0.8430 (ttmm)
REVERT: K  473 ASP cc_start: 0.8077 (m-30) cc_final: 0.7644 (m-30)
REVERT: K  486 LYS cc_start: 0.8457 (ttpp) cc_final: 0.8013 (ttpp)
REVERT: K  508 LYS cc_start: 0.8261 (mttp) cc_final: 0.7903 (mtpt)
REVERT: K  525 ASP cc_start: 0.7622 (t0) cc_final: 0.7408 (t0)
REVERT: K  530 SER cc_start: 0.9137 (t) cc_final: 0.8902 (p)
REVERT: L  474 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7653 (t0)
REVERT: L  530 SER cc_start: 0.8995 (t) cc_final: 0.8659 (p)
REVERT: M  525 ASP cc_start: 0.7710 (t0) cc_final: 0.7459 (t0)
REVERT: M  530 SER cc_start: 0.8968 (t) cc_final: 0.8675 (m)
REVERT: N  473 ASP cc_start: 0.7587 (m-30) cc_final: 0.6753 (m-30)
REVERT: N  534 GLN cc_start: 0.7811 (tm-30) cc_final: 0.7527 (tm-30)
REVERT: O  477 ASP cc_start: 0.8277 (m-30) cc_final: 0.8014 (m-30)
REVERT: O  530 SER cc_start: 0.8921 (t) cc_final: 0.8591 (p)
REVERT: P  473 ASP cc_start: 0.7807 (m-30) cc_final: 0.7251 (m-30)
REVERT: P  477 ASP cc_start: 0.8414 (m-30) cc_final: 0.8145 (m-30)
REVERT: P  479 GLU cc_start: 0.7596 (mp0) cc_final: 0.7224 (mp0)
REVERT: P  525 ASP cc_start: 0.8025 (t0) cc_final: 0.7816 (t0)
  outliers start: 26
  outliers final: 5
  residues processed: 516
  average time/residue: 0.1213
  time to fit residues: 84.0370
Evaluate side-chains
  490 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 483
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  515 ASP
Chi-restraints excluded: chain D residue  512 LEU
Chi-restraints excluded: chain D residue  523 GLU
Chi-restraints excluded: chain E residue  512 LEU
Chi-restraints excluded: chain E residue  523 GLU
Chi-restraints excluded: chain F residue  490 GLU
Chi-restraints excluded: chain L residue  474 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 117 optimal weight:    0.2980
   chunk 17 optimal weight:    3.9990
   chunk 96 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 114 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 478 ASN
G 478 ASN
H 458 HIS
I 478 ASN
J 484 ASN
L 476 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.095460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.085967 restraints weight = 17721.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.089201 restraints weight = 8641.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.091223 restraints weight = 4826.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.092543 restraints weight = 2911.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.093431 restraints weight = 1840.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  11136  Z= 0.214
  Angle     :  0.586   7.764  14912  Z= 0.318
  Chirality :  0.039   0.161   1680
  Planarity :  0.004   0.030   1984
  Dihedral  :  3.430  13.116   1472
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 12.74 %
    Favored  : 84.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.23), residues: 1328
  helix:  1.07 (0.15), residues: 1216
  sheet:  None (None), residues: 0
  loop : -1.07 (0.47), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 519 
 TYR   0.013   0.002   TYR E 531 
 PHE   0.012   0.002   PHE C 453 
 HIS   0.003   0.001   HIS P 458 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 (11136)
  covalent geometry    : angle       0.58567 (14912)
  hydrogen bonds       : bond        0.04275 (  784)
  hydrogen bonds       : angle       4.47489 ( 2352)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  527 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 488
  time to evaluate  : 0.469 
Fit side-chains
REVERT: C  525 ASP cc_start: 0.8039 (t0) cc_final: 0.7493 (t0)
REVERT: A  525 ASP cc_start: 0.7875 (t0) cc_final: 0.7653 (t0)
REVERT: B  473 ASP cc_start: 0.7983 (m-30) cc_final: 0.7407 (m-30)
REVERT: B  474 ASP cc_start: 0.7982 (t70) cc_final: 0.7553 (t0)
REVERT: B  477 ASP cc_start: 0.7700 (m-30) cc_final: 0.7390 (m-30)
REVERT: B  483 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7569 (tp30)
REVERT: B  525 ASP cc_start: 0.8126 (t0) cc_final: 0.7742 (t0)
REVERT: D  460 GLN cc_start: 0.7735 (mm110) cc_final: 0.6808 (mp10)
REVERT: D  469 LYS cc_start: 0.8705 (mmmm) cc_final: 0.8428 (mmmm)
REVERT: D  474 ASP cc_start: 0.8243 (t70) cc_final: 0.7600 (t70)
REVERT: D  478 ASN cc_start: 0.8770 (m110) cc_final: 0.8328 (m-40)
REVERT: D  523 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7889 (mp0)
REVERT: D  525 ASP cc_start: 0.8068 (t0) cc_final: 0.7675 (t0)
REVERT: D  530 SER cc_start: 0.8925 (t) cc_final: 0.8617 (p)
REVERT: E  469 LYS cc_start: 0.8620 (mmtm) cc_final: 0.8250 (mmmm)
REVERT: E  473 ASP cc_start: 0.7987 (m-30) cc_final: 0.7222 (m-30)
REVERT: E  477 ASP cc_start: 0.8190 (m-30) cc_final: 0.7813 (m-30)
REVERT: E  525 ASP cc_start: 0.7743 (t0) cc_final: 0.7371 (t0)
REVERT: E  530 SER cc_start: 0.8816 (t) cc_final: 0.8400 (m)
REVERT: F  477 ASP cc_start: 0.7916 (m-30) cc_final: 0.7536 (m-30)
REVERT: G  462 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8375 (tt0)
REVERT: G  473 ASP cc_start: 0.8236 (m-30) cc_final: 0.7781 (m-30)
REVERT: G  477 ASP cc_start: 0.7859 (m-30) cc_final: 0.7623 (m-30)
REVERT: G  500 GLU cc_start: 0.8029 (tp30) cc_final: 0.7219 (tp30)
REVERT: H  525 ASP cc_start: 0.7692 (t0) cc_final: 0.7492 (t0)
REVERT: I  474 ASP cc_start: 0.7635 (t70) cc_final: 0.7303 (t0)
REVERT: I  478 ASN cc_start: 0.8880 (m-40) cc_final: 0.8644 (m-40)
REVERT: I  491 GLN cc_start: 0.8752 (pp30) cc_final: 0.8242 (pp30)
REVERT: I  495 ARG cc_start: 0.8796 (ptm-80) cc_final: 0.8426 (ttp-110)
REVERT: I  525 ASP cc_start: 0.7865 (t0) cc_final: 0.7621 (t0)
REVERT: I  530 SER cc_start: 0.8930 (t) cc_final: 0.8695 (m)
REVERT: J  473 ASP cc_start: 0.7882 (m-30) cc_final: 0.7531 (m-30)
REVERT: J  479 GLU cc_start: 0.8008 (mp0) cc_final: 0.7644 (mp0)
REVERT: J  505 MET cc_start: 0.8105 (mtp) cc_final: 0.7890 (mtp)
REVERT: J  534 GLN cc_start: 0.8067 (tm-30) cc_final: 0.7852 (tm-30)
REVERT: K  473 ASP cc_start: 0.8269 (m-30) cc_final: 0.7805 (m-30)
REVERT: K  486 LYS cc_start: 0.8520 (ttpp) cc_final: 0.8152 (tttm)
REVERT: K  495 ARG cc_start: 0.8242 (ptm-80) cc_final: 0.8017 (ttp-110)
REVERT: K  525 ASP cc_start: 0.7913 (t0) cc_final: 0.7521 (t0)
REVERT: K  530 SER cc_start: 0.9108 (t) cc_final: 0.8842 (p)
REVERT: L  530 SER cc_start: 0.8930 (t) cc_final: 0.8582 (p)
REVERT: M  525 ASP cc_start: 0.7971 (t0) cc_final: 0.7649 (t0)
REVERT: M  530 SER cc_start: 0.8925 (t) cc_final: 0.8673 (m)
REVERT: M  534 GLN cc_start: 0.7928 (pp30) cc_final: 0.7571 (pp30)
REVERT: N  473 ASP cc_start: 0.7640 (m-30) cc_final: 0.6829 (m-30)
REVERT: N  474 ASP cc_start: 0.7421 (t0) cc_final: 0.7087 (t0)
REVERT: N  477 ASP cc_start: 0.8040 (m-30) cc_final: 0.7756 (m-30)
REVERT: N  478 ASN cc_start: 0.8875 (m-40) cc_final: 0.8509 (m110)
REVERT: N  523 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8036 (mt-10)
REVERT: N  525 ASP cc_start: 0.7905 (t0) cc_final: 0.7694 (t0)
REVERT: N  534 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7667 (tm-30)
REVERT: O  477 ASP cc_start: 0.8201 (m-30) cc_final: 0.7897 (m-30)
REVERT: O  525 ASP cc_start: 0.7677 (t0) cc_final: 0.7458 (t0)
REVERT: O  530 SER cc_start: 0.8948 (t) cc_final: 0.8531 (p)
REVERT: P  473 ASP cc_start: 0.7998 (m-30) cc_final: 0.7440 (m-30)
REVERT: P  525 ASP cc_start: 0.8228 (t0) cc_final: 0.7836 (t0)
  outliers start: 39
  outliers final: 18
  residues processed: 498
  average time/residue: 0.1274
  time to fit residues: 84.4939
Evaluate side-chains
  494 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 473
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  515 ASP
Chi-restraints excluded: chain D residue  462 GLN
Chi-restraints excluded: chain D residue  523 GLU
Chi-restraints excluded: chain E residue  462 GLN
Chi-restraints excluded: chain E residue  468 LEU
Chi-restraints excluded: chain E residue  512 LEU
Chi-restraints excluded: chain E residue  515 ASP
Chi-restraints excluded: chain E residue  523 GLU
