Starting phenix.real_space_refine
on Wed Sep 17 06:20:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jik_61508/09_2025/9jik_61508.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jik_61508/09_2025/9jik_61508.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jik_61508/09_2025/9jik_61508.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jik_61508/09_2025/9jik_61508.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jik_61508/09_2025/9jik_61508.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jik_61508/09_2025/9jik_61508.map"
  }
  resolution = 2.91
  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=   0.001 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    3694      2.51       5
     N     998      2.21       5
     O    1136      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5850
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1175
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 151, 1169
          Classifications: {'peptide': 151}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 143}
      Conformer: "B"
        Number of residues, atoms: 151, 1169
          Classifications: {'peptide': 151}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 143}
          bond proxies already assigned to first conformer: 1199
    Chain: "L"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 798
          Classifications: {'peptide': 108}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 952
          Classifications: {'peptide': 124}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
    Chain: "B"
      Number of atoms: 1175
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 151, 1169
          Classifications: {'peptide': 151}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 143}
      Conformer: "B"
        Number of residues, atoms: 151, 1169
          Classifications: {'peptide': 151}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 143}
          bond proxies already assigned to first conformer: 1199
    Chain: "D"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 798
          Classifications: {'peptide': 108}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 100}
    Chain: "C"
      Number of atoms: 952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 952
          Classifications: {'peptide': 124}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  ASER A 474 " occ=0.51
      ... (10 atoms not shown)
      pdb=" OG BSER A 474 " occ=0.49
    residue:
      pdb=" N  ASER B 474 " occ=0.51
      ... (10 atoms not shown)
      pdb=" OG BSER B 474 " occ=0.49
  Time building chain proxies: 2.01, per 1000 atoms: 0.34
  Number of scatterers: 5850
  At special positions: 0
  Unit cell: (111.15, 68.9, 84.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      22     16.00
     O    1136      8.00
     N     998      7.00
     C    3694      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  89 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  89 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03

  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: 0.45
  Conformation dependent library (CDL) restraints added in 317.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1376

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 22 sheets defined
      2.1% alpha, 43.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 501 through 503
      No H-bonds generated for 'chain 'A' and resid 501 through 503'
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.742A  pdb=" N   THR H  91 " --> pdb=" O   THR H  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 501 through 503
      No H-bonds generated for 'chain 'B' and resid 501 through 503'
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.742A  pdb=" N   THR C  91 " --> pdb=" O   THR C  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 453 through 454
    Processing sheet with id=AA2, first strand: chain 'A' and resid 459 through 460
      removed outlier: 4.746A  pdb=" N   VAL A 584 " --> pdb=" O   SER A 466 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   SER A 466 " --> pdb=" O   VAL A 584 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   SER A 472 " --> pdb=" O   HIS A 479 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   HIS A 479 " --> pdb=" O   SER A 472 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   TRP A 559 " --> pdb=" O   TYR A 571 " (cutoff:3.500A)
      removed outlier: 5.555A  pdb=" N   SER A 573 " --> pdb=" O   SER A 557 " (cutoff:3.500A)
      removed outlier: 8.101A  pdb=" N   SER A 557 " --> pdb=" O   SER A 573 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   TRP A 562 " --> pdb=" O   VAL A 524 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   VAL A 524 " --> pdb=" O   TRP A 562 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   HIS A 516 " --> pdb=" O   GLN A 527 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 459 through 460
      removed outlier: 4.452A  pdb=" N   PHE A 536 " --> pdb=" O   GLY A 545 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 488 through 490
    Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 12
      removed outlier: 3.694A  pdb=" N   ALA L  12 " --> pdb=" O   THR L 108 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 17 through 23
      removed outlier: 3.743A  pdb=" N   ALA L  72 " --> pdb=" O   CYS L  22 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 46 through 49
      removed outlier: 6.485A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.761A  pdb=" N   VAL H  34 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   TRP H  50 " --> pdb=" O   VAL H  34 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR H  59 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 101 through 102
    Processing sheet with id=AB3, first strand: chain 'B' and resid 453 through 454
    Processing sheet with id=AB4, first strand: chain 'B' and resid 459 through 460
      removed outlier: 4.786A  pdb=" N   VAL B 584 " --> pdb=" O   SER B 466 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   SER B 466 " --> pdb=" O   VAL B 584 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   SER B 472 " --> pdb=" O   HIS B 479 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   HIS B 479 " --> pdb=" O   SER B 472 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   TRP B 559 " --> pdb=" O   TYR B 571 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   TRP B 562 " --> pdb=" O   VAL B 524 " (cutoff:3.500A)
      removed outlier: 5.028A  pdb=" N   VAL B 524 " --> pdb=" O   TRP B 562 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   HIS B 516 " --> pdb=" O   GLN B 527 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 459 through 460
      removed outlier: 4.627A  pdb=" N   PHE B 536 " --> pdb=" O   GLY B 545 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 488 through 490
    Processing sheet with id=AB7, first strand: chain 'D' and resid 9 through 12
      removed outlier: 3.693A  pdb=" N   ALA D  12 " --> pdb=" O   THR D 108 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 17 through 23
      removed outlier: 3.743A  pdb=" N   ALA D  72 " --> pdb=" O   CYS D  22 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 46 through 49
      removed outlier: 6.485A  pdb=" N   TRP D  36 " --> pdb=" O   LEU D  48 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 3 through 6
    Processing sheet with id=AC2, first strand: chain 'C' and resid 3 through 6
    Processing sheet with id=AC3, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.761A  pdb=" N   VAL C  34 " --> pdb=" O   TRP C  50 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   TRP C  50 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   TRP C  36 " --> pdb=" O   MET C  48 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR C  59 " --> pdb=" O   TRP C  50 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 101 through 102

    214 hydrogen bonds defined for protein.
    540 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.09

  Time building geometry restraints manager: 0.63 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1828
        1.34 -     1.45: 1128
        1.45 -     1.57: 3020
        1.57 -     1.69: 0
        1.69 -     1.80: 34
  Bond restraints: 6010
  Sorted by residual:
  bond pdb=" N   PRO H 106 "
       pdb=" CD  PRO H 106 "
    ideal  model  delta    sigma   weight residual
    1.473  1.522 -0.049 1.40e-02 5.10e+03 1.24e+01
  bond pdb=" N   PRO B 583 "
       pdb=" CD  PRO B 583 "
    ideal  model  delta    sigma   weight residual
    1.474  1.511 -0.037 1.40e-02 5.10e+03 6.91e+00
  bond pdb=" CG  MET B 531 "
       pdb=" SD  MET B 531 "
    ideal  model  delta    sigma   weight residual
    1.803  1.762  0.041 2.50e-02 1.60e+03 2.74e+00
  bond pdb=" CG  MET A 531 "
       pdb=" SD  MET A 531 "
    ideal  model  delta    sigma   weight residual
    1.803  1.764  0.039 2.50e-02 1.60e+03 2.39e+00
  bond pdb=" CB  PRO B 583 "
       pdb=" CG  PRO B 583 "
    ideal  model  delta    sigma   weight residual
    1.506  1.446  0.060 3.90e-02 6.57e+02 2.38e+00
  ... (remaining 6005 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 7932
        1.98 -     3.96: 240
        3.96 -     5.94: 48
        5.94 -     7.91: 4
        7.91 -     9.89: 2
  Bond angle restraints: 8226
  Sorted by residual:
  angle pdb=" C   ASP D  51 "
        pdb=" N   ASN D  52 "
        pdb=" CA  ASN D  52 "
      ideal   model   delta    sigma   weight residual
     121.54  131.43   -9.89 1.91e+00 2.74e-01 2.68e+01
  angle pdb=" C   ASP L  51 "
        pdb=" N   ASN L  52 "
        pdb=" CA  ASN L  52 "
      ideal   model   delta    sigma   weight residual
     121.54  131.43   -9.89 1.91e+00 2.74e-01 2.68e+01
  angle pdb=" C   GLY B 582 "
        pdb=" N   PRO B 583 "
        pdb=" CD  PRO B 583 "
      ideal   model   delta    sigma   weight residual
     120.60  113.56    7.04 2.20e+00 2.07e-01 1.02e+01
  angle pdb=" C   ASN L  53 "
        pdb=" N   LYS L  54 "
        pdb=" CA  LYS L  54 "
