Starting phenix.real_space_refine
on Sun Aug 24 14:49:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8avd_15679/08_2025/8avd_15679.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8avd_15679/08_2025/8avd_15679.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8avd_15679/08_2025/8avd_15679.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8avd_15679/08_2025/8avd_15679.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8avd_15679/08_2025/8avd_15679.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8avd_15679/08_2025/8avd_15679.cif"
  }
  resolution = 4.42
  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=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 9439 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     Ni      3      6.56       5
     S      60      5.16       5
     C    8127      2.51       5
     N    2154      2.21       5
     O    2433      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12777
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1077
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 133}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 3181
          Classifications: {'peptide': 399}
          Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 372}
    Chain: "C"
      Number of atoms: 1077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1077
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 133}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 3181
          Classifications: {'peptide': 399}
          Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 372}
    Chain: "E"
      Number of atoms: 1077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1077
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 133}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 3181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 3181
          Classifications: {'peptide': 399}
          Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 372}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NI': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NI': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NI': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.59, per 1000 atoms: 0.20
  Number of scatterers: 12777
  At special positions: 0
  Unit cell: (132.64, 144.246, 126.008, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ni      3     28.00
     S      60     16.00
     O    2433      8.00
     N    2154      7.00
     C    8127      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 117 " - pdb=" SG  CYS A 167 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 350 " - pdb=" SG  CYS B 410 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 411 " - pdb=" SG  CYS B 416 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 434 " - pdb=" SG  CYS B 445 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 471 " - pdb=" SG  CYS B 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 486 " - pdb=" SG  CYS B 496 " distance=2.06
    Simple disulfide: pdb=" SG  CYS C 117 " - pdb=" SG  CYS C 167 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 350 " - pdb=" SG  CYS D 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 411 " - pdb=" SG  CYS D 416 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 434 " - pdb=" SG  CYS D 445 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 471 " - pdb=" SG  CYS D 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 486 " - pdb=" SG  CYS D 496 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 117 " - pdb=" SG  CYS E 167 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 350 " - pdb=" SG  CYS F 410 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 411 " - pdb=" SG  CYS F 416 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 434 " - pdb=" SG  CYS F 445 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 471 " - pdb=" SG  CYS F 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 486 " - pdb=" SG  CYS F 496 " distance=2.08

  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: 0.86
  Conformation dependent library (CDL) restraints added in 543.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3102

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 30 sheets defined
      21.2% alpha, 31.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 44
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 4.029A  pdb=" N   SER A  50 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 88
      removed outlier: 3.979A  pdb=" N   SER A  88 " --> pdb=" O   GLN A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 116
    Processing helix  chain 'A' and resid 130 through 138
      removed outlier: 3.691A  pdb=" N   VAL A 134 " --> pdb=" O   SER A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 160
    Processing helix  chain 'B' and resid 375 through 377
      No H-bonds generated for 'chain 'B' and resid 375 through 377'
    Processing helix  chain 'B' and resid 528 through 533
      removed outlier: 3.936A  pdb=" N   VAL B 533 " --> pdb=" O   ASP B 530 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 23 through 45
    Processing helix  chain 'C' and resid 45 through 50
      removed outlier: 4.090A  pdb=" N   SER C  50 " --> pdb=" O   SER C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 71 through 89