Chi-restraints excluded: chain F residue  462 GLN
Chi-restraints excluded: chain F residue  465 MET
Chi-restraints excluded: chain F residue  490 GLU
Chi-restraints excluded: chain G residue  462 GLN
Chi-restraints excluded: chain G residue  465 MET
Chi-restraints excluded: chain H residue  512 LEU
Chi-restraints excluded: chain I residue  468 LEU
Chi-restraints excluded: chain I residue  515 ASP
Chi-restraints excluded: chain K residue  462 GLN
Chi-restraints excluded: chain K residue  512 LEU
Chi-restraints excluded: chain M residue  462 GLN
Chi-restraints excluded: chain N residue  468 LEU
Chi-restraints excluded: chain N residue  523 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 72 optimal weight:    8.9990
   chunk 15 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 88 optimal weight:    7.9990
   chunk 41 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 114 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
C 484 ASN
A 478 ASN
G 478 ASN
H 462 GLN
I 478 ASN
J 535 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.097699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.088602 restraints weight = 17396.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.091744 restraints weight = 8538.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.093738 restraints weight = 4732.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.095000 restraints weight = 2826.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.095869 restraints weight = 1771.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.3411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11136  Z= 0.124
  Angle     :  0.501   7.242  14912  Z= 0.273
  Chirality :  0.035   0.124   1680
  Planarity :  0.003   0.033   1984
  Dihedral  :  3.243  12.983   1472
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 15.34 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.23), residues: 1328
  helix:  1.36 (0.15), residues: 1200
  sheet:  None (None), residues: 0
  loop : -0.55 (0.41), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 519 
 TYR   0.007   0.001   TYR H 527 
 PHE   0.007   0.001   PHE D 453 
 HIS   0.002   0.001   HIS P 458 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (11136)
  covalent geometry    : angle       0.50051 (14912)
  hydrogen bonds       : bond        0.03412 (  784)
  hydrogen bonds       : angle       4.43993 ( 2352)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  532 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 494
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  477 ASP cc_start: 0.8045 (m-30) cc_final: 0.7827 (m-30)
REVERT: C  525 ASP cc_start: 0.7857 (t0) cc_final: 0.7326 (t0)
REVERT: A  474 ASP cc_start: 0.7644 (t0) cc_final: 0.7439 (t0)
REVERT: A  520 SER cc_start: 0.8814 (t) cc_final: 0.8585 (m)
REVERT: A  525 ASP cc_start: 0.7850 (t0) cc_final: 0.7550 (t0)
REVERT: B  473 ASP cc_start: 0.7978 (m-30) cc_final: 0.7342 (m-30)
REVERT: B  474 ASP cc_start: 0.7890 (t70) cc_final: 0.7490 (t0)
REVERT: B  477 ASP cc_start: 0.7714 (m-30) cc_final: 0.7421 (m-30)
REVERT: B  525 ASP cc_start: 0.7974 (t0) cc_final: 0.7595 (t0)
REVERT: D  474 ASP cc_start: 0.8150 (t70) cc_final: 0.7544 (t70)
REVERT: D  478 ASN cc_start: 0.8689 (m110) cc_final: 0.8262 (m-40)
REVERT: D  523 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7886 (mp0)
REVERT: D  525 ASP cc_start: 0.7873 (t0) cc_final: 0.7561 (t0)
REVERT: D  530 SER cc_start: 0.8908 (t) cc_final: 0.8646 (p)
REVERT: E  469 LYS cc_start: 0.8563 (mmtm) cc_final: 0.8222 (mmmm)
REVERT: E  473 ASP cc_start: 0.7953 (m-30) cc_final: 0.7134 (m-30)
REVERT: E  477 ASP cc_start: 0.8254 (m-30) cc_final: 0.7894 (m-30)
REVERT: E  505 MET cc_start: 0.7865 (mtp) cc_final: 0.7588 (mtt)
REVERT: E  525 ASP cc_start: 0.7560 (t0) cc_final: 0.7301 (t0)
REVERT: E  530 SER cc_start: 0.8811 (t) cc_final: 0.8438 (m)
REVERT: F  477 ASP cc_start: 0.7937 (m-30) cc_final: 0.7564 (m-30)
REVERT: G  473 ASP cc_start: 0.8398 (m-30) cc_final: 0.7766 (m-30)
REVERT: G  477 ASP cc_start: 0.7922 (m-30) cc_final: 0.7628 (m-30)
REVERT: G  500 GLU cc_start: 0.8049 (tp30) cc_final: 0.7587 (tp30)
REVERT: I  486 LYS cc_start: 0.8700 (ttpp) cc_final: 0.8484 (ttpp)
REVERT: I  491 GLN cc_start: 0.8773 (pp30) cc_final: 0.8314 (pp30)
REVERT: I  495 ARG cc_start: 0.8765 (ptm-80) cc_final: 0.8406 (ttp-110)
REVERT: I  530 SER cc_start: 0.8967 (t) cc_final: 0.8686 (m)
REVERT: J  473 ASP cc_start: 0.7792 (m-30) cc_final: 0.7416 (m-30)
REVERT: J  477 ASP cc_start: 0.7900 (m-30) cc_final: 0.7497 (m-30)
REVERT: J  478 ASN cc_start: 0.8944 (m-40) cc_final: 0.8648 (m-40)
REVERT: J  479 GLU cc_start: 0.7955 (mp0) cc_final: 0.7607 (mp0)
REVERT: J  486 LYS cc_start: 0.8731 (ttpp) cc_final: 0.8443 (ttmm)
REVERT: J  505 MET cc_start: 0.7956 (mtp) cc_final: 0.7751 (mtp)
REVERT: J  534 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7703 (tm-30)
REVERT: K  473 ASP cc_start: 0.8191 (m-30) cc_final: 0.7725 (m-30)
REVERT: K  486 LYS cc_start: 0.8477 (ttpp) cc_final: 0.8177 (tttm)
REVERT: K  525 ASP cc_start: 0.7745 (t0) cc_final: 0.7368 (t0)
REVERT: K  530 SER cc_start: 0.9149 (t) cc_final: 0.8865 (p)
REVERT: L  530 SER cc_start: 0.8941 (t) cc_final: 0.8614 (p)
REVERT: M  477 ASP cc_start: 0.7846 (m-30) cc_final: 0.7572 (m-30)
REVERT: M  479 GLU cc_start: 0.7512 (mp0) cc_final: 0.7304 (mp0)
REVERT: M  525 ASP cc_start: 0.7775 (t0) cc_final: 0.7456 (t0)
REVERT: M  530 SER cc_start: 0.8888 (t) cc_final: 0.8674 (m)
REVERT: M  534 GLN cc_start: 0.7829 (pp30) cc_final: 0.7522 (pp30)
REVERT: N  473 ASP cc_start: 0.7540 (m-30) cc_final: 0.6762 (m-30)
REVERT: N  477 ASP cc_start: 0.7998 (m-30) cc_final: 0.7727 (m-30)
REVERT: N  487 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7853 (mt-10)
REVERT: N  534 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7620 (tm-30)
REVERT: O  477 ASP cc_start: 0.8250 (m-30) cc_final: 0.7945 (m-30)
REVERT: O  525 ASP cc_start: 0.7551 (t0) cc_final: 0.7195 (t0)
REVERT: O  530 SER cc_start: 0.8996 (t) cc_final: 0.8625 (p)
REVERT: P  473 ASP cc_start: 0.7820 (m-30) cc_final: 0.7410 (m-30)
REVERT: P  477 ASP cc_start: 0.8403 (m-30) cc_final: 0.7850 (m-30)
REVERT: P  479 GLU cc_start: 0.7543 (mp0) cc_final: 0.7172 (mp0)
REVERT: P  525 ASP cc_start: 0.8113 (t0) cc_final: 0.7903 (t0)
REVERT: P  534 GLN cc_start: 0.7714 (pp30) cc_final: 0.7497 (pp30)
  outliers start: 38
  outliers final: 18
  residues processed: 505
  average time/residue: 0.1233
  time to fit residues: 83.3557
Evaluate side-chains
  489 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 470
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  462 GLN
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain B residue  515 ASP
Chi-restraints excluded: chain D residue  523 GLU
Chi-restraints excluded: chain E residue  462 GLN
Chi-restraints excluded: chain E residue  468 LEU
Chi-restraints excluded: chain E residue  491 GLN
Chi-restraints excluded: chain G residue  465 MET
Chi-restraints excluded: chain I residue  468 LEU
Chi-restraints excluded: chain K residue  462 GLN
Chi-restraints excluded: chain L residue  491 GLN
Chi-restraints excluded: chain L residue  525 ASP
Chi-restraints excluded: chain N residue  491 GLN
Chi-restraints excluded: chain N residue  515 ASP
Chi-restraints excluded: chain N residue  523 GLU
Chi-restraints excluded: chain N residue  530 SER
Chi-restraints excluded: chain P residue  482 THR
Chi-restraints excluded: chain P residue  512 LEU
Chi-restraints excluded: chain P residue  530 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   chunk 97 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 122 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0770
   overall best weight:    1.0144

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

Flipped N/Q/H residues before XYZ refinement:
D 458 HIS
E 476 GLN
G 478 ASN
H 462 GLN