      ideal   model   delta    sigma   weight residual
     122.73  118.04    4.69 1.62e+00 3.81e-01 8.37e+00
  angle pdb=" C   ASN D  53 "
        pdb=" N   LYS D  54 "
        pdb=" CA  LYS D  54 "
      ideal   model   delta    sigma   weight residual
     122.73  118.06    4.67 1.62e+00 3.81e-01 8.32e+00
  ... (remaining 8221 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.24: 3330
       17.24 -    34.49: 86
       34.49 -    51.73: 16
       51.73 -    68.97: 2
       68.97 -    86.21: 8
  Dihedral angle restraints: 3442
    sinusoidal: 1260
      harmonic: 2182
  Sorted by residual:
  dihedral pdb=" CA  PRO A 465 "
           pdb=" C   PRO A 465 "
           pdb=" N   SER A 466 "
           pdb=" CA  SER A 466 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -136.80  -43.20     0      5.00e+00 4.00e-02 7.47e+01
  dihedral pdb=" CA  PRO B 465 "
           pdb=" C   PRO B 465 "
           pdb=" N   SER B 466 "
           pdb=" CA  SER B 466 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -139.08  -40.92     0      5.00e+00 4.00e-02 6.70e+01
  dihedral pdb=" CA  VAL H 104 "
           pdb=" C   VAL H 104 "
           pdb=" N   VAL H 105 "
           pdb=" CA  VAL H 105 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.68  -31.32     0      5.00e+00 4.00e-02 3.92e+01
  ... (remaining 3439 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 550
       0.041 -    0.082: 256
       0.082 -    0.123: 71
       0.123 -    0.164: 33
       0.164 -    0.204: 8
  Chirality restraints: 918
  Sorted by residual:
  chirality pdb=" CG  LEU A 523 "
            pdb=" CB  LEU A 523 "
            pdb=" CD1 LEU A 523 "
            pdb=" CD2 LEU A 523 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CG  LEU B 523 "
            pdb=" CB  LEU B 523 "
            pdb=" CD1 LEU B 523 "
            pdb=" CD2 LEU B 523 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CB  THR B 519 "
            pdb=" CA  THR B 519 "
            pdb=" OG1 THR B 519 "
            pdb=" CG2 THR B 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 915 not shown)

  Planarity restraints: 1040
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL H 105 "    0.069 5.00e-02 4.00e+02   1.03e-01 1.70e+01
        pdb=" N   PRO H 106 "   -0.178 5.00e-02 4.00e+02
        pdb=" CA  PRO H 106 "    0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO H 106 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 582 "    0.067 5.00e-02 4.00e+02   1.01e-01 1.64e+01
        pdb=" N   PRO B 583 "   -0.175 5.00e-02 4.00e+02
        pdb=" CA  PRO B 583 "    0.060 5.00e-02 4.00e+02
        pdb=" CD  PRO B 583 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 105 "   -0.041 5.00e-02 4.00e+02   6.14e-02 6.04e+00
        pdb=" N   PRO C 106 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO C 106 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C 106 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 1037 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 1866
        2.84 -     3.35: 4696
        3.35 -     3.87: 10169
        3.87 -     4.38: 11532
        4.38 -     4.90: 20683
  Nonbonded interactions: 48946
  Sorted by model distance:
  nonbonded pdb=" OH  TYR D  37 "
            pdb=" O   VAL C 110 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" O   THR A 542 "
            pdb=" OG  SER B 555 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" OH  TYR L  37 "
            pdb=" O   VAL H 110 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" O   PRO A 465 "
            pdb=" OG  SER A 484 "
     model   vdw
     2.366 3.040
  nonbonded pdb=" OG  SER A 555 "
            pdb=" O   THR B 542 "
     model   vdw
     2.373 3.040
  ... (remaining 48941 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'L'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'H'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.49 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.290
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
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      :  0.007   0.060   6014  Z= 0.296
  Angle     :  0.838   9.892   8234  Z= 0.466
  Chirality :  0.055   0.204    918
  Planarity :  0.008   0.103   1040
  Dihedral  :  9.666  86.210   2054
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.55 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.82 (0.28), residues: 760
  helix:  None (None), residues: 0
  sheet: -1.81 (0.26), residues: 340
  loop : -1.88 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG L  55 
 TYR   0.033   0.003   TYR A 482 
 PHE   0.023   0.005   PHE B 536 
 TRP   0.040   0.004   TRP H  50 
 HIS   0.005   0.001   HIS L  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00650 ( 6010)
  covalent geometry    : angle       0.83797 ( 8226)
  SS BOND              : bond        0.00589 (    4)
  SS BOND              : angle       0.55805 (    8)
  hydrogen bonds       : bond        0.26751 (  190)