      removed outlier: 3.930A  pdb=" N   SER C  88 " --> pdb=" O   GLN C  84 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU C  89 " --> pdb=" O   VAL C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 116
    Processing helix  chain 'C' and resid 130 through 138
      removed outlier: 3.518A  pdb=" N   VAL C 134 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 160
    Processing helix  chain 'D' and resid 375 through 377
      No H-bonds generated for 'chain 'D' and resid 375 through 377'
    Processing helix  chain 'D' and resid 528 through 533
      removed outlier: 3.936A  pdb=" N   VAL D 533 " --> pdb=" O   ASP D 530 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 23 through 45
    Processing helix  chain 'E' and resid 45 through 50
      removed outlier: 3.917A  pdb=" N   SER E  50 " --> pdb=" O   SER E  46 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 71 through 89
      removed outlier: 3.892A  pdb=" N   SER E  88 " --> pdb=" O   GLN E  84 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU E  89 " --> pdb=" O   VAL E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 91 through 116
    Processing helix  chain 'E' and resid 130 through 138
    Processing helix  chain 'E' and resid 138 through 160
    Processing helix  chain 'F' and resid 375 through 377
      No H-bonds generated for 'chain 'F' and resid 375 through 377'
    Processing helix  chain 'F' and resid 528 through 533
      removed outlier: 3.920A  pdb=" N   VAL F 533 " --> pdb=" O   ASP F 530 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58
    Processing sheet with id=AA2, first strand: chain 'B' and resid 240 through 246
      removed outlier: 6.086A  pdb=" N   GLY B 241 " --> pdb=" O   ASP B 257 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   ASP B 257 " --> pdb=" O   GLY B 241 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 279 through 286
    Processing sheet with id=AA4, first strand: chain 'B' and resid 331 through 334
    Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 341
      removed outlier: 3.546A  pdb=" N   ILE B 338 " --> pdb=" O   GLU B 422 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 416 through 417
      removed outlier: 7.128A  pdb=" N   CYS B 416 " --> pdb=" O   THR C  58 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 432 through 436
    Processing sheet with id=AA8, first strand: chain 'B' and resid 482 through 484
      removed outlier: 4.264A  pdb=" N   LEU B 462 " --> pdb=" O   LYS B 484 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 482 through 484
      removed outlier: 4.264A  pdb=" N   LEU B 462 " --> pdb=" O   LYS B 484 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 539 through 545
      removed outlier: 5.344A  pdb=" N   ASN B 540 " --> pdb=" O   GLU B 557 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   GLU B 557 " --> pdb=" O   ASN B 540 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 582 through 586
    Processing sheet with id=AB3, first strand: chain 'D' and resid 240 through 246
      removed outlier: 5.959A  pdb=" N   GLY D 241 " --> pdb=" O   ASP D 257 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   ASP D 257 " --> pdb=" O   GLY D 241 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 279 through 286
    Processing sheet with id=AB5, first strand: chain 'D' and resid 331 through 334
    Processing sheet with id=AB6, first strand: chain 'D' and resid 337 through 341
    Processing sheet with id=AB7, first strand: chain 'D' and resid 416 through 417
      removed outlier: 7.020A  pdb=" N   CYS D 416 " --> pdb=" O   THR E  58 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'D' and resid 433 through 436
    Processing sheet with id=AB9, first strand: chain 'D' and resid 482 through 484
      removed outlier: 4.759A  pdb=" N   LEU D 462 " --> pdb=" O   LYS D 484 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 482 through 484
      removed outlier: 4.759A  pdb=" N   LEU D 462 " --> pdb=" O   LYS D 484 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 539 through 545
      removed outlier: 5.262A  pdb=" N   ASN D 540 " --> pdb=" O   GLU D 557 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   GLU D 557 " --> pdb=" O   ASN D 540 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 582 through 586
    Processing sheet with id=AC4, first strand: chain 'F' and resid 240 through 246
      removed outlier: 6.008A  pdb=" N   GLY F 241 " --> pdb=" O   ASP F 257 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   ASP F 257 " --> pdb=" O   GLY F 241 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'F' and resid 279 through 286
    Processing sheet with id=AC6, first strand: chain 'F' and resid 331 through 334
    Processing sheet with id=AC7, first strand: chain 'F' and resid 337 through 341
      removed outlier: 3.670A  pdb=" N   ILE F 338 " --> pdb=" O   GLU F 422 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'F' and resid 432 through 436
    Processing sheet with id=AC9, first strand: chain 'F' and resid 482 through 483
    Processing sheet with id=AD1, first strand: chain 'F' and resid 482 through 483
    Processing sheet with id=AD2, first strand: chain 'F' and resid 539 through 545
      removed outlier: 5.427A  pdb=" N   ASN F 540 " --> pdb=" O   GLU F 557 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   GLU F 557 " --> pdb=" O   ASN F 540 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'F' and resid 582 through 586