H 535 GLN
I 478 ASN
L 476 GLN
N 476 GLN
P 476 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.098285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.089176 restraints weight = 17268.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.092274 restraints weight = 8577.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.094256 restraints weight = 4798.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.095512 restraints weight = 2888.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.096367 restraints weight = 1821.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.3599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11136  Z= 0.130
  Angle     :  0.511   8.177  14912  Z= 0.278
  Chirality :  0.035   0.126   1680
  Planarity :  0.003   0.027   1984
  Dihedral  :  3.217  13.502   1472
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 16.31 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.22), residues: 1328
  helix:  1.41 (0.15), residues: 1200
  sheet:  None (None), residues: 0
  loop : -0.60 (0.40), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 519 
 TYR   0.007   0.001   TYR H 527 
 PHE   0.009   0.001   PHE D 453 
 HIS   0.002   0.000   HIS P 458 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (11136)
  covalent geometry    : angle       0.51085 (14912)
  hydrogen bonds       : bond        0.03427 (  784)
  hydrogen bonds       : angle       4.39135 ( 2352)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  528 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 485
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  477 ASP cc_start: 0.7966 (m-30) cc_final: 0.7751 (m-30)
REVERT: C  525 ASP cc_start: 0.7917 (t0) cc_final: 0.7351 (t0)
REVERT: A  525 ASP cc_start: 0.7842 (t0) cc_final: 0.7524 (t0)
REVERT: B  473 ASP cc_start: 0.8017 (m-30) cc_final: 0.7386 (m-30)
REVERT: B  474 ASP cc_start: 0.7944 (t70) cc_final: 0.7363 (t0)
REVERT: B  477 ASP cc_start: 0.7657 (m-30) cc_final: 0.7433 (m-30)
REVERT: B  478 ASN cc_start: 0.8521 (m-40) cc_final: 0.7839 (m110)
REVERT: B  525 ASP cc_start: 0.7916 (t0) cc_final: 0.7528 (t0)
REVERT: D  462 GLN cc_start: 0.8706 (tt0) cc_final: 0.8333 (tt0)
REVERT: D  474 ASP cc_start: 0.8167 (t70) cc_final: 0.7558 (t70)
REVERT: D  478 ASN cc_start: 0.8687 (m110) cc_final: 0.8298 (m-40)
REVERT: D  523 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7887 (mp0)
REVERT: D  525 ASP cc_start: 0.7860 (t0) cc_final: 0.7572 (t0)
REVERT: D  530 SER cc_start: 0.8937 (t) cc_final: 0.8665 (p)
REVERT: E  469 LYS cc_start: 0.8547 (mmtm) cc_final: 0.8218 (mmmm)
REVERT: E  473 ASP cc_start: 0.7963 (m-30) cc_final: 0.7160 (m-30)
REVERT: E  477 ASP cc_start: 0.8238 (m-30) cc_final: 0.7892 (m-30)
REVERT: E  478 ASN cc_start: 0.8846 (m-40) cc_final: 0.8602 (m110)
REVERT: E  505 MET cc_start: 0.7884 (mtp) cc_final: 0.7559 (mtt)
REVERT: E  525 ASP cc_start: 0.7554 (t0) cc_final: 0.7085 (t0)
REVERT: E  530 SER cc_start: 0.8786 (t) cc_final: 0.8464 (m)
REVERT: F  477 ASP cc_start: 0.7912 (m-30) cc_final: 0.7538 (m-30)
REVERT: G  473 ASP cc_start: 0.8401 (m-30) cc_final: 0.7798 (m-30)
REVERT: G  477 ASP cc_start: 0.7987 (m-30) cc_final: 0.7766 (m-30)
REVERT: G  500 GLU cc_start: 0.7953 (tp30) cc_final: 0.7488 (tp30)
REVERT: H  525 ASP cc_start: 0.7582 (t0) cc_final: 0.7286 (t0)
REVERT: I  491 GLN cc_start: 0.8768 (pp30) cc_final: 0.8263 (pp30)
REVERT: I  495 ARG cc_start: 0.8752 (ptm-80) cc_final: 0.8434 (ttp-110)
REVERT: I  530 SER cc_start: 0.8953 (t) cc_final: 0.8700 (m)
REVERT: J  473 ASP cc_start: 0.7796 (m-30) cc_final: 0.7341 (m-30)
REVERT: J  477 ASP cc_start: 0.7878 (m-30) cc_final: 0.7435 (m-30)
REVERT: J  478 ASN cc_start: 0.8952 (m-40) cc_final: 0.8625 (m-40)
REVERT: J  479 GLU cc_start: 0.7956 (mp0) cc_final: 0.7585 (mp0)
REVERT: J  505 MET cc_start: 0.7948 (mtp) cc_final: 0.7725 (mtp)
REVERT: J  534 GLN cc_start: 0.7972 (tm-30) cc_final: 0.7663 (tm-30)
REVERT: K  469 LYS cc_start: 0.8633 (mmtp) cc_final: 0.8227 (mmtp)
REVERT: K  473 ASP cc_start: 0.8214 (m-30) cc_final: 0.7733 (m-30)
REVERT: K  486 LYS cc_start: 0.8403 (ttpp) cc_final: 0.8183 (tttm)
REVERT: K  525 ASP cc_start: 0.7740 (t0) cc_final: 0.7357 (t0)
REVERT: K  530 SER cc_start: 0.9144 (t) cc_final: 0.8869 (p)
REVERT: L  479 GLU cc_start: 0.7781 (mp0) cc_final: 0.7539 (mp0)
REVERT: L  530 SER cc_start: 0.8947 (t) cc_final: 0.8644 (p)
REVERT: M  477 ASP cc_start: 0.7854 (m-30) cc_final: 0.7564 (m-30)
REVERT: M  479 GLU cc_start: 0.7521 (mp0) cc_final: 0.7285 (mp0)
REVERT: M  525 ASP cc_start: 0.7792 (t0) cc_final: 0.7453 (t0)
REVERT: M  534 GLN cc_start: 0.7784 (pp30) cc_final: 0.7549 (pp30)
REVERT: N  473 ASP cc_start: 0.7580 (m-30) cc_final: 0.6751 (m-30)
REVERT: N  477 ASP cc_start: 0.8083 (m-30) cc_final: 0.7808 (m-30)
REVERT: N  487 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7885 (mt-10)
REVERT: N  534 GLN cc_start: 0.7851 (tm-30) cc_final: 0.7590 (tm-30)
REVERT: O  474 ASP cc_start: 0.7485 (t0) cc_final: 0.7165 (t0)
REVERT: O  477 ASP cc_start: 0.8315 (m-30) cc_final: 0.8036 (m-30)
REVERT: O  520 SER cc_start: 0.8804 (t) cc_final: 0.8568 (m)
REVERT: O  530 SER cc_start: 0.9015 (t) cc_final: 0.8653 (p)
REVERT: P  473 ASP cc_start: 0.7884 (m-30) cc_final: 0.7405 (m-30)
REVERT: P  477 ASP cc_start: 0.8408 (m-30) cc_final: 0.7745 (m-30)
REVERT: P  479 GLU cc_start: 0.7589 (mp0) cc_final: 0.7204 (mp0)
REVERT: P  525 ASP cc_start: 0.8095 (t0) cc_final: 0.7876 (t0)
REVERT: P  534 GLN cc_start: 0.7700 (pp30) cc_final: 0.7392 (pp30)
  outliers start: 43
  outliers final: 25
  residues processed: 499
  average time/residue: 0.1215
  time to fit residues: 81.3636
Evaluate side-chains
  499 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 473
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  462 GLN
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain B residue  515 ASP
Chi-restraints excluded: chain D residue  523 GLU
Chi-restraints excluded: chain E residue  462 GLN
Chi-restraints excluded: chain E residue  468 LEU
Chi-restraints excluded: chain E residue  491 GLN
Chi-restraints excluded: chain E residue  515 ASP
Chi-restraints excluded: chain F residue  462 GLN
Chi-restraints excluded: chain F residue  490 GLU
Chi-restraints excluded: chain G residue  465 MET
Chi-restraints excluded: chain G residue  525 ASP
Chi-restraints excluded: chain I residue  468 LEU
Chi-restraints excluded: chain K residue  462 GLN
Chi-restraints excluded: chain K residue  465 MET
Chi-restraints excluded: chain L residue  491 GLN
Chi-restraints excluded: chain L residue  505 MET
Chi-restraints excluded: chain L residue  525 ASP
Chi-restraints excluded: chain M residue  462 GLN
Chi-restraints excluded: chain N residue  462 GLN
Chi-restraints excluded: chain N residue  515 ASP
Chi-restraints excluded: chain N residue  523 GLU
Chi-restraints excluded: chain N residue  530 SER
Chi-restraints excluded: chain O residue  523 GLU
Chi-restraints excluded: chain P residue  515 ASP
Chi-restraints excluded: chain P residue  530 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 124 optimal weight:    0.0470
   chunk 50 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0060
   chunk 72 optimal weight:   10.0000
   chunk 76 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 96 optimal weight:    6.9990
   chunk 68 optimal weight:    2.9990
   chunk 108 optimal weight:    0.6980
   chunk 104 optimal weight:    7.9990
   overall best weight:    0.9496

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

Flipped N/Q/H residues before XYZ refinement:
B 462 GLN
E 476 GLN
F 476 GLN
H 462 GLN
I 534 GLN
L 535 GLN
