Starting phenix.real_space_refine
on Wed Sep 17 06:23:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jii_61506/09_2025/9jii_61506.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jii_61506/09_2025/9jii_61506.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jii_61506/09_2025/9jii_61506.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jii_61506/09_2025/9jii_61506.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jii_61506/09_2025/9jii_61506.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jii_61506/09_2025/9jii_61506.cif"
  }
  resolution = 2.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.016
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    3738      2.51       5
     N    1006      2.21       5
     O    1162      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  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: 5928
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1186
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 152, 1174
          Classifications: {'peptide': 152}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 143}
      Conformer: "B"
        Number of residues, atoms: 152, 1174
          Classifications: {'peptide': 152}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 143}
          bond proxies already assigned to first conformer: 1197
    Chain: "L"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 821
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 957
          Classifications: {'peptide': 125}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 121}
    Chain: "B"
      Number of atoms: 1186
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 152, 1174
          Classifications: {'peptide': 152}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 143}
      Conformer: "B"
        Number of residues, atoms: 152, 1174
          Classifications: {'peptide': 152}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 143}
          bond proxies already assigned to first conformer: 1197
    Chain: "E"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 821
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 102}
    Chain: "F"
      Number of atoms: 957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 957
          Classifications: {'peptide': 125}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 121}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N  ASER A 474 " occ=0.32
      ... (10 atoms not shown)
      pdb=" OG BSER A 474 " occ=0.68
    residue:
      pdb=" N  ASER A 502 " occ=0.52
      ... (10 atoms not shown)
      pdb=" OG BSER A 502 " occ=0.48
    residue:
      pdb=" N  ASER B 474 " occ=0.55
      ... (10 atoms not shown)
      pdb=" OG BSER B 474 " occ=0.45
    residue:
      pdb=" N  ASER B 502 " occ=0.52
      ... (10 atoms not shown)
      pdb=" OG BSER B 502 " occ=0.48
  Time building chain proxies: 1.97, per 1000 atoms: 0.33
  Number of scatterers: 5928
  At special positions: 0
  Unit cell: (118.95, 82.55, 88.4, 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    1162      8.00
     N    1006      7.00
     C    3738      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=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.22
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  96 " distance=2.16

  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: 0.48
  Conformation dependent library (CDL) restraints added in 447.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1400

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 12 sheets defined
      4.3% alpha, 28.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  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 'A' and resid 504 through 507
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.676A  pdb=" N   GLU L  84 " --> pdb=" O   THR L  81 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 31
    Processing helix  chain 'B' and resid 501 through 503
      No H-bonds generated for 'chain 'B' and resid 501 through 503'
    Processing helix  chain 'B' and resid 504 through 507
    Processing helix  chain 'E' and resid 80 through 84
      removed outlier: 3.703A  pdb=" N   GLU E  84 " --> pdb=" O   THR E  81 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 28 through 32
      removed outlier: 3.833A  pdb=" N   TYR F  32 " --> pdb=" O   PHE F  29 " (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 473
      removed outlier: 4.432A  pdb=" N   SER A 472 " --> pdb=" O   HIS A 479 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   HIS A 479 " --> pdb=" O   SER A 472 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 479 through 484
    current: chain 'A' and resid 496 through 499
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 496 through 499
    current: chain 'A' and resid 523 through 538
      removed outlier: 4.496A  pdb=" N   PHE A 536 " --> pdb=" O   GLY A 545 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 544 through 545
    current: chain 'A' and resid 567 through 573
    Processing sheet with id=AA3, first strand: chain 'L' and resid 9 through 11
  WARNING: can't find start of bonding for strands!
    previous: chain 'L' and resid 9 through 11
    current: chain 'L' and resid 46 through 49
  WARNING: can't find start of bonding for strands!
    previous: chain 'L' and resid 46 through 49
    current: chain 'L' and resid 98 through 101
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'L' and resid 17 through 23
    Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12
  WARNING: can't find start of bonding for strands!
    previous: chain 'H' and resid 10 through 12
    current: chain 'H' and resid 46 through 52
  WARNING: can't find start of bonding for strands!
    previous: chain 'H' and resid 58 through 60
    current: chain 'H' and resid 110 through 115
    Processing sheet with id=AA7, first strand: chain 'B' and resid 453 through 454
    Processing sheet with id=AA8, first strand: chain 'B' and resid 459 through 473
      removed outlier: 4.396A  pdb=" N   SER B 472 " --> pdb=" O   HIS B 479 " (cutoff:3.500A)
      removed outlier: 5.545A  pdb=" N   HIS B 479 " --> pdb=" O   SER B 472 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 479 through 484
    current: chain 'B' and resid 496 through 499
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 496 through 499
    current: chain 'B' and resid 523 through 538
      removed outlier: 4.595A  pdb=" N   PHE B 536 " --> pdb=" O   GLY B 545 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 544 through 545
    current: chain 'B' and resid 567 through 573
    Processing sheet with id=AA9, first strand: chain 'E' and resid 9 through 11
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 9 through 11
    current: chain 'E' and resid 45 through 49
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 45 through 49
    current: chain 'E' and resid 98 through 101
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'E' and resid 17 through 22
    Processing sheet with id=AB2, first strand: chain 'F' and resid 3 through 6
    Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 12
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 10 through 12
    current: chain 'F' and resid 46 through 51
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 58 through 60
    current: chain 'F' and resid 110 through 115