    615 hydrogen bonds defined for protein.
    1635 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.10

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        1.15 -     1.30: 2092
        1.30 -     1.46: 4085
        1.46 -     1.61: 6810
        1.61 -     1.76: 1
        1.76 -     1.92: 77
  Bond restraints: 13065
  Sorted by residual:
  bond pdb=" CG  ASN A 103 "
       pdb=" OD1 ASN A 103 "
    ideal  model  delta    sigma   weight residual
    1.231  1.150  0.081 1.90e-02 2.77e+03 1.83e+01
  bond pdb=" CG  LYS E  74 "
       pdb=" CD  LYS E  74 "
    ideal  model  delta    sigma   weight residual
    1.520  1.404  0.116 3.00e-02 1.11e+03 1.50e+01
  bond pdb=" CG  ASN A 103 "
       pdb=" ND2 ASN A 103 "
    ideal  model  delta    sigma   weight residual
    1.328  1.247  0.081 2.10e-02 2.27e+03 1.48e+01
  bond pdb=" CB  CYS B 486 "
       pdb=" SG  CYS B 486 "
    ideal  model  delta    sigma   weight residual
    1.808  1.917 -0.109 3.30e-02 9.18e+02 1.10e+01
  bond pdb=" CB  THR C  58 "
       pdb=" CG2 THR C  58 "
    ideal  model  delta    sigma   weight residual
    1.521  1.417  0.104 3.30e-02 9.18e+02 9.85e+00
  ... (remaining 13060 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.98: 17738
        5.98 -    11.96: 60
       11.96 -    17.93: 7
       17.93 -    23.91: 2
       23.91 -    29.89: 1
  Bond angle restraints: 17808
  Sorted by residual:
  angle pdb=" CA  CYS F 486 "
        pdb=" CB  CYS F 486 "
        pdb=" SG  CYS F 486 "
      ideal   model   delta    sigma   weight residual
     114.40  144.29  -29.89 2.30e+00 1.89e-01 1.69e+02
  angle pdb=" CA  CYS F 496 "
        pdb=" CB  CYS F 496 "
        pdb=" SG  CYS F 496 "
      ideal   model   delta    sigma   weight residual
     114.40  134.97  -20.57 2.30e+00 1.89e-01 8.00e+01
  angle pdb=" C   CYS F 496 "
        pdb=" CA  CYS F 496 "
        pdb=" CB  CYS F 496 "
      ideal   model   delta    sigma   weight residual
     110.16  122.15  -11.99 1.66e+00 3.63e-01 5.22e+01
  angle pdb=" CG  LYS E  74 "
        pdb=" CD  LYS E  74 "
        pdb=" CE  LYS E  74 "
      ideal   model   delta    sigma   weight residual
     111.30   95.52   15.78 2.30e+00 1.89e-01 4.71e+01
  angle pdb=" C   CYS F 486 "
        pdb=" CA  CYS F 486 "
        pdb=" CB  CYS F 486 "
      ideal   model   delta    sigma   weight residual
     109.37  121.89  -12.52 1.83e+00 2.99e-01 4.68e+01
  ... (remaining 17803 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 7333
       17.65 -    35.30: 511
       35.30 -    52.95: 78
       52.95 -    70.59: 37
       70.59 -    88.24: 12
  Dihedral angle restraints: 7971
    sinusoidal: 3198
      harmonic: 4773
  Sorted by residual:
  dihedral pdb=" CB  CYS F 486 "
           pdb=" SG  CYS F 486 "
           pdb=" SG  CYS F 496 "
           pdb=" CB  CYS F 496 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -16.56  -69.44     1      1.00e+01 1.00e-02 6.23e+01
  dihedral pdb=" CB  CYS B 486 "
           pdb=" SG  CYS B 486 "
           pdb=" SG  CYS B 496 "
           pdb=" CB  CYS B 496 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   31.72   61.28     1      1.00e+01 1.00e-02 4.99e+01
  dihedral pdb=" C   CYS F 486 "
           pdb=" N   CYS F 486 "
           pdb=" CA  CYS F 486 "
           pdb=" CB  CYS F 486 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.14   16.54     0      2.50e+00 1.60e-01 4.38e+01
  ... (remaining 7968 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.127: 1979
       0.127 -    0.253: 76
       0.253 -    0.380: 4
       0.380 -    0.507: 1
       0.507 -    0.633: 4
  Chirality restraints: 2064
  Sorted by residual:
  chirality pdb=" CB  THR C  58 "
            pdb=" CA  THR C  58 "
            pdb=" OG1 THR C  58 "
            pdb=" CG2 THR C  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    1.92    0.63 2.00e-01 2.50e+01 1.00e+01
  chirality pdb=" CB  ILE E  69 "
            pdb=" CA  ILE E  69 "
            pdb=" CG1 ILE E  69 "
            pdb=" CG2 ILE E  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.06    0.59 2.00e-01 2.50e+01 8.59e+00
  chirality pdb=" CA  CYS F 486 "
            pdb=" N   CYS F 486 "
            pdb=" C   CYS F 486 "
            pdb=" CB  CYS F 486 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.95    0.56 2.00e-01 2.50e+01 7.77e+00
  ... (remaining 2061 not shown)

  Planarity restraints: 2259
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A  63 "    0.073 5.00e-02 4.00e+02   1.08e-01 1.87e+01
        pdb=" N   PRO A  64 "   -0.187 5.00e-02 4.00e+02
        pdb=" CA  PRO A  64 "    0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO A  64 "    0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 103 "    0.020 2.00e-02 2.50e+03   4.23e-02 1.79e+01
        pdb=" CG  ASN A 103 "   -0.073 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 103 "    0.028 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 103 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE E  63 "    0.059 5.00e-02 4.00e+02   8.74e-02 1.22e+01
        pdb=" N   PRO E  64 "   -0.151 5.00e-02 4.00e+02
        pdb=" CA  PRO E  64 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO E  64 "    0.047 5.00e-02 4.00e+02
  ... (remaining 2256 not shown)

  Histogram of nonbonded interaction distances:
        1.78 -     2.40: 39
        2.40 -     3.03: 7364
        3.03 -     3.65: 19511
        3.65 -     4.28: 28279
        4.28 -     4.90: 46720
  Nonbonded interactions: 101913
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG E  41 "
            pdb=" O   TYR F 439 "
     model   vdw
     1.776 3.120
  nonbonded pdb=" ND2 ASN A 103 "
            pdb=" N   LEU B 504 "
     model   vdw
     1.888 3.200
  nonbonded pdb=" OH  TYR B 409 "
            pdb=" CB  SER C 141 "
     model   vdw
     1.972 3.440
  nonbonded pdb=" NH1 ARG B 512 "
            pdb=" OD1 ASN B 514 "
     model   vdw
     2.071 3.120
  nonbonded pdb=" OE1 GLU B 274 "
            pdb=" NH1 ARG B 280 "
     model   vdw
     2.129 3.120
  ... (remaining 101908 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
}

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:             0.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.440
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.116  13083  Z= 0.215
  Angle     :  1.106  29.888  17844  Z= 0.589
  Chirality :  0.064   0.633   2064
  Planarity :  0.006   0.108   2259
  Dihedral  : 13.218  88.242   4815
  Min Nonbonded Distance : 1.776