P 476 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.098023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.088962 restraints weight = 17457.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.092161 restraints weight = 8281.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.094178 restraints weight = 4489.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.095438 restraints weight = 2624.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.096270 restraints weight = 1616.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.3743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11136  Z= 0.128
  Angle     :  0.516   8.515  14912  Z= 0.282
  Chirality :  0.035   0.128   1680
  Planarity :  0.003   0.034   1984
  Dihedral  :  3.227  13.583   1472
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 17.45 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.22), residues: 1328
  helix:  1.46 (0.15), residues: 1200
  sheet:  None (None), residues: 0
  loop : -0.57 (0.41), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG I 533 
 TYR   0.007   0.001   TYR H 527 
 PHE   0.007   0.001   PHE K 453 
 HIS   0.002   0.000   HIS D 458 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (11136)
  covalent geometry    : angle       0.51641 (14912)
  hydrogen bonds       : bond        0.03352 (  784)
  hydrogen bonds       : angle       4.40658 ( 2352)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  526 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 479
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
REVERT: A  520 SER cc_start: 0.8952 (t) cc_final: 0.8749 (m)
REVERT: A  525 ASP cc_start: 0.7792 (t0) cc_final: 0.7447 (t0)
REVERT: B  473 ASP cc_start: 0.7990 (m-30) cc_final: 0.7432 (m-30)
REVERT: B  474 ASP cc_start: 0.7945 (t70) cc_final: 0.7482 (t0)
REVERT: B  525 ASP cc_start: 0.7890 (t0) cc_final: 0.7495 (t0)
REVERT: D  478 ASN cc_start: 0.8690 (m110) cc_final: 0.8269 (m-40)
REVERT: D  523 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7909 (mp0)
REVERT: D  525 ASP cc_start: 0.7856 (t0) cc_final: 0.7558 (t0)
REVERT: D  530 SER cc_start: 0.8910 (t) cc_final: 0.8597 (p)
REVERT: E  469 LYS cc_start: 0.8558 (mmtm) cc_final: 0.8206 (mmmm)
REVERT: E  473 ASP cc_start: 0.8080 (m-30) cc_final: 0.7214 (m-30)
REVERT: E  477 ASP cc_start: 0.8266 (m-30) cc_final: 0.7889 (m-30)
REVERT: E  478 ASN cc_start: 0.8836 (m-40) cc_final: 0.8622 (m110)
REVERT: E  505 MET cc_start: 0.7903 (mtp) cc_final: 0.7572 (mtt)
REVERT: E  525 ASP cc_start: 0.7530 (t0) cc_final: 0.7038 (t0)
REVERT: E  530 SER cc_start: 0.8809 (t) cc_final: 0.8480 (m)
REVERT: F  477 ASP cc_start: 0.7885 (m-30) cc_final: 0.7497 (m-30)
REVERT: F  520 SER cc_start: 0.8843 (t) cc_final: 0.8341 (m)
REVERT: F  534 GLN cc_start: 0.7642 (tm-30) cc_final: 0.7333 (pp30)
REVERT: G  473 ASP cc_start: 0.8428 (m-30) cc_final: 0.7818 (m-30)
REVERT: G  477 ASP cc_start: 0.8045 (m-30) cc_final: 0.7834 (m-30)
REVERT: G  500 GLU cc_start: 0.7906 (tp30) cc_final: 0.7438 (tp30)
REVERT: H  525 ASP cc_start: 0.7566 (t0) cc_final: 0.7213 (t0)
REVERT: I  491 GLN cc_start: 0.8790 (pp30) cc_final: 0.8298 (pp30)
REVERT: I  495 ARG cc_start: 0.8732 (ptm-80) cc_final: 0.8415 (ttp-110)
REVERT: I  530 SER cc_start: 0.8806 (t) cc_final: 0.8597 (m)
REVERT: J  473 ASP cc_start: 0.7763 (m-30) cc_final: 0.7341 (m-30)
REVERT: J  477 ASP cc_start: 0.7838 (m-30) cc_final: 0.7404 (m-30)
REVERT: J  478 ASN cc_start: 0.8934 (m-40) cc_final: 0.8631 (m-40)
REVERT: J  479 GLU cc_start: 0.7932 (mp0) cc_final: 0.7557 (mp0)
REVERT: J  486 LYS cc_start: 0.8711 (ttpp) cc_final: 0.8387 (ttmm)
REVERT: J  505 MET cc_start: 0.7987 (mtp) cc_final: 0.7749 (mtp)
REVERT: J  534 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7665 (tm-30)
REVERT: K  469 LYS cc_start: 0.8614 (mmtp) cc_final: 0.8222 (mmtp)
REVERT: K  473 ASP cc_start: 0.8245 (m-30) cc_final: 0.7783 (m-30)
REVERT: K  525 ASP cc_start: 0.7632 (t0) cc_final: 0.7262 (t0)
REVERT: K  530 SER cc_start: 0.9124 (t) cc_final: 0.8854 (p)
REVERT: L  479 GLU cc_start: 0.7794 (mp0) cc_final: 0.7524 (mp0)
REVERT: L  530 SER cc_start: 0.8963 (t) cc_final: 0.8632 (p)
REVERT: M  477 ASP cc_start: 0.7890 (m-30) cc_final: 0.7613 (m-30)
REVERT: M  479 GLU cc_start: 0.7494 (mp0) cc_final: 0.7265 (mp0)
REVERT: M  534 GLN cc_start: 0.7811 (pp30) cc_final: 0.7594 (pp30)
REVERT: N  473 ASP cc_start: 0.7550 (m-30) cc_final: 0.6677 (m-30)
REVERT: N  477 ASP cc_start: 0.8112 (m-30) cc_final: 0.7808 (m-30)
REVERT: N  478 ASN cc_start: 0.8831 (m-40) cc_final: 0.8494 (m110)
REVERT: N  487 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7897 (mt-10)
REVERT: N  523 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7972 (mt-10)
REVERT: N  534 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7653 (tm-30)
REVERT: O  477 ASP cc_start: 0.8334 (m-30) cc_final: 0.8055 (m-30)
REVERT: O  525 ASP cc_start: 0.7620 (t0) cc_final: 0.7350 (t0)
REVERT: O  530 SER cc_start: 0.9031 (t) cc_final: 0.8687 (p)
REVERT: P  473 ASP cc_start: 0.7968 (m-30) cc_final: 0.7449 (m-30)
REVERT: P  477 ASP cc_start: 0.8397 (m-30) cc_final: 0.7705 (m-30)
REVERT: P  479 GLU cc_start: 0.7612 (mp0) cc_final: 0.7238 (mp0)
REVERT: P  525 ASP cc_start: 0.8036 (t0) cc_final: 0.7772 (t0)
REVERT: P  534 GLN cc_start: 0.7808 (pp30) cc_final: 0.7434 (pp30)
  outliers start: 47
  outliers final: 30
  residues processed: 494
  average time/residue: 0.1243
  time to fit residues: 82.0509
Evaluate side-chains
  501 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 469
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  462 GLN
Chi-restraints excluded: chain C residue  505 MET
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain B residue  515 ASP
Chi-restraints excluded: chain D residue  523 GLU
Chi-restraints excluded: chain E residue  462 GLN
Chi-restraints excluded: chain E residue  468 LEU
Chi-restraints excluded: chain E residue  491 GLN
Chi-restraints excluded: chain E residue  515 ASP
Chi-restraints excluded: chain F residue  462 GLN
Chi-restraints excluded: chain G residue  465 MET
Chi-restraints excluded: chain G residue  525 ASP
Chi-restraints excluded: chain H residue  500 GLU
Chi-restraints excluded: chain I residue  462 GLN
Chi-restraints excluded: chain I residue  468 LEU
Chi-restraints excluded: chain I residue  534 GLN
Chi-restraints excluded: chain K residue  462 GLN
Chi-restraints excluded: chain K residue  465 MET
Chi-restraints excluded: chain K residue  468 LEU
Chi-restraints excluded: chain K residue  522 SER
Chi-restraints excluded: chain L residue  491 GLN
Chi-restraints excluded: chain L residue  505 MET
Chi-restraints excluded: chain L residue  525 ASP
Chi-restraints excluded: chain M residue  462 GLN
Chi-restraints excluded: chain N residue  462 GLN
Chi-restraints excluded: chain N residue  491 GLN
Chi-restraints excluded: chain N residue  523 GLU
Chi-restraints excluded: chain O residue  496 GLN
Chi-restraints excluded: chain O residue  512 LEU
Chi-restraints excluded: chain O residue  523 GLU
Chi-restraints excluded: chain P residue  515 ASP
Chi-restraints excluded: chain P residue  530 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 98 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 125 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9990
   chunk 8 optimal weight:   10.0000
   chunk 86 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 462 GLN
E 476 GLN
F 476 GLN
** H 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 534 GLN
P 476 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.098600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.089517 restraints weight = 17316.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.092727 restraints weight = 8228.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.094709 restraints weight = 4455.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.095969 restraints weight = 2607.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.096821 restraints weight = 1608.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.3855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  11136  Z= 0.129
  Angle     :  0.535   9.388  14912  Z= 0.293