  hydrogen bonds       : angle      10.18118 (  540)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A  496 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8202 (mm-40)
REVERT: H   27 TYR cc_start: 0.8283 (p90) cc_final: 0.7991 (p90)
REVERT: H   78 THR cc_start: 0.7992 (m) cc_final: 0.7612 (p)
REVERT: B  463 THR cc_start: 0.7817 (t) cc_final: 0.7239 (m)
REVERT: D   10 VAL cc_start: 0.8336 (p) cc_final: 0.8092 (m)
REVERT: C    5 VAL cc_start: 0.8316 (t) cc_final: 0.8082 (p)
REVERT: C   53 VAL cc_start: 0.7681 (t) cc_final: 0.7442 (t)
REVERT: C   76 THR cc_start: 0.7979 (p) cc_final: 0.7570 (t)
REVERT: C  122 VAL cc_start: 0.8297 (t) cc_final: 0.7842 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.2180
  time to fit residues: 35.2108
Evaluate side-chains
  114 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
H   6 GLN
H  39 GLN
D   6 GLN
D  39 HIS
C   6 GLN
C  39 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.110529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.096253 restraints weight = 21415.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 3.14
r_work: 0.2993 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2990
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2990 r_free = 0.2990    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2990 r_free = 0.2990    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2990
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   6014  Z= 0.276
  Angle     :  0.723  10.257   8234  Z= 0.380
  Chirality :  0.047   0.166    918
  Planarity :  0.007   0.064   1040
  Dihedral  :  7.641  88.161    836
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  :  9.21 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.03 (0.29), residues: 760
  helix:  None (None), residues: 0
  sheet: -1.13 (0.27), residues: 382
  loop : -1.48 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 449 
 TYR   0.027   0.003   TYR H  99 
 PHE   0.020   0.003   PHE C 111 
 TRP   0.040   0.003   TRP C  50 
 HIS   0.012   0.002   HIS L  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00621 ( 6010)
  covalent geometry    : angle       0.72178 ( 8226)
  SS BOND              : bond        0.00467 (    4)
  SS BOND              : angle       1.27771 (    8)
  hydrogen bonds       : bond        0.04902 (  190)
  hydrogen bonds       : angle       6.98843 (  540)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A  535 ASN cc_start: 0.8125 (t0) cc_final: 0.7772 (t0)
REVERT: A  569 TYR cc_start: 0.8278 (m-10) cc_final: 0.8075 (m-80)
REVERT: H   27 TYR cc_start: 0.8405 (p90) cc_final: 0.8132 (p90)
REVERT: H   76 THR cc_start: 0.7877 (p) cc_final: 0.7605 (m)
REVERT: B  466 SER cc_start: 0.8397 (p) cc_final: 0.8196 (p)
REVERT: C    5 VAL cc_start: 0.8510 (t) cc_final: 0.8305 (p)
REVERT: C   76 THR cc_start: 0.7928 (p) cc_final: 0.7618 (t)
REVERT: C   81 MET cc_start: 0.7861 (tmm) cc_final: 0.7644 (tmt)
REVERT: C   93 VAL cc_start: 0.8174 (t) cc_final: 0.7791 (p)
REVERT: C  116 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7622 (pt0)
REVERT: C  122 VAL cc_start: 0.8467 (t) cc_final: 0.8086 (p)
  outliers start: 24
  outliers final: 15
  residues processed: 127
  average time/residue: 0.2061
  time to fit residues: 29.4300
Evaluate side-chains
  125 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  488 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   43 THR
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  542 THR
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue   26 ASN
Chi-restraints excluded: chain D residue   94 SER
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   88 THR
Chi-restraints excluded: chain C residue  116 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 47 optimal weight:    0.2980
   chunk 43 optimal weight:    0.0970
   chunk 11 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0070
   chunk 32 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0670
   overall best weight:    0.2134

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

Flipped N/Q/H residues before XYZ refinement:
L  39 HIS
D   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.115931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.102646 restraints weight = 15952.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 2.64
r_work: 0.3107 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3126
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3126
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6014  Z= 0.112
  Angle     :  0.555  11.071   8234  Z= 0.288
  Chirality :  0.043   0.143    918
  Planarity :  0.005   0.054   1040
  Dihedral  :  6.871  89.781    836
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 12.86 %
    Favored  : 84.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -1.58 (0.30), residues: 760
  helix:  None (None), residues: 0
  sheet: -0.79 (0.27), residues: 382
  loop : -1.23 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  55 
 TYR   0.013   0.001   TYR H  99 
 PHE   0.011   0.002   PHE C 111 
 TRP   0.018   0.002   TRP C  50 