Molprobity Statistics.
  All-atom Clashscore : 15.37
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  5.25 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.68 (0.19), residues: 1599
  helix: -0.38 (0.26), residues: 300
  sheet:  0.20 (0.19), residues: 546
  loop : -0.90 (0.21), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.029   0.002   ARG B 310 
 TYR   0.031   0.003   TYR B 470 
 PHE   0.029   0.002   PHE B 502 
 TRP   0.023   0.002   TRP F 447 
 HIS   0.007   0.001   HIS C  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 (13065)
  covalent geometry    : angle       1.09439 (17808)
  SS BOND              : bond        0.01468 (   18)
  SS BOND              : angle       3.71075 (   36)
  hydrogen bonds       : bond        0.12041 (  577)
  hydrogen bonds       : angle       6.73107 ( 1635)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.9656 (mm) cc_final: 0.9434 (mp)
REVERT: A  110 LEU cc_start: 0.8700 (mm) cc_final: 0.8374 (mm)
REVERT: A  143 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8797 (tm-30)
REVERT: C   30 ASP cc_start: 0.8730 (m-30) cc_final: 0.8506 (m-30)
REVERT: C  106 ASP cc_start: 0.8934 (m-30) cc_final: 0.8654 (m-30)
REVERT: C  156 ASP cc_start: 0.9073 (m-30) cc_final: 0.8829 (m-30)
REVERT: D  584 HIS cc_start: 0.9178 (t70) cc_final: 0.8862 (t-170)
REVERT: E   69 ILE cc_start: 0.8398 (tp) cc_final: 0.8122 (pt)
REVERT: F  302 TYR cc_start: 0.8494 (m-80) cc_final: 0.8049 (m-80)
REVERT: F  366 TRP cc_start: 0.7657 (m100) cc_final: 0.7429 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.0806
  time to fit residues: 18.0691
Evaluate side-chains
  92 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    0.6980
   chunk 149 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  67 HIS
A 103 ASN
A 159 GLN
B 461 GLN
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 103 ASN
** E  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 103 ASN
E 155 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.076903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.061229 restraints weight = 71324.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.061480 restraints weight = 38630.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.062990 restraints weight = 25657.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.062786 restraints weight = 18021.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.063283 restraints weight = 17470.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.1242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.095  13083  Z= 0.142
  Angle     :  0.688  13.365  17844  Z= 0.352
  Chirality :  0.047   0.378   2064
  Planarity :  0.004   0.049   2259
  Dihedral  :  5.323  63.425   1740
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.49 %
    Favored  : 97.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.20), residues: 1599
  helix:  1.31 (0.29), residues: 306
  sheet:  0.59 (0.18), residues: 566
  loop : -0.15 (0.23), residues: 727

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 280 
 TYR   0.015   0.001   TYR B 470 
 PHE   0.012   0.001   PHE B 502 
 TRP   0.008   0.001   TRP D 367 
 HIS   0.011   0.001   HIS E  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (13065)
  covalent geometry    : angle       0.68250 (17808)
  SS BOND              : bond        0.00856 (   18)
  SS BOND              : angle       2.00411 (   36)
  hydrogen bonds       : bond        0.04478 (  577)
  hydrogen bonds       : angle       5.69852 ( 1635)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 135
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8649 (mm-30)
REVERT: A  143 GLU cc_start: 0.9158 (tm-30) cc_final: 0.8875 (tm-30)
REVERT: B  509 MET cc_start: 0.9333 (mpp) cc_final: 0.9097 (mpp)
REVERT: C   37 THR cc_start: 0.9564 (m) cc_final: 0.9270 (m)
REVERT: C  106 ASP cc_start: 0.8946 (m-30) cc_final: 0.8685 (m-30)
REVERT: C  156 ASP cc_start: 0.9160 (m-30) cc_final: 0.8946 (m-30)
REVERT: D  584 HIS cc_start: 0.9067 (t70) cc_final: 0.8726 (t-170)
REVERT: E   35 ILE cc_start: 0.9678 (mt) cc_final: 0.9224 (tt)
REVERT: F  302 TYR cc_start: 0.8492 (m-80) cc_final: 0.7975 (m-80)
REVERT: F  366 TRP cc_start: 0.7639 (m100) cc_final: 0.7205 (m100)
  outliers start: 2
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0706
  time to fit residues: 15.1993
Evaluate side-chains
  84 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 118 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 111 optimal weight:    0.5980
   chunk 141 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 83 optimal weight:    0.2980
   chunk 151 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
B 461 GLN
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.075074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.059800 restraints weight = 71249.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.059265 restraints weight = 40310.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.060600 restraints weight = 27823.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.061169 restraints weight = 18977.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.061304 restraints weight = 17755.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.1935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13083  Z= 0.142
  Angle     :  0.621  11.971  17844  Z= 0.320
  Chirality :  0.044   0.245   2064
  Planarity :  0.004   0.034   2259
  Dihedral  :  5.234  65.638   1740
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.36 %
    Favored  : 96.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.21), residues: 1599
  helix:  1.70 (0.29), residues: 306
  sheet:  0.81 (0.19), residues: 593
  loop :  0.21 (0.25), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 105 
 TYR   0.015   0.001   TYR D 424 
 PHE   0.008   0.001   PHE D 403 
 TRP   0.009   0.001   TRP F 556 
 HIS   0.007   0.001   HIS A  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (13065)
  covalent geometry    : angle       0.61539 (17808)
  SS BOND              : bond        0.00309 (   18)
  SS BOND              : angle       1.98884 (   36)
  hydrogen bonds       : bond        0.03916 (  577)
  hydrogen bonds       : angle       5.39301 ( 1635)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 120
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8579 (mm-30)
REVERT: A  143 GLU cc_start: 0.9282 (tm-30) cc_final: 0.9017 (tm-30)
REVERT: B  461 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8793 (pp30)
REVERT: C   37 THR cc_start: 0.9537 (m) cc_final: 0.9186 (m)
REVERT: C  106 ASP cc_start: 0.8954 (m-30) cc_final: 0.8691 (m-30)
REVERT: C  156 ASP cc_start: 0.9145 (m-30) cc_final: 0.8842 (m-30)
REVERT: D  252 LEU cc_start: 0.9026 (tt) cc_final: 0.8744 (tt)
REVERT: D  584 HIS cc_start: 0.9144 (t70) cc_final: 0.8803 (t-170)
REVERT: E   35 ILE cc_start: 0.9611 (mt) cc_final: 0.9383 (tt)
REVERT: E   76 ASP cc_start: 0.8734 (t0) cc_final: 0.8439 (t0)
REVERT: F  302 TYR cc_start: 0.8497 (m-80) cc_final: 0.8097 (m-80)
REVERT: F  366 TRP cc_start: 0.7710 (m100) cc_final: 0.7242 (m100)
  outliers start: 2
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0836
  time to fit residues: 15.7494
Evaluate side-chains
  78 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 66 optimal weight:   10.0000
   chunk 77 optimal weight:    5.9990
   chunk 148 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 103 optimal weight:    0.8980
   chunk 63 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 104 optimal weight:    4.9990
   chunk 89 optimal weight:    0.3980
   overall best weight:    2.6586