    82 hydrogen bonds defined for protein.
    204 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: 0.81

  Time building geometry restraints manager: 0.65 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 958
        1.28 -     1.41: 1625
        1.41 -     1.55: 3466
        1.55 -     1.68: 1
        1.68 -     1.81: 36
  Bond restraints: 6086
  Sorted by residual:
  bond pdb=" C   ALA B 544 "
       pdb=" O   ALA B 544 "
    ideal  model  delta    sigma   weight residual
    1.234  1.146  0.088 1.26e-02 6.30e+03 4.90e+01
  bond pdb=" C   ALA A 544 "
       pdb=" O   ALA A 544 "
    ideal  model  delta    sigma   weight residual
    1.234  1.160  0.074 1.26e-02 6.30e+03 3.49e+01
  bond pdb=" C   SER L  64 "
       pdb=" N   ALA L  65 "
    ideal  model  delta    sigma   weight residual
    1.331  1.265  0.066 1.22e-02 6.72e+03 2.94e+01
  bond pdb=" CA  ALA B 544 "
       pdb=" C   ALA B 544 "
    ideal  model  delta    sigma   weight residual
    1.522  1.458  0.064 1.21e-02 6.83e+03 2.78e+01
  bond pdb=" CA  ALA A 544 "
       pdb=" C   ALA A 544 "
    ideal  model  delta    sigma   weight residual
    1.522  1.462  0.059 1.21e-02 6.83e+03 2.39e+01
  ... (remaining 6081 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 7941
        1.33 -     2.67: 296
        2.67 -     4.00: 60
        4.00 -     5.33: 16
        5.33 -     6.67: 9
  Bond angle restraints: 8322
  Sorted by residual:
  angle pdb=" O   ALA B 544 "
        pdb=" C   ALA B 544 "
        pdb=" N   GLY B 545 "
      ideal   model   delta    sigma   weight residual
     123.24  128.97   -5.73 1.23e+00 6.61e-01 2.17e+01
  angle pdb=" CA  ALA B 544 "
        pdb=" C   ALA B 544 "
        pdb=" O   ALA B 544 "
      ideal   model   delta    sigma   weight residual
     121.11  115.71    5.40 1.17e+00 7.31e-01 2.13e+01
  angle pdb=" O   ALA A 544 "
        pdb=" C   ALA A 544 "
        pdb=" N   GLY A 545 "
      ideal   model   delta    sigma   weight residual
     123.24  128.25   -5.01 1.23e+00 6.61e-01 1.66e+01
  angle pdb=" CA  ALA A 544 "
        pdb=" C   ALA A 544 "
        pdb=" O   ALA A 544 "
      ideal   model   delta    sigma   weight residual
     121.11  116.77    4.34 1.17e+00 7.31e-01 1.38e+01
  angle pdb=" N   ILE L  29 "
        pdb=" CA  ILE L  29 "
        pdb=" C   ILE L  29 "
      ideal   model   delta    sigma   weight residual
     111.81  108.88    2.93 8.60e-01 1.35e+00 1.16e+01
  ... (remaining 8317 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.43: 3149
       16.43 -    32.86: 266
       32.86 -    49.29: 70
       49.29 -    65.72: 25
       65.72 -    82.15: 8
  Dihedral angle restraints: 3518
    sinusoidal: 1298
      harmonic: 2220
  Sorted by residual:
  dihedral pdb=" CD  ARG H  72 "
           pdb=" NE  ARG H  72 "
           pdb=" CZ  ARG H  72 "
           pdb=" NH1 ARG H  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -53.36   53.36     1      1.00e+01 1.00e-02 3.87e+01