 HIS   0.003   0.001   HIS L  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 6010)
  covalent geometry    : angle       0.55468 ( 8226)
  SS BOND              : bond        0.00140 (    4)
  SS BOND              : angle       0.91895 (    8)
  hydrogen bonds       : bond        0.03296 (  190)
  hydrogen bonds       : angle       6.19119 (  540)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.229 
Fit side-chains
REVERT: H   27 TYR cc_start: 0.8372 (p90) cc_final: 0.8127 (p90)
REVERT: H   48 MET cc_start: 0.8308 (mtp) cc_final: 0.8054 (mmm)
REVERT: C    5 VAL cc_start: 0.8487 (t) cc_final: 0.8277 (p)
REVERT: C  116 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7547 (pt0)
  outliers start: 15
  outliers final: 7
  residues processed: 112
  average time/residue: 0.2175
  time to fit residues: 27.1391
Evaluate side-chains
  111 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain B residue  542 THR
Chi-restraints excluded: chain D residue   26 ASN
Chi-restraints excluded: chain D residue   94 SER
Chi-restraints excluded: chain C residue  116 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 61 optimal weight:    0.4980
   chunk 26 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 73 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B 585 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.113643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.099059 restraints weight = 24630.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 3.34
r_work: 0.3024 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3036
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3036
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6014  Z= 0.185
  Angle     :  0.612  11.096   8234  Z= 0.316
  Chirality :  0.044   0.142    918
  Planarity :  0.005   0.047   1040
  Dihedral  :  6.937  86.222    836
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 14.60 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -1.43 (0.30), residues: 760
  helix:  None (None), residues: 0
  sheet: -0.63 (0.27), residues: 382
  loop : -1.20 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 449 
 TYR   0.016   0.002   TYR H  99 
 PHE   0.014   0.002   PHE A 536 
 TRP   0.021   0.002   TRP C  50 
 HIS   0.004   0.001   HIS A 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 6010)
  covalent geometry    : angle       0.61147 ( 8226)
  SS BOND              : bond        0.00243 (    4)
  SS BOND              : angle       1.15804 (    8)
  hydrogen bonds       : bond        0.03524 (  190)
  hydrogen bonds       : angle       6.06997 (  540)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.212 
Fit side-chains
REVERT: H   27 TYR cc_start: 0.8373 (p90) cc_final: 0.8141 (p90)
REVERT: H   48 MET cc_start: 0.8385 (mtp) cc_final: 0.8147 (mmm)
REVERT: C    5 VAL cc_start: 0.8520 (t) cc_final: 0.8306 (p)
REVERT: C   81 MET cc_start: 0.7919 (tmm) cc_final: 0.7698 (tmt)
REVERT: C   93 VAL cc_start: 0.8158 (t) cc_final: 0.7807 (p)
REVERT: C  116 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7688 (pt0)
  outliers start: 17
  outliers final: 14
  residues processed: 113
  average time/residue: 0.2264
  time to fit residues: 28.3935
Evaluate side-chains
  116 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  488 THR
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain B residue  542 THR
Chi-restraints excluded: chain D residue   26 ASN
Chi-restraints excluded: chain D residue   94 SER
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   88 THR
Chi-restraints excluded: chain C residue  116 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 73 optimal weight:    0.4980
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 585 ASN
D   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.112942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.098415 restraints weight = 24062.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 3.26
r_work: 0.3031 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3036
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3036
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   6014  Z= 0.248
  Angle     :  0.661  11.627   8234  Z= 0.342
  Chirality :  0.045   0.147    918
  Planarity :  0.005   0.046   1040
  Dihedral  :  7.123  81.938    836
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 14.76 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -1.31 (0.30), residues: 760
  helix:  None (None), residues: 0
  sheet: -0.46 (0.28), residues: 382
  loop : -1.25 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 449 
 TYR   0.018   0.002   TYR H  99 
 PHE   0.017   0.002   PHE A 536 
 TRP   0.021   0.002   TRP A 561 
 HIS   0.008   0.001   HIS A 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00567 ( 6010)
  covalent geometry    : angle       0.66033 ( 8226)
  SS BOND              : bond        0.00396 (    4)
  SS BOND              : angle       1.24197 (    8)
  hydrogen bonds       : bond        0.03789 (  190)
  hydrogen bonds       : angle       6.14160 (  540)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.220 