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

Flipped N/Q/H residues before XYZ refinement:
B 461 GLN
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 461 GLN
E  43 ASN
E 160 GLN
F 461 GLN
F 478 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.071645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.055163 restraints weight = 70697.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.056791 restraints weight = 47488.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.057767 restraints weight = 23755.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.057701 restraints weight = 18549.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.058020 restraints weight = 17701.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  13083  Z= 0.211
  Angle     :  0.654   9.913  17844  Z= 0.340
  Chirality :  0.044   0.236   2064
  Planarity :  0.004   0.040   2259
  Dihedral  :  5.465  70.230   1740
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  3.70 %
    Favored  : 96.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.21), residues: 1599
  helix:  1.56 (0.29), residues: 306
  sheet:  0.80 (0.20), residues: 594
  loop :  0.26 (0.25), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 512 
 TYR   0.015   0.002   TYR B 470 
 PHE   0.013   0.002   PHE D 403 
 TRP   0.015   0.001   TRP B 367 
 HIS   0.006   0.001   HIS F 478 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 (13065)
  covalent geometry    : angle       0.65138 (17808)
  SS BOND              : bond        0.00358 (   18)
  SS BOND              : angle       1.45306 (   36)
  hydrogen bonds       : bond        0.04069 (  577)
  hydrogen bonds       : angle       5.48431 ( 1635)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8505 (mm-30)
REVERT: A  143 GLU cc_start: 0.9331 (tm-30) cc_final: 0.8985 (tm-30)
REVERT: B  461 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8740 (pp30)
REVERT: C   37 THR cc_start: 0.9512 (m) cc_final: 0.9101 (m)
REVERT: C  106 ASP cc_start: 0.8907 (m-30) cc_final: 0.8607 (m-30)
REVERT: C  156 ASP cc_start: 0.9091 (m-30) cc_final: 0.8772 (m-30)
REVERT: D  584 HIS cc_start: 0.9265 (t70) cc_final: 0.8864 (t-170)
REVERT: E  103 ASN cc_start: 0.9386 (m-40) cc_final: 0.9160 (t0)
REVERT: F  366 TRP cc_start: 0.7890 (m100) cc_final: 0.7487 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0759
  time to fit residues: 14.1627
Evaluate side-chains
  86 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 14 optimal weight:   30.0000
   chunk 55 optimal weight:    0.8980
   chunk 158 optimal weight:    5.9990
   chunk 93 optimal weight:    0.8980
   chunk 68 optimal weight:    9.9990
   chunk 92 optimal weight:    0.9980
   chunk 79 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 44 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    2.3584