  Chirality :  0.035   0.126   1680
  Planarity :  0.003   0.038   1984
  Dihedral  :  3.248  13.404   1472
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 18.34 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.22), residues: 1328
  helix:  1.45 (0.15), residues: 1200
  sheet:  None (None), residues: 0
  loop : -0.53 (0.41), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 519 
 TYR   0.006   0.001   TYR H 527 
 PHE   0.007   0.001   PHE K 453 
 HIS   0.001   0.001   HIS D 458 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (11136)
  covalent geometry    : angle       0.53477 (14912)
  hydrogen bonds       : bond        0.03364 (  784)
  hydrogen bonds       : angle       4.44485 ( 2352)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  525 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 482
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  486 LYS cc_start: 0.9002 (ttpp) cc_final: 0.8783 (ttmm)
REVERT: C  520 SER cc_start: 0.8599 (t) cc_final: 0.8395 (m)
REVERT: A  474 ASP cc_start: 0.7795 (t0) cc_final: 0.7532 (t0)
REVERT: A  525 ASP cc_start: 0.7782 (t0) cc_final: 0.7424 (t0)
REVERT: B  473 ASP cc_start: 0.7896 (m-30) cc_final: 0.7398 (m-30)
REVERT: B  474 ASP cc_start: 0.7882 (t70) cc_final: 0.7444 (t0)
REVERT: B  525 ASP cc_start: 0.7871 (t0) cc_final: 0.7482 (t0)
REVERT: B  534 GLN cc_start: 0.7394 (mp10) cc_final: 0.7145 (mp10)
REVERT: D  462 GLN cc_start: 0.8638 (tt0) cc_final: 0.8402 (tt0)
REVERT: D  474 ASP cc_start: 0.8151 (t70) cc_final: 0.7758 (t70)
REVERT: D  478 ASN cc_start: 0.8691 (m110) cc_final: 0.8226 (m-40)
REVERT: D  523 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7943 (mp0)
REVERT: D  525 ASP cc_start: 0.7858 (t0) cc_final: 0.7559 (t0)
REVERT: D  530 SER cc_start: 0.8916 (t) cc_final: 0.8609 (p)
REVERT: E  469 LYS cc_start: 0.8554 (mmtm) cc_final: 0.8203 (mmmm)
REVERT: E  473 ASP cc_start: 0.8097 (m-30) cc_final: 0.7124 (m-30)
REVERT: E  477 ASP cc_start: 0.8255 (m-30) cc_final: 0.7863 (m-30)
REVERT: E  505 MET cc_start: 0.7891 (mtp) cc_final: 0.7559 (mtt)
REVERT: E  525 ASP cc_start: 0.7485 (t0) cc_final: 0.6994 (t0)
REVERT: E  530 SER cc_start: 0.8795 (t) cc_final: 0.8479 (m)
REVERT: F  477 ASP cc_start: 0.7924 (m-30) cc_final: 0.7530 (m-30)
REVERT: F  520 SER cc_start: 0.8835 (t) cc_final: 0.8371 (m)
REVERT: F  534 GLN cc_start: 0.7586 (tm-30) cc_final: 0.7353 (pp30)
REVERT: G  473 ASP cc_start: 0.8424 (m-30) cc_final: 0.7815 (m-30)
REVERT: G  477 ASP cc_start: 0.8068 (m-30) cc_final: 0.7842 (m-30)
REVERT: G  500 GLU cc_start: 0.7869 (tp30) cc_final: 0.7372 (tp30)
REVERT: H  525 ASP cc_start: 0.7521 (t0) cc_final: 0.7209 (t0)
REVERT: I  491 GLN cc_start: 0.8782 (pp30) cc_final: 0.8301 (pp30)
REVERT: I  495 ARG cc_start: 0.8727 (ptm-80) cc_final: 0.8429 (ttp-110)
REVERT: J  473 ASP cc_start: 0.7758 (m-30) cc_final: 0.7185 (m-30)
REVERT: J  477 ASP cc_start: 0.7885 (m-30) cc_final: 0.7360 (m-30)
REVERT: J  478 ASN cc_start: 0.8927 (m-40) cc_final: 0.8625 (m-40)
REVERT: J  479 GLU cc_start: 0.7918 (mp0) cc_final: 0.7568 (mp0)
REVERT: J  486 LYS cc_start: 0.8672 (ttpp) cc_final: 0.8426 (ttmm)
REVERT: J  505 MET cc_start: 0.8006 (mtp) cc_final: 0.7775 (mtp)
REVERT: J  534 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7650 (tm-30)
REVERT: K  473 ASP cc_start: 0.8219 (m-30) cc_final: 0.7726 (m-30)
REVERT: K  505 MET cc_start: 0.8236 (mtp) cc_final: 0.7874 (mtp)
REVERT: K  525 ASP cc_start: 0.7648 (t0) cc_final: 0.7326 (t0)
REVERT: K  530 SER cc_start: 0.9150 (t) cc_final: 0.8872 (p)
REVERT: L  479 GLU cc_start: 0.7795 (mp0) cc_final: 0.7557 (mp0)
REVERT: L  530 SER cc_start: 0.8983 (t) cc_final: 0.8630 (p)
REVERT: M  477 ASP cc_start: 0.7869 (m-30) cc_final: 0.7591 (m-30)
REVERT: M  479 GLU cc_start: 0.7430 (mp0) cc_final: 0.7216 (mp0)
REVERT: M  525 ASP cc_start: 0.7729 (t0) cc_final: 0.7397 (t0)
REVERT: N  473 ASP cc_start: 0.7569 (m-30) cc_final: 0.6708 (m-30)
REVERT: N  477 ASP cc_start: 0.8145 (m-30) cc_final: 0.7838 (m-30)
REVERT: N  478 ASN cc_start: 0.8855 (m-40) cc_final: 0.8546 (m110)
REVERT: N  487 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7918 (mt-10)
REVERT: N  523 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7956 (mt-10)
REVERT: N  534 GLN cc_start: 0.7892 (tm-30) cc_final: 0.7668 (tm-30)
REVERT: O  477 ASP cc_start: 0.8362 (m-30) cc_final: 0.8082 (m-30)
REVERT: O  508 LYS cc_start: 0.7951 (mttm) cc_final: 0.7675 (mmtm)
REVERT: O  525 ASP cc_start: 0.7567 (t0) cc_final: 0.7198 (t0)
REVERT: O  530 SER cc_start: 0.9019 (t) cc_final: 0.8692 (p)
REVERT: P  473 ASP cc_start: 0.7932 (m-30) cc_final: 0.7452 (m-30)
REVERT: P  477 ASP cc_start: 0.8436 (m-30) cc_final: 0.7717 (m-30)
REVERT: P  479 GLU cc_start: 0.7622 (mp0) cc_final: 0.7229 (mp0)
REVERT: P  525 ASP cc_start: 0.8020 (t0) cc_final: 0.7752 (t0)
REVERT: P  534 GLN cc_start: 0.7848 (pp30) cc_final: 0.7447 (pp30)
  outliers start: 43
  outliers final: 26
  residues processed: 496
  average time/residue: 0.1253
  time to fit residues: 83.2913
Evaluate side-chains
  501 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 473
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  462 GLN
Chi-restraints excluded: chain C residue  505 MET
Chi-restraints excluded: chain B residue  515 ASP
Chi-restraints excluded: chain D residue  523 GLU
Chi-restraints excluded: chain E residue  462 GLN
Chi-restraints excluded: chain E residue  491 GLN
Chi-restraints excluded: chain F residue  462 GLN
Chi-restraints excluded: chain F residue  490 GLU
Chi-restraints excluded: chain G residue  465 MET
Chi-restraints excluded: chain G residue  523 GLU
Chi-restraints excluded: chain G residue  525 ASP
Chi-restraints excluded: chain I residue  462 GLN
Chi-restraints excluded: chain I residue  468 LEU
Chi-restraints excluded: chain I residue  534 GLN
Chi-restraints excluded: chain K residue  456 GLU
Chi-restraints excluded: chain K residue  462 GLN
Chi-restraints excluded: chain K residue  465 MET
Chi-restraints excluded: chain K residue  468 LEU
Chi-restraints excluded: chain L residue  491 GLN
Chi-restraints excluded: chain L residue  505 MET
Chi-restraints excluded: chain L residue  525 ASP
Chi-restraints excluded: chain N residue  462 GLN
Chi-restraints excluded: chain N residue  491 GLN
Chi-restraints excluded: chain N residue  523 GLU
Chi-restraints excluded: chain O residue  496 GLN
Chi-restraints excluded: chain O residue  523 GLU
Chi-restraints excluded: chain P residue  487 GLU
Chi-restraints excluded: chain P residue  530 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 127 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 119 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 62 optimal weight:    0.5980
   chunk 65 optimal weight:    3.9990
   chunk 116 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
E 476 GLN
F 476 GLN
** H 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 478 ASN
I 534 GLN
P 476 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.099039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.089949 restraints weight = 17224.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.093150 restraints weight = 8155.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.095139 restraints weight = 4435.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.096411 restraints weight = 2607.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.097260 restraints weight = 1609.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.3974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  11136  Z= 0.131
  Angle     :  0.557   9.780  14912  Z= 0.306
  Chirality :  0.035   0.143   1680
  Planarity :  0.004   0.031   1984
  Dihedral  :  3.259  13.916   1472
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 20.13 %
    Favored  : 76.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.22), residues: 1328
  helix:  1.44 (0.15), residues: 1200