Fit side-chains
REVERT: H   48 MET cc_start: 0.8430 (mtp) cc_final: 0.8191 (mmm)
REVERT: D   40 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7914 (mp)
REVERT: C    5 VAL cc_start: 0.8518 (t) cc_final: 0.8311 (p)
REVERT: C   93 VAL cc_start: 0.8186 (t) cc_final: 0.7846 (p)
REVERT: C  116 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7640 (pt0)
  outliers start: 22
  outliers final: 17
  residues processed: 115
  average time/residue: 0.2234
  time to fit residues: 28.6896
Evaluate side-chains
  121 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  488 THR
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain H residue    9 THR
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain B residue  542 THR
Chi-restraints excluded: chain D residue   26 ASN
Chi-restraints excluded: chain D residue   40 LEU
Chi-restraints excluded: chain D residue   94 SER
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   88 THR
Chi-restraints excluded: chain C residue  116 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 13 optimal weight:    0.4980
   chunk 24 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9990
   chunk 61 optimal weight:    0.4980
   chunk 30 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 585 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.112869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.099074 restraints weight = 19821.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 2.97
r_work: 0.3074 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3062
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3062
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6014  Z= 0.196
  Angle     :  0.627  11.975   8234  Z= 0.320
  Chirality :  0.044   0.143    918
  Planarity :  0.005   0.047   1040
  Dihedral  :  6.826  77.621    836
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 15.71 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -1.20 (0.30), residues: 760
  helix:  None (None), residues: 0
  sheet: -0.35 (0.27), residues: 402
  loop : -1.25 (0.30), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 449 
 TYR   0.022   0.002   TYR A 569 
 PHE   0.014   0.002   PHE A 536 
 TRP   0.022   0.002   TRP A 561 
 HIS   0.005   0.001   HIS A 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 6010)
  covalent geometry    : angle       0.62641 ( 8226)
  SS BOND              : bond        0.00277 (    4)
  SS BOND              : angle       1.15007 (    8)
  hydrogen bonds       : bond        0.03493 (  190)
  hydrogen bonds       : angle       5.99650 (  540)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.172 
Fit side-chains
REVERT: H   48 MET cc_start: 0.8394 (mtp) cc_final: 0.8182 (mmm)
REVERT: D   40 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7862 (mp)
REVERT: C    5 VAL cc_start: 0.8505 (t) cc_final: 0.8289 (p)
REVERT: C   93 VAL cc_start: 0.8161 (t) cc_final: 0.7828 (p)
REVERT: C  116 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7605 (pt0)
  outliers start: 22
  outliers final: 16
  residues processed: 117
  average time/residue: 0.2087
  time to fit residues: 27.2810
Evaluate side-chains
  126 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  488 THR
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain B residue  531 MET
Chi-restraints excluded: chain B residue  542 THR
Chi-restraints excluded: chain D residue   26 ASN
Chi-restraints excluded: chain D residue   40 LEU
Chi-restraints excluded: chain C residue    9 THR
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue  116 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 13 optimal weight:    0.2980
   chunk 24 optimal weight:    0.3980
   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 585 ASN
D   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.113281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.099347 restraints weight = 21188.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 3.04
r_work: 0.3046 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3045
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3045
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.3049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6014  Z= 0.191
  Angle     :  0.626  11.994   8234  Z= 0.320
  Chirality :  0.044   0.143    918
  Planarity :  0.005   0.048   1040
  Dihedral  :  6.681  73.996    836
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 15.56 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -1.16 (0.30), residues: 760
  helix:  None (None), residues: 0
  sheet: -0.29 (0.28), residues: 384
  loop : -1.23 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  55 
 TYR   0.022   0.002   TYR A 569 
 PHE   0.017   0.002   PHE A 536 
 TRP   0.025   0.002   TRP H  50 
 HIS   0.005   0.001   HIS A 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 6010)
  covalent geometry    : angle       0.62578 ( 8226)
  SS BOND              : bond        0.00266 (    4)
  SS BOND              : angle       1.08396 (    8)