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

Flipped N/Q/H residues before XYZ refinement:
B 461 GLN
B 489 GLN
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 305 GLN
F 465 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.071158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.056044 restraints weight = 72547.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.057663 restraints weight = 47787.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.057523 restraints weight = 24324.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.057473 restraints weight = 20696.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.057657 restraints weight = 18834.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.3343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13083  Z= 0.185
  Angle     :  0.629  10.313  17844  Z= 0.325
  Chirality :  0.044   0.352   2064
  Planarity :  0.005   0.077   2259
  Dihedral  :  5.372  63.217   1740
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.95 %
    Favored  : 97.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.21), residues: 1599
  helix:  1.55 (0.29), residues: 306
  sheet:  0.80 (0.20), residues: 607
  loop :  0.36 (0.26), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG F 280 
 TYR   0.021   0.002   TYR D 424 
 PHE   0.013   0.002   PHE F 334 
 TRP   0.008   0.001   TRP F 556 
 HIS   0.013   0.002   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (13065)
  covalent geometry    : angle       0.62751 (17808)
  SS BOND              : bond        0.00377 (   18)
  SS BOND              : angle       1.16825 (   36)
  hydrogen bonds       : bond        0.03845 (  577)
  hydrogen bonds       : angle       5.33410 ( 1635)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8410 (mm-30)
REVERT: B  461 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8762 (pp30)
REVERT: B  632 MET cc_start: 0.4996 (ptt) cc_final: 0.4655 (ptt)
REVERT: C   36 LYS cc_start: 0.9084 (pptt) cc_final: 0.8863 (pptt)
REVERT: C   37 THR cc_start: 0.9565 (m) cc_final: 0.9191 (m)
REVERT: C  106 ASP cc_start: 0.9081 (m-30) cc_final: 0.8786 (m-30)
REVERT: C  156 ASP cc_start: 0.9005 (m-30) cc_final: 0.8666 (m-30)
REVERT: D  584 HIS cc_start: 0.9226 (t70) cc_final: 0.9007 (t70)
REVERT: E   76 ASP cc_start: 0.9140 (t0) cc_final: 0.8916 (t0)
REVERT: F  366 TRP cc_start: 0.7969 (m100) cc_final: 0.7553 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0801
  time to fit residues: 13.9828
Evaluate side-chains
  77 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 156 optimal weight:   10.0000
   chunk 47 optimal weight:    9.9990
   chunk 34 optimal weight:    0.0070
   chunk 124 optimal weight:    8.9990
   chunk 133 optimal weight:    2.9990
   chunk 111 optimal weight:    0.6980
   chunk 105 optimal weight:    5.9990
   chunk 137 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 131 optimal weight:    0.9990
   chunk 121 optimal weight:    9.9990
   overall best weight:    1.1202

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

Flipped N/Q/H residues before XYZ refinement:
B 461 GLN
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 103 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.070597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.053480 restraints weight = 71770.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.055501 restraints weight = 49024.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.056240 restraints weight = 24105.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.056564 restraints weight = 18366.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.056759 restraints weight = 18224.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.3542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13083  Z= 0.120
  Angle     :  0.583  10.500  17844  Z= 0.299
  Chirality :  0.044   0.236   2064
  Planarity :  0.004   0.061   2259
  Dihedral  :  5.165  58.758   1740
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.88 %
    Favored  : 98.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.21), residues: 1599
  helix:  1.73 (0.29), residues: 306
  sheet:  0.86 (0.20), residues: 609
  loop :  0.41 (0.26), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  41 
 TYR   0.014   0.001   TYR D 424 
 PHE   0.011   0.001   PHE F 334 
 TRP   0.008   0.001   TRP F 556 
 HIS   0.003   0.001   HIS F 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (13065)
  covalent geometry    : angle       0.58231 (17808)
  SS BOND              : bond        0.00502 (   18)
  SS BOND              : angle       0.88874 (   36)
  hydrogen bonds       : bond        0.03684 (  577)
  hydrogen bonds       : angle       5.02845 ( 1635)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  461 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8761 (pp30)
REVERT: B  632 MET cc_start: 0.5133 (ptt) cc_final: 0.4461 (ptt)
REVERT: C   36 LYS cc_start: 0.9053 (pptt) cc_final: 0.8825 (pptt)
REVERT: C   37 THR cc_start: 0.9577 (m) cc_final: 0.9222 (m)
REVERT: C  156 ASP cc_start: 0.9098 (m-30) cc_final: 0.8791 (m-30)
REVERT: D  584 HIS cc_start: 0.9238 (t70) cc_final: 0.9023 (t70)
  outliers start: 1
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0828
  time to fit residues: 14.6611
Evaluate side-chains
  77 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 141 optimal weight:    0.9980
   chunk 122 optimal weight:    6.9990
   chunk 58 optimal weight:    0.8980
   chunk 90 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 128 optimal weight:    9.9990
   chunk 89 optimal weight:    6.9990
   chunk 82 optimal weight:    1.9990
   chunk 99 optimal weight:    6.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
B 461 GLN
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 103 ASN
F 567 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.070545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.053571 restraints weight = 71358.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.055616 restraints weight = 46455.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.055881 restraints weight = 23385.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.055897 restraints weight = 20817.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.056206 restraints weight = 19264.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.3757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13083  Z= 0.125
  Angle     :  0.602  11.561  17844  Z= 0.307
  Chirality :  0.045   0.231   2064
  Planarity :  0.004   0.053   2259
  Dihedral  :  5.109  57.526   1740
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.87 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.21), residues: 1599
  helix:  1.89 (0.30), residues: 303
  sheet:  0.83 (0.21), residues: 579
  loop :  0.37 (0.25), residues: 717