  sheet:  None (None), residues: 0
  loop : -0.41 (0.43), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 519 
 TYR   0.007   0.001   TYR F 527 
 PHE   0.007   0.001   PHE K 453 
 HIS   0.002   0.001   HIS D 458 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (11136)
  covalent geometry    : angle       0.55728 (14912)
  hydrogen bonds       : bond        0.03358 (  784)
  hydrogen bonds       : angle       4.47555 ( 2352)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  512 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 476
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  486 LYS cc_start: 0.9016 (ttpp) cc_final: 0.8803 (ttmm)
REVERT: A  525 ASP cc_start: 0.7779 (t0) cc_final: 0.7427 (t0)
REVERT: B  473 ASP cc_start: 0.7796 (m-30) cc_final: 0.7393 (m-30)
REVERT: B  474 ASP cc_start: 0.7877 (t70) cc_final: 0.7487 (t0)
REVERT: B  525 ASP cc_start: 0.7867 (t0) cc_final: 0.7476 (t0)
REVERT: B  534 GLN cc_start: 0.7412 (mp10) cc_final: 0.7176 (mp10)
REVERT: D  474 ASP cc_start: 0.8115 (t70) cc_final: 0.7734 (t70)
REVERT: D  478 ASN cc_start: 0.8701 (m110) cc_final: 0.8234 (m-40)
REVERT: D  523 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7925 (mp0)
REVERT: D  525 ASP cc_start: 0.7719 (t0) cc_final: 0.7465 (t0)
REVERT: D  530 SER cc_start: 0.8949 (t) cc_final: 0.8636 (p)
REVERT: E  469 LYS cc_start: 0.8546 (mmtm) cc_final: 0.8181 (mmmm)
REVERT: E  473 ASP cc_start: 0.8003 (m-30) cc_final: 0.7402 (m-30)
REVERT: E  505 MET cc_start: 0.7934 (mtp) cc_final: 0.7618 (mtt)
REVERT: E  525 ASP cc_start: 0.7469 (t0) cc_final: 0.6971 (t0)
REVERT: E  530 SER cc_start: 0.8783 (t) cc_final: 0.8485 (m)
REVERT: F  477 ASP cc_start: 0.7948 (m-30) cc_final: 0.7519 (m-30)
REVERT: F  534 GLN cc_start: 0.7591 (tm-30) cc_final: 0.7333 (pp30)
REVERT: G  473 ASP cc_start: 0.8408 (m-30) cc_final: 0.7810 (m-30)
REVERT: G  477 ASP cc_start: 0.8066 (m-30) cc_final: 0.7836 (m-30)
REVERT: G  500 GLU cc_start: 0.7861 (tp30) cc_final: 0.7594 (tp30)
REVERT: H  525 ASP cc_start: 0.7488 (t0) cc_final: 0.7161 (t0)
REVERT: I  491 GLN cc_start: 0.8760 (pp30) cc_final: 0.8244 (pp30)
REVERT: I  495 ARG cc_start: 0.8713 (ptm-80) cc_final: 0.8353 (ttp-110)
REVERT: J  473 ASP cc_start: 0.7746 (m-30) cc_final: 0.7142 (m-30)
REVERT: J  477 ASP cc_start: 0.7925 (m-30) cc_final: 0.7392 (m-30)
REVERT: J  478 ASN cc_start: 0.8947 (m-40) cc_final: 0.8628 (m-40)
REVERT: J  479 GLU cc_start: 0.7914 (mp0) cc_final: 0.7539 (mp0)
REVERT: J  505 MET cc_start: 0.8029 (mtp) cc_final: 0.7803 (mtp)
REVERT: J  534 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7625 (tm-30)
REVERT: K  473 ASP cc_start: 0.8214 (m-30) cc_final: 0.7712 (m-30)
REVERT: K  505 MET cc_start: 0.8241 (mtp) cc_final: 0.7901 (mtp)
REVERT: K  525 ASP cc_start: 0.7636 (t0) cc_final: 0.7293 (t0)
REVERT: K  530 SER cc_start: 0.9152 (t) cc_final: 0.8878 (p)
REVERT: L  479 GLU cc_start: 0.7751 (mp0) cc_final: 0.7513 (mp0)
REVERT: L  486 LYS cc_start: 0.9013 (ttpp) cc_final: 0.8742 (ttpp)
REVERT: L  530 SER cc_start: 0.8997 (t) cc_final: 0.8641 (p)
REVERT: M  477 ASP cc_start: 0.7886 (m-30) cc_final: 0.7628 (m-30)
REVERT: M  479 GLU cc_start: 0.7446 (mp0) cc_final: 0.7224 (mp0)
REVERT: M  525 ASP cc_start: 0.7655 (t0) cc_final: 0.7283 (t0)
REVERT: N  469 LYS cc_start: 0.8516 (mmmm) cc_final: 0.7949 (mmmm)
REVERT: N  473 ASP cc_start: 0.7507 (m-30) cc_final: 0.6677 (m-30)
REVERT: N  477 ASP cc_start: 0.8157 (m-30) cc_final: 0.7831 (m-30)
REVERT: N  478 ASN cc_start: 0.8863 (m-40) cc_final: 0.8522 (m110)
REVERT: N  487 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7787 (mt-10)
REVERT: N  534 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7674 (tm-30)
REVERT: O  477 ASP cc_start: 0.8407 (m-30) cc_final: 0.8107 (m-30)
REVERT: O  525 ASP cc_start: 0.7558 (t0) cc_final: 0.7161 (t0)
REVERT: O  530 SER cc_start: 0.9015 (t) cc_final: 0.8695 (p)
REVERT: P  473 ASP cc_start: 0.7983 (m-30) cc_final: 0.7436 (m-30)
REVERT: P  477 ASP cc_start: 0.8429 (m-30) cc_final: 0.7706 (m-30)
REVERT: P  479 GLU cc_start: 0.7621 (mp0) cc_final: 0.7231 (mp0)
REVERT: P  523 GLU cc_start: 0.8021 (pp20) cc_final: 0.7794 (pp20)
REVERT: P  525 ASP cc_start: 0.8008 (t0) cc_final: 0.7743 (t0)
REVERT: P  534 GLN cc_start: 0.7875 (pp30) cc_final: 0.7430 (pp30)
  outliers start: 36
  outliers final: 28
  residues processed: 487
  average time/residue: 0.1187
  time to fit residues: 78.0680
Evaluate side-chains
  492 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 463
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  462 GLN
Chi-restraints excluded: chain C residue  505 MET
Chi-restraints excluded: chain B residue  515 ASP
Chi-restraints excluded: chain D residue  523 GLU
Chi-restraints excluded: chain E residue  462 GLN
Chi-restraints excluded: chain E residue  491 GLN
Chi-restraints excluded: chain F residue  462 GLN
Chi-restraints excluded: chain F residue  490 GLU
Chi-restraints excluded: chain G residue  465 MET
Chi-restraints excluded: chain G residue  523 GLU
Chi-restraints excluded: chain G residue  525 ASP
Chi-restraints excluded: chain I residue  462 GLN
Chi-restraints excluded: chain I residue  468 LEU
Chi-restraints excluded: chain I residue  534 GLN
Chi-restraints excluded: chain K residue  456 GLU
Chi-restraints excluded: chain K residue  462 GLN
Chi-restraints excluded: chain K residue  465 MET
Chi-restraints excluded: chain K residue  468 LEU
Chi-restraints excluded: chain K residue  522 SER
Chi-restraints excluded: chain L residue  491 GLN
Chi-restraints excluded: chain L residue  525 ASP
Chi-restraints excluded: chain M residue  462 GLN
Chi-restraints excluded: chain N residue  462 GLN
Chi-restraints excluded: chain N residue  491 GLN
Chi-restraints excluded: chain N residue  515 ASP
Chi-restraints excluded: chain O residue  496 GLN
Chi-restraints excluded: chain O residue  523 GLU
Chi-restraints excluded: chain P residue  487 GLU
Chi-restraints excluded: chain P residue  530 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 60 optimal weight:    0.5980
   chunk 15 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 111 optimal weight:    6.9990
   chunk 7 optimal weight:    0.4980
   chunk 25 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
D 535 GLN
E 478 ASN
F 476 GLN
H 476 GLN
I 478 ASN
I 534 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.100567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.091240 restraints weight = 17194.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 18)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.094423 restraints weight = 8446.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.096451 restraints weight = 4684.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.097748 restraints weight = 2806.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.098619 restraints weight = 1766.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.4116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  11136  Z= 0.125
  Angle     :  0.564  11.241  14912  Z= 0.309
  Chirality :  0.035   0.145   1680
  Planarity :  0.003   0.030   1984
  Dihedral  :  3.268  13.968   1472
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 20.21 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.82 (0.22), residues: 1328
  helix:  1.43 (0.15), residues: 1200
  sheet:  None (None), residues: 0
  loop : -0.42 (0.42), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 519 
 TYR   0.006   0.001   TYR F 527 
 PHE   0.006   0.001   PHE K 453 
 HIS   0.002   0.001   HIS A 458 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (11136)
  covalent geometry    : angle       0.56449 (14912)
  hydrogen bonds       : bond        0.03241 (  784)
  hydrogen bonds       : angle       4.53504 ( 2352)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  510 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 471