  hydrogen bonds       : bond        0.03439 (  190)
  hydrogen bonds       : angle       5.94198 (  540)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.249 
Fit side-chains
REVERT: D   40 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7845 (mp)
REVERT: C    5 VAL cc_start: 0.8499 (t) cc_final: 0.8276 (p)
REVERT: C   93 VAL cc_start: 0.8157 (t) cc_final: 0.7815 (p)
REVERT: C  116 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7614 (pt0)
  outliers start: 22
  outliers final: 18
  residues processed: 118
  average time/residue: 0.2201
  time to fit residues: 28.9682
Evaluate side-chains
  124 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  488 THR
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  542 THR
Chi-restraints excluded: chain D residue   26 ASN
Chi-restraints excluded: chain D residue   40 LEU
Chi-restraints excluded: chain C residue    9 THR
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue  116 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 585 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.112966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.098775 restraints weight = 24097.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 3.25
r_work: 0.3038 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3042
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3042 r_free = 0.3042    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3042 r_free = 0.3042    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3042
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   6014  Z= 0.239
  Angle     :  0.663  11.925   8234  Z= 0.339
  Chirality :  0.045   0.146    918
  Planarity :  0.005   0.045   1040
  Dihedral  :  6.754  70.933    836
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 14.76 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -1.10 (0.30), residues: 760
  helix:  None (None), residues: 0
  sheet: -0.24 (0.28), residues: 382
  loop : -1.20 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  38 
 TYR   0.019   0.002   TYR C  94 
 PHE   0.015   0.002   PHE A 536 
 TRP   0.024   0.002   TRP H  50 
 HIS   0.006   0.001   HIS A 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00545 ( 6010)
  covalent geometry    : angle       0.66240 ( 8226)
  SS BOND              : bond        0.00413 (    4)
  SS BOND              : angle       1.10977 (    8)
  hydrogen bonds       : bond        0.03717 (  190)
  hydrogen bonds       : angle       6.01078 (  540)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.245 
Fit side-chains
REVERT: H   72 THR cc_start: 0.8285 (p) cc_final: 0.7914 (t)
REVERT: D   40 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7898 (mp)
REVERT: C    5 VAL cc_start: 0.8525 (t) cc_final: 0.8311 (p)
REVERT: C   93 VAL cc_start: 0.8200 (t) cc_final: 0.7862 (p)
REVERT: C  116 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7641 (pt0)
  outliers start: 26
  outliers final: 18
  residues processed: 119
  average time/residue: 0.2137
  time to fit residues: 28.5644
Evaluate side-chains
  125 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  488 THR
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  542 THR
Chi-restraints excluded: chain D residue   26 ASN
Chi-restraints excluded: chain D residue   40 LEU
Chi-restraints excluded: chain C residue    9 THR
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue  116 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 68 optimal weight:    0.1980
   chunk 61 optimal weight:    0.2980
   chunk 45 optimal weight:    0.2980
   chunk 11 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A 496 GLN
B 585 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.115218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.101728 restraints weight = 21502.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 3.04
r_work: 0.3084 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3078
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3078
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6014  Z= 0.156
  Angle     :  0.602  12.035   8234  Z= 0.305
  Chirality :  0.043   0.141    918
  Planarity :  0.004   0.043   1040
  Dihedral  :  6.292  66.920    836
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 16.03 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -1.11 (0.30), residues: 760
  helix:  None (None), residues: 0
  sheet: -0.25 (0.28), residues: 380
  loop : -1.20 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  55 
 TYR   0.014   0.002   TYR C  94 
 PHE   0.012   0.002   PHE A 536 
 TRP   0.024   0.002   TRP B 561 
 HIS   0.003   0.001   HIS A 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 6010)
  covalent geometry    : angle       0.60142 ( 8226)
  SS BOND              : bond        0.00176 (    4)
  SS BOND              : angle       0.88081 (    8)
  hydrogen bonds       : bond        0.03206 (  190)
  hydrogen bonds       : angle       5.80250 (  540)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.243 