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E 105 
 TYR   0.012   0.001   TYR D 424 
 PHE   0.012   0.001   PHE D 326 
 TRP   0.039   0.001   TRP F 366 
 HIS   0.003   0.001   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (13065)
  covalent geometry    : angle       0.60033 (17808)
  SS BOND              : bond        0.00227 (   18)
  SS BOND              : angle       1.10780 (   36)
  hydrogen bonds       : bond        0.03530 (  577)
  hydrogen bonds       : angle       4.98534 ( 1635)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8418 (mm-30)
REVERT: B  461 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8790 (pp30)
REVERT: B  632 MET cc_start: 0.5448 (ptt) cc_final: 0.4698 (ptt)
REVERT: C  106 ASP cc_start: 0.8870 (t0) cc_final: 0.8529 (t0)
REVERT: C  156 ASP cc_start: 0.9137 (m-30) cc_final: 0.8850 (m-30)
REVERT: D  310 ARG cc_start: 0.8960 (tmm-80) cc_final: 0.8672 (tmm-80)
REVERT: D  320 TRP cc_start: 0.7710 (m100) cc_final: 0.7490 (m100)
REVERT: D  584 HIS cc_start: 0.9247 (t70) cc_final: 0.9033 (t70)
  outliers start: 2
  outliers final: 0
  residues processed: 107
  average time/residue: 0.0853
  time to fit residues: 14.0119
Evaluate side-chains
  79 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 75 optimal weight:   30.0000
   chunk 63 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 21 optimal weight:    9.9990
   chunk 137 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   chunk 83 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 103 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
B 461 GLN
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  83 GLN
D 305 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.068828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.052254 restraints weight = 73313.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.053727 restraints weight = 50941.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.054646 restraints weight = 27853.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.054581 restraints weight = 21204.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.055002 restraints weight = 20905.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.4290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13083  Z= 0.179
  Angle     :  0.642  11.280  17844  Z= 0.329
  Chirality :  0.044   0.258   2064
  Planarity :  0.005   0.102   2259
  Dihedral  :  5.256  57.843   1740
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.08 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.22), residues: 1599
  helix:  1.66 (0.30), residues: 303
  sheet:  0.79 (0.21), residues: 579
  loop :  0.32 (0.25), residues: 717

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D 446 
 TYR   0.013   0.002   TYR F 619 
 PHE   0.019   0.002   PHE D 493 
 TRP   0.023   0.001   TRP B 447 
 HIS   0.007   0.001   HIS F 478 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (13065)
  covalent geometry    : angle       0.63961 (17808)
  SS BOND              : bond        0.00304 (   18)
  SS BOND              : angle       1.34517 (   36)
  hydrogen bonds       : bond        0.03733 (  577)
  hydrogen bonds       : angle       5.23004 ( 1635)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.488 
Fit side-chains
REVERT: A  102 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8496 (mm-30)
REVERT: A  166 GLU cc_start: 0.8384 (pm20) cc_final: 0.7968 (pm20)
REVERT: B  461 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8796 (pp30)
REVERT: B  632 MET cc_start: 0.6138 (ptt) cc_final: 0.5564 (ptt)
REVERT: C   36 LYS cc_start: 0.9054 (pptt) cc_final: 0.8739 (pptt)
REVERT: C   37 THR cc_start: 0.9576 (m) cc_final: 0.9288 (m)
REVERT: C  106 ASP cc_start: 0.8884 (t0) cc_final: 0.8566 (t0)
REVERT: C  156 ASP cc_start: 0.9128 (m-30) cc_final: 0.8801 (m-30)
REVERT: D  310 ARG cc_start: 0.8859 (tmm-80) cc_final: 0.8579 (tmm-80)
REVERT: D  584 HIS cc_start: 0.9258 (t70) cc_final: 0.9055 (t70)
REVERT: F  376 GLU cc_start: 0.9315 (pm20) cc_final: 0.9113 (pm20)
  outliers start: 1
  outliers final: 0
  residues processed: 104
  average time/residue: 0.0730
  time to fit residues: 12.2863
Evaluate side-chains
  73 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 102 optimal weight:    5.9990
   chunk 76 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   chunk 109 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   chunk 67 optimal weight:    4.9990
   chunk 148 optimal weight:    7.9990
   chunk 116 optimal weight:    8.9990
   chunk 150 optimal weight:    5.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 103 ASN
F 363 GLN
** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.065520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.049620 restraints weight = 78093.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.050811 restraints weight = 54002.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.051368 restraints weight = 27789.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.051282 restraints weight = 22389.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.051878 restraints weight = 21269.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.5304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  13083  Z= 0.314
  Angle     :  0.803  10.440  17844  Z= 0.418
  Chirality :  0.048   0.251   2064
  Planarity :  0.006   0.135   2259
  Dihedral  :  5.963  58.333   1740
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 20.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.21), residues: 1599
  helix:  0.79 (0.28), residues: 300
  sheet:  0.56 (0.21), residues: 566
  loop : -0.01 (0.25), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG D 446 
 TYR   0.051   0.003   TYR C  82 
 PHE   0.025   0.003   PHE E 113 
 TRP   0.022   0.002   TRP F 367 
 HIS   0.013   0.003   HIS F 478 