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  491 GLN cc_start: 0.8103 (pp30) cc_final: 0.7836 (pp30)
REVERT: A  460 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7925 (mm-40)
REVERT: A  525 ASP cc_start: 0.7673 (t0) cc_final: 0.7334 (t0)
REVERT: B  469 LYS cc_start: 0.8508 (mmmm) cc_final: 0.8270 (mmmm)
REVERT: B  473 ASP cc_start: 0.7804 (m-30) cc_final: 0.7417 (m-30)
REVERT: B  474 ASP cc_start: 0.7880 (t70) cc_final: 0.7191 (t0)
REVERT: B  478 ASN cc_start: 0.8365 (m-40) cc_final: 0.7733 (m110)
REVERT: B  525 ASP cc_start: 0.7849 (t0) cc_final: 0.7444 (t0)
REVERT: B  534 GLN cc_start: 0.7442 (mp10) cc_final: 0.7193 (mp10)
REVERT: D  462 GLN cc_start: 0.8444 (tt0) cc_final: 0.8220 (tt0)
REVERT: D  474 ASP cc_start: 0.8119 (t70) cc_final: 0.7345 (t0)
REVERT: D  478 ASN cc_start: 0.8677 (m110) cc_final: 0.8069 (m-40)
REVERT: D  523 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7918 (mp0)
REVERT: D  525 ASP cc_start: 0.7653 (t0) cc_final: 0.7429 (t0)
REVERT: D  530 SER cc_start: 0.8929 (t) cc_final: 0.8606 (p)
REVERT: E  469 LYS cc_start: 0.8484 (mmtm) cc_final: 0.8081 (mmmm)
REVERT: E  473 ASP cc_start: 0.7942 (m-30) cc_final: 0.7389 (m-30)
REVERT: E  505 MET cc_start: 0.7912 (mtp) cc_final: 0.7642 (mtt)
REVERT: E  525 ASP cc_start: 0.7438 (t0) cc_final: 0.6967 (t0)
REVERT: E  530 SER cc_start: 0.8757 (t) cc_final: 0.8477 (m)
REVERT: F  477 ASP cc_start: 0.7972 (m-30) cc_final: 0.7585 (m-30)
REVERT: F  534 GLN cc_start: 0.7605 (tm-30) cc_final: 0.7327 (pp30)
REVERT: G  473 ASP cc_start: 0.8416 (m-30) cc_final: 0.7830 (m-30)
REVERT: G  477 ASP cc_start: 0.8076 (m-30) cc_final: 0.7854 (m-30)
REVERT: G  500 GLU cc_start: 0.7850 (tp30) cc_final: 0.7508 (tp30)
REVERT: H  525 ASP cc_start: 0.7425 (t0) cc_final: 0.7167 (t0)
REVERT: H  530 SER cc_start: 0.8781 (m) cc_final: 0.8250 (p)
REVERT: I  491 GLN cc_start: 0.8759 (pp30) cc_final: 0.8253 (pp30)
REVERT: I  495 ARG cc_start: 0.8671 (ptm-80) cc_final: 0.8341 (ttp-110)
REVERT: J  473 ASP cc_start: 0.7744 (m-30) cc_final: 0.7157 (m-30)
REVERT: J  477 ASP cc_start: 0.7915 (m-30) cc_final: 0.7370 (m-30)
REVERT: J  478 ASN cc_start: 0.8928 (m-40) cc_final: 0.8603 (m-40)
REVERT: J  479 GLU cc_start: 0.7898 (mp0) cc_final: 0.7527 (mp0)
REVERT: J  486 LYS cc_start: 0.8629 (ttpp) cc_final: 0.8371 (ttmm)
REVERT: J  505 MET cc_start: 0.8043 (mtp) cc_final: 0.7840 (mtp)
REVERT: J  534 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7595 (tm-30)
REVERT: K  473 ASP cc_start: 0.8220 (m-30) cc_final: 0.7726 (m-30)
REVERT: K  493 LYS cc_start: 0.8855 (mmmm) cc_final: 0.8566 (mmmt)
REVERT: K  505 MET cc_start: 0.8236 (mtp) cc_final: 0.7889 (mtp)
REVERT: K  525 ASP cc_start: 0.7574 (t0) cc_final: 0.7260 (t0)
REVERT: K  530 SER cc_start: 0.9130 (t) cc_final: 0.8856 (p)
REVERT: L  479 GLU cc_start: 0.7752 (mp0) cc_final: 0.7515 (mp0)
REVERT: L  530 SER cc_start: 0.8974 (t) cc_final: 0.8607 (p)
REVERT: M  477 ASP cc_start: 0.7893 (m-30) cc_final: 0.7605 (m-30)
REVERT: M  479 GLU cc_start: 0.7450 (mp0) cc_final: 0.7231 (mp0)
REVERT: M  525 ASP cc_start: 0.7649 (t0) cc_final: 0.7260 (t0)
REVERT: N  469 LYS cc_start: 0.8473 (mmmm) cc_final: 0.7921 (mmmm)
REVERT: N  473 ASP cc_start: 0.7495 (m-30) cc_final: 0.6659 (m-30)
REVERT: N  477 ASP cc_start: 0.8173 (m-30) cc_final: 0.7839 (m-30)
REVERT: N  478 ASN cc_start: 0.8833 (m-40) cc_final: 0.8480 (m110)
REVERT: N  486 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8034 (tttt)
REVERT: N  487 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7898 (mt-10)
REVERT: N  490 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7617 (mt-10)
REVERT: N  523 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8000 (mt-10)
REVERT: N  534 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7660 (tm-30)
REVERT: O  477 ASP cc_start: 0.8428 (m-30) cc_final: 0.8113 (m-30)
REVERT: O  525 ASP cc_start: 0.7555 (t0) cc_final: 0.7162 (t0)
REVERT: O  530 SER cc_start: 0.8978 (t) cc_final: 0.8650 (p)
REVERT: O  533 ARG cc_start: 0.7099 (ttm-80) cc_final: 0.6888 (ttt90)
REVERT: P  473 ASP cc_start: 0.7982 (m-30) cc_final: 0.7429 (m-30)
REVERT: P  477 ASP cc_start: 0.8441 (m-30) cc_final: 0.7698 (m-30)
REVERT: P  479 GLU cc_start: 0.7635 (mp0) cc_final: 0.7246 (mp0)
REVERT: P  523 GLU cc_start: 0.7956 (pp20) cc_final: 0.7746 (pp20)
REVERT: P  525 ASP cc_start: 0.8005 (t0) cc_final: 0.7742 (t0)
REVERT: P  534 GLN cc_start: 0.7866 (pp30) cc_final: 0.7421 (pp30)
  outliers start: 39
  outliers final: 28
  residues processed: 484
  average time/residue: 0.1192
  time to fit residues: 77.4191
Evaluate side-chains
  489 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 458
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  462 GLN
Chi-restraints excluded: chain C residue  505 MET
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain B residue  515 ASP
Chi-restraints excluded: chain D residue  523 GLU
Chi-restraints excluded: chain E residue  462 GLN
Chi-restraints excluded: chain E residue  491 GLN
Chi-restraints excluded: chain F residue  462 GLN
Chi-restraints excluded: chain G residue  456 GLU
Chi-restraints excluded: chain G residue  465 MET
Chi-restraints excluded: chain G residue  525 ASP
Chi-restraints excluded: chain I residue  462 GLN
Chi-restraints excluded: chain I residue  468 LEU
Chi-restraints excluded: chain I residue  534 GLN
Chi-restraints excluded: chain K residue  456 GLU
Chi-restraints excluded: chain K residue  462 GLN
Chi-restraints excluded: chain K residue  465 MET
Chi-restraints excluded: chain K residue  468 LEU
Chi-restraints excluded: chain K residue  522 SER
Chi-restraints excluded: chain L residue  491 GLN
Chi-restraints excluded: chain L residue  525 ASP
Chi-restraints excluded: chain M residue  462 GLN
Chi-restraints excluded: chain M residue  468 LEU
Chi-restraints excluded: chain N residue  462 GLN
Chi-restraints excluded: chain N residue  486 LYS
Chi-restraints excluded: chain N residue  491 GLN
Chi-restraints excluded: chain N residue  515 ASP
Chi-restraints excluded: chain N residue  523 GLU
Chi-restraints excluded: chain O residue  523 GLU
Chi-restraints excluded: chain P residue  482 THR
Chi-restraints excluded: chain P residue  487 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 85 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 126 optimal weight:    0.9980
   chunk 104 optimal weight:    6.9990
   chunk 72 optimal weight:   10.0000
   chunk 124 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 87 optimal weight:    0.5980
   chunk 116 optimal weight:    5.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
F 476 GLN
H 499 ASN
I 478 ASN
I 534 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.099996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.091037 restraints weight = 17387.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.094105 restraints weight = 8558.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.096065 restraints weight = 4753.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.097296 restraints weight = 2838.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.098128 restraints weight = 1786.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.4186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  11136  Z= 0.134
  Angle     :  0.579  11.325  14912  Z= 0.318
  Chirality :  0.036   0.160   1680
  Planarity :  0.004   0.034   1984
  Dihedral  :  3.329  14.270   1472
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 20.62 %
    Favored  : 76.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.80 (0.22), residues: 1328
  helix:  1.42 (0.15), residues: 1200
  sheet:  None (None), residues: 0
  loop : -0.42 (0.43), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 519 
 TYR   0.007   0.001   TYR F 527 
 PHE   0.007   0.001   PHE K 453 
 HIS   0.002   0.001   HIS A 458 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (11136)