Fit side-chains
REVERT: H   48 MET cc_start: 0.8266 (mmm) cc_final: 0.7821 (mmm)
REVERT: D   40 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7808 (mp)
REVERT: C    5 VAL cc_start: 0.8523 (t) cc_final: 0.8288 (p)
REVERT: C   93 VAL cc_start: 0.8167 (t) cc_final: 0.7848 (p)
REVERT: C  116 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7596 (pt0)
  outliers start: 20
  outliers final: 18
  residues processed: 113
  average time/residue: 0.2304
  time to fit residues: 28.9063
Evaluate side-chains
  123 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  488 THR
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  542 THR
Chi-restraints excluded: chain D residue   26 ASN
Chi-restraints excluded: chain D residue   40 LEU
Chi-restraints excluded: chain C residue    9 THR
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue  116 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 69 optimal weight:    0.3980
   chunk 34 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 496 GLN
B 585 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.113183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.098705 restraints weight = 29503.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 3.60
r_work: 0.3028 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3013
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3013 r_free = 0.3013    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3013 r_free = 0.3013    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3013
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.3261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   6014  Z= 0.222
  Angle     :  0.655  12.003   8234  Z= 0.334
  Chirality :  0.045   0.143    918
  Planarity :  0.005   0.042   1040
  Dihedral  :  6.418  63.232    836
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 15.56 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -1.10 (0.30), residues: 760
  helix:  None (None), residues: 0
  sheet: -0.24 (0.28), residues: 380
  loop : -1.21 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  38 
 TYR   0.017   0.002   TYR C  94 
 PHE   0.015   0.002   PHE A 536 
 TRP   0.023   0.002   TRP B 561 
 HIS   0.005   0.001   HIS A 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 6010)
  covalent geometry    : angle       0.65430 ( 8226)
  SS BOND              : bond        0.00352 (    4)
  SS BOND              : angle       0.95680 (    8)
  hydrogen bonds       : bond        0.03584 (  190)
  hydrogen bonds       : angle       5.94035 (  540)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.213 
Fit side-chains
REVERT: H   72 THR cc_start: 0.8307 (p) cc_final: 0.7914 (t)
REVERT: D   40 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7872 (mp)
REVERT: C    5 VAL cc_start: 0.8538 (t) cc_final: 0.8308 (p)
REVERT: C   93 VAL cc_start: 0.8199 (t) cc_final: 0.7875 (p)
REVERT: C  116 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7640 (pt0)
  outliers start: 22
  outliers final: 19
  residues processed: 116
  average time/residue: 0.2169
  time to fit residues: 28.2352
Evaluate side-chains
  126 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  488 THR
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  542 THR
Chi-restraints excluded: chain D residue   26 ASN
Chi-restraints excluded: chain D residue   40 LEU
Chi-restraints excluded: chain C residue    9 THR
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue  116 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0770
   chunk 37 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
A 496 GLN
B 585 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.114346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.101860 restraints weight = 16107.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.53
r_work: 0.3101 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3107
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3107
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   6014  Z= 0.212
  Angle     :  0.648  11.980   8234  Z= 0.330
  Chirality :  0.045   0.143    918
  Planarity :  0.005   0.042   1040
  Dihedral  :  6.315  59.151    836
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 15.71 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -1.04 (0.30), residues: 760
  helix:  None (None), residues: 0
  sheet: -0.22 (0.28), residues: 378
  loop : -1.13 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG H  38 
 TYR   0.018   0.002   TYR H  94 
 PHE   0.015   0.002   PHE A 536 
 TRP   0.024   0.002   TRP B 561 
 HIS   0.004   0.001   HIS A 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 6010)
  covalent geometry    : angle       0.64762 ( 8226)
  SS BOND              : bond        0.00335 (    4)
  SS BOND              : angle       0.90677 (    8)
  hydrogen bonds       : bond        0.03487 (  190)
  hydrogen bonds       : angle       5.94752 (  540)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1890.53 seconds
wall clock time: 33 minutes 8.61 seconds (1988.61 seconds total)