Details of bonding type rmsd
  covalent geometry    : bond        0.00649 (13065)
  covalent geometry    : angle       0.80093 (17808)
  SS BOND              : bond        0.00396 (   18)
  SS BOND              : angle       1.42621 (   36)
  hydrogen bonds       : bond        0.04563 (  577)
  hydrogen bonds       : angle       6.05653 ( 1635)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 LEU cc_start: 0.8970 (mt) cc_final: 0.8759 (mt)
REVERT: A  102 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8855 (mm-30)
REVERT: A  143 GLU cc_start: 0.9400 (tm-30) cc_final: 0.8982 (tm-30)
REVERT: B  632 MET cc_start: 0.6732 (ptt) cc_final: 0.6292 (ptt)
REVERT: C   30 ASP cc_start: 0.9237 (m-30) cc_final: 0.8942 (m-30)
REVERT: C  156 ASP cc_start: 0.9165 (m-30) cc_final: 0.8852 (m-30)
REVERT: D  310 ARG cc_start: 0.8907 (tmm-80) cc_final: 0.8622 (tmm-80)
REVERT: E   61 ASP cc_start: 0.8561 (p0) cc_final: 0.8353 (p0)
REVERT: F  384 ASP cc_start: 0.8345 (m-30) cc_final: 0.7763 (p0)
REVERT: F  429 ASN cc_start: 0.8978 (m-40) cc_final: 0.8768 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.0754
  time to fit residues: 11.2972
Evaluate side-chains
  67 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0670
   chunk 50 optimal weight:    0.0770
   chunk 9 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 133 optimal weight:    0.7980
   chunk 4 optimal weight:    0.3980
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.4676

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

Flipped N/Q/H residues before XYZ refinement:
B 461 GLN
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 103 ASN
F 349 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.068508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.052751 restraints weight = 75887.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.053682 restraints weight = 51613.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.054453 restraints weight = 26275.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.054395 restraints weight = 20961.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.054591 restraints weight = 19821.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.5124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13083  Z= 0.119
  Angle     :  0.642  11.859  17844  Z= 0.328
  Chirality :  0.046   0.198   2064
  Planarity :  0.004   0.102   2259
  Dihedral  :  5.285  39.372   1740
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.20 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.22), residues: 1599
  helix:  1.34 (0.30), residues: 300
  sheet:  0.70 (0.21), residues: 580
  loop :  0.29 (0.26), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F 280 
 TYR   0.020   0.001   TYR C  82 
 PHE   0.023   0.002   PHE F 334 
 TRP   0.009   0.001   TRP D 510 
 HIS   0.005   0.001   HIS B 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (13065)
  covalent geometry    : angle       0.64060 (17808)
  SS BOND              : bond        0.00399 (   18)
  SS BOND              : angle       1.12583 (   36)
  hydrogen bonds       : bond        0.03824 (  577)
  hydrogen bonds       : angle       5.40741 ( 1635)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 108
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8374 (mm-30)
REVERT: A  143 GLU cc_start: 0.9379 (tm-30) cc_final: 0.8908 (tm-30)
REVERT: B  461 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8683 (pp30)
REVERT: C   30 ASP cc_start: 0.9167 (m-30) cc_final: 0.8851 (m-30)
REVERT: C   36 LYS cc_start: 0.9022 (pptt) cc_final: 0.8748 (pptt)
REVERT: C   37 THR cc_start: 0.9585 (m) cc_final: 0.9236 (m)
REVERT: C  106 ASP cc_start: 0.9285 (t0) cc_final: 0.9017 (t0)
REVERT: C  156 ASP cc_start: 0.9164 (m-30) cc_final: 0.8849 (m-30)
REVERT: D  310 ARG cc_start: 0.8811 (tmm-80) cc_final: 0.8547 (tmm-80)
REVERT: D  584 HIS cc_start: 0.9522 (t70) cc_final: 0.9268 (t70)
REVERT: E  162 ASP cc_start: 0.8613 (m-30) cc_final: 0.8386 (p0)
REVERT: F  384 ASP cc_start: 0.8357 (m-30) cc_final: 0.7884 (p0)
REVERT: F  509 MET cc_start: 0.9127 (mpp) cc_final: 0.8827 (mpp)
  outliers start: 2
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0820
  time to fit residues: 13.8336
Evaluate side-chains
  79 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 91 optimal weight:    0.6980
   chunk 19 optimal weight:    7.9990
   chunk 29 optimal weight:    0.7980
   chunk 13 optimal weight:    0.1980
   chunk 1 optimal weight:    1.9990
   chunk 152 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 115 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 150 optimal weight:    0.4980
   chunk 46 optimal weight:    8.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B 461 GLN
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 349 HIS
F 465 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.068806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.053059 restraints weight = 74516.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.053992 restraints weight = 52252.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.054281 restraints weight = 28916.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.054405 restraints weight = 24901.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.054690 restraints weight = 22190.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.5141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13083  Z= 0.114
  Angle     :  0.616  13.012  17844  Z= 0.314
  Chirality :  0.045   0.212   2064
  Planarity :  0.004   0.089   2259
  Dihedral  :  4.927  37.548   1740
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.07 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.22), residues: 1599
  helix:  1.37 (0.29), residues: 300
  sheet:  0.79 (0.21), residues: 580
  loop :  0.35 (0.26), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 446 
 TYR   0.016   0.001   TYR C  82 
 PHE   0.016   0.001   PHE F 334 
 TRP   0.008   0.001   TRP B 447 
 HIS   0.010   0.001   HIS F 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (13065)
  covalent geometry    : angle       0.61488 (17808)
  SS BOND              : bond        0.00235 (   18)
  SS BOND              : angle       1.06046 (   36)
  hydrogen bonds       : bond        0.03576 (  577)
  hydrogen bonds       : angle       5.20030 ( 1635)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1603.18 seconds
wall clock time: 28 minutes 46.00 seconds (1726.00 seconds total)