  covalent geometry    : angle       0.57949 (14912)
  hydrogen bonds       : bond        0.03318 (  784)
  hydrogen bonds       : angle       4.54834 ( 2352)

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  497 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 462
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  491 GLN cc_start: 0.8052 (pp30) cc_final: 0.7777 (pp30)
REVERT: A  525 ASP cc_start: 0.7713 (t0) cc_final: 0.7363 (t0)
REVERT: B  474 ASP cc_start: 0.7742 (t70) cc_final: 0.7240 (t0)
REVERT: B  478 ASN cc_start: 0.8340 (m-40) cc_final: 0.7747 (m110)
REVERT: B  525 ASP cc_start: 0.7915 (t0) cc_final: 0.7500 (t0)
REVERT: B  534 GLN cc_start: 0.7460 (mp10) cc_final: 0.7209 (mp10)
REVERT: D  462 GLN cc_start: 0.8460 (tt0) cc_final: 0.8223 (tt0)
REVERT: D  478 ASN cc_start: 0.8662 (m110) cc_final: 0.8380 (m-40)
REVERT: D  530 SER cc_start: 0.8979 (t) cc_final: 0.8679 (p)
REVERT: E  469 LYS cc_start: 0.8484 (mmtm) cc_final: 0.8093 (mmmm)
REVERT: E  473 ASP cc_start: 0.7948 (m-30) cc_final: 0.7417 (m-30)
REVERT: E  505 MET cc_start: 0.7961 (mtp) cc_final: 0.7683 (mtt)
REVERT: E  525 ASP cc_start: 0.7430 (t0) cc_final: 0.6982 (t0)
REVERT: E  530 SER cc_start: 0.8783 (t) cc_final: 0.8503 (m)
REVERT: F  477 ASP cc_start: 0.7980 (m-30) cc_final: 0.7601 (m-30)
REVERT: F  534 GLN cc_start: 0.7601 (tm-30) cc_final: 0.7343 (pp30)
REVERT: G  473 ASP cc_start: 0.8431 (m-30) cc_final: 0.7808 (m-30)
REVERT: G  477 ASP cc_start: 0.8073 (m-30) cc_final: 0.7849 (m-30)
REVERT: G  500 GLU cc_start: 0.7797 (tp30) cc_final: 0.7492 (tp30)
REVERT: H  525 ASP cc_start: 0.7424 (t0) cc_final: 0.7196 (t0)
REVERT: H  530 SER cc_start: 0.8828 (m) cc_final: 0.8290 (p)
REVERT: I  491 GLN cc_start: 0.8751 (pp30) cc_final: 0.8226 (pp30)
REVERT: I  495 ARG cc_start: 0.8664 (ptm-80) cc_final: 0.8353 (ttp-110)
REVERT: J  473 ASP cc_start: 0.7740 (m-30) cc_final: 0.7149 (m-30)
REVERT: J  477 ASP cc_start: 0.7964 (m-30) cc_final: 0.7430 (m-30)
REVERT: J  478 ASN cc_start: 0.8923 (m-40) cc_final: 0.8602 (m-40)
REVERT: J  479 GLU cc_start: 0.7893 (mp0) cc_final: 0.7555 (mp0)
REVERT: J  486 LYS cc_start: 0.8640 (ttpp) cc_final: 0.8395 (ttmm)
REVERT: J  505 MET cc_start: 0.8031 (mtp) cc_final: 0.7796 (mtp)
REVERT: J  534 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7568 (tm-30)
REVERT: K  473 ASP cc_start: 0.8200 (m-30) cc_final: 0.7709 (m-30)
REVERT: K  493 LYS cc_start: 0.8843 (mmmm) cc_final: 0.8576 (mmmt)
REVERT: K  505 MET cc_start: 0.8269 (mtp) cc_final: 0.7912 (mtp)
REVERT: K  525 ASP cc_start: 0.7589 (t0) cc_final: 0.7282 (t0)
REVERT: K  530 SER cc_start: 0.9152 (t) cc_final: 0.8884 (p)
REVERT: L  479 GLU cc_start: 0.7730 (mp0) cc_final: 0.7508 (mp0)
REVERT: L  530 SER cc_start: 0.9009 (t) cc_final: 0.8649 (p)
REVERT: M  477 ASP cc_start: 0.7906 (m-30) cc_final: 0.7616 (m-30)
REVERT: M  525 ASP cc_start: 0.7694 (t0) cc_final: 0.7329 (t0)
REVERT: N  469 LYS cc_start: 0.8466 (mmmm) cc_final: 0.7925 (mmmm)
REVERT: N  473 ASP cc_start: 0.7466 (m-30) cc_final: 0.6614 (m-30)
REVERT: N  477 ASP cc_start: 0.8160 (m-30) cc_final: 0.7828 (m-30)
REVERT: N  478 ASN cc_start: 0.8857 (m-40) cc_final: 0.8505 (m110)
REVERT: N  486 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.7947 (tttt)
REVERT: N  487 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7944 (mt-10)
REVERT: N  490 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7550 (mt-10)
REVERT: N  523 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7995 (mt-10)
REVERT: N  534 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7620 (tm-30)
REVERT: O  477 ASP cc_start: 0.8395 (m-30) cc_final: 0.8112 (m-30)
REVERT: O  525 ASP cc_start: 0.7464 (t0) cc_final: 0.7121 (t0)
REVERT: O  530 SER cc_start: 0.8992 (t) cc_final: 0.8680 (p)
REVERT: P  473 ASP cc_start: 0.7965 (m-30) cc_final: 0.7386 (m-30)
REVERT: P  477 ASP cc_start: 0.8445 (m-30) cc_final: 0.7698 (m-30)
REVERT: P  479 GLU cc_start: 0.7621 (mp0) cc_final: 0.7243 (mp0)
REVERT: P  523 GLU cc_start: 0.7969 (pp20) cc_final: 0.7761 (pp20)
REVERT: P  525 ASP cc_start: 0.7998 (t0) cc_final: 0.7756 (t0)
REVERT: P  534 GLN cc_start: 0.7852 (pp30) cc_final: 0.7383 (pp30)
  outliers start: 35
  outliers final: 30
  residues processed: 473
  average time/residue: 0.1226
  time to fit residues: 77.7722
Evaluate side-chains
  484 residues out of total 1232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 452
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  462 GLN
Chi-restraints excluded: chain C residue  505 MET
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain B residue  515 ASP
Chi-restraints excluded: chain B residue  523 GLU
Chi-restraints excluded: chain D residue  523 GLU
Chi-restraints excluded: chain E residue  462 GLN
Chi-restraints excluded: chain E residue  491 GLN
Chi-restraints excluded: chain F residue  462 GLN
Chi-restraints excluded: chain G residue  456 GLU
Chi-restraints excluded: chain G residue  465 MET
Chi-restraints excluded: chain G residue  523 GLU
Chi-restraints excluded: chain G residue  525 ASP
Chi-restraints excluded: chain I residue  462 GLN
Chi-restraints excluded: chain I residue  468 LEU
Chi-restraints excluded: chain I residue  534 GLN
Chi-restraints excluded: chain K residue  456 GLU
Chi-restraints excluded: chain K residue  462 GLN
Chi-restraints excluded: chain K residue  465 MET
Chi-restraints excluded: chain K residue  468 LEU
Chi-restraints excluded: chain K residue  522 SER
Chi-restraints excluded: chain L residue  491 GLN
Chi-restraints excluded: chain L residue  525 ASP
Chi-restraints excluded: chain M residue  462 GLN
Chi-restraints excluded: chain M residue  468 LEU
Chi-restraints excluded: chain N residue  462 GLN
Chi-restraints excluded: chain N residue  486 LYS
Chi-restraints excluded: chain N residue  515 ASP
Chi-restraints excluded: chain N residue  523 GLU
Chi-restraints excluded: chain O residue  456 GLU
Chi-restraints excluded: chain O residue  523 GLU
Chi-restraints excluded: chain P residue  487 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 64 optimal weight:    8.9990
   chunk 112 optimal weight:    8.9990
   chunk 27 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9990
   chunk 113 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 111 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
F 476 GLN
I 534 GLN
K 458 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.096685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.087710 restraints weight = 17557.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.090625 restraints weight = 8733.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.092594 restraints weight = 5008.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.093858 restraints weight = 3028.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.094690 restraints weight = 1920.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.4040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  11136  Z= 0.193
  Angle     :  0.643  11.637  14912  Z= 0.353
  Chirality :  0.040   0.201   1680
  Planarity :  0.004   0.035   1984
  Dihedral  :  3.557  14.379   1472
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 20.37 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.23), residues: 1328
  helix:  1.19 (0.15), residues: 1216
  sheet:  None (None), residues: 0
  loop : -0.91 (0.47), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 519 
 TYR   0.009   0.002   TYR F 527 
 PHE   0.009   0.002   PHE C 453 
 HIS   0.002   0.001   HIS A 458 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 (11136)
  covalent geometry    : angle       0.64337 (14912)
  hydrogen bonds       : bond        0.03891 (  784)
  hydrogen bonds       : angle       4.59877 ( 2352)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2286.41 seconds
wall clock time: 40 minutes 3.96 seconds (2403.96 seconds total)