  dihedral pdb=" CD  ARG H  38 "
           pdb=" NE  ARG H  38 "
           pdb=" CZ  ARG H  38 "
           pdb=" NH1 ARG H  38 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -48.61   48.61     1      1.00e+01 1.00e-02 3.25e+01
  dihedral pdb=" CA  GLN F  65 "
           pdb=" C   GLN F  65 "
           pdb=" N   GLY F  66 "
           pdb=" CA  GLY F  66 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.17   25.83     0      5.00e+00 4.00e-02 2.67e+01
  ... (remaining 3515 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 478
       0.028 -    0.057: 258
       0.057 -    0.085: 113
       0.085 -    0.113: 49
       0.113 -    0.142: 20
  Chirality restraints: 918
  Sorted by residual:
  chirality pdb=" CB  THR B 542 "
            pdb=" CA  THR B 542 "
            pdb=" OG1 THR B 542 "
            pdb=" CG2 THR B 542 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 5.01e-01
  chirality pdb=" CA  ILE A 490 "
            pdb=" N   ILE A 490 "
            pdb=" C   ILE A 490 "
            pdb=" CB  ILE A 490 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.92e-01
  chirality pdb=" CA  ALA E  65 "
            pdb=" N   ALA E  65 "
            pdb=" C   ALA E  65 "
            pdb=" CB  ALA E  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.35    0.13 2.00e-01 2.50e+01 4.41e-01
  ... (remaining 915 not shown)

  Planarity restraints: 1060
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H  72 "    0.876 9.50e-02 1.11e+02   3.93e-01 9.36e+01
        pdb=" NE  ARG H  72 "   -0.053 2.00e-02 2.50e+03
        pdb=" CZ  ARG H  72 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG H  72 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG H  72 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H  38 "    0.820 9.50e-02 1.11e+02   3.68e-01 8.21e+01
        pdb=" NE  ARG H  38 "   -0.049 2.00e-02 2.50e+03
        pdb=" CZ  ARG H  38 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG H  38 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG H  38 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG F  38 "   -0.669 9.50e-02 1.11e+02   3.00e-01 5.49e+01
        pdb=" NE  ARG F  38 "    0.040 2.00e-02 2.50e+03
        pdb=" CZ  ARG F  38 "    0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG F  38 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG F  38 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 1057 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 92
        2.65 -     3.21: 5353
        3.21 -     3.77: 9400
        3.77 -     4.34: 13656
        4.34 -     4.90: 22177
  Nonbonded interactions: 50678
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 491 "
            pdb=" OG1 THR A 494 "
     model   vdw
     2.083 3.040
  nonbonded pdb=" OD1 ASN B 491 "
            pdb=" OG1 THR B 494 "
     model   vdw
     2.102 3.040
  nonbonded pdb=" O   TYR H  32 "
            pdb=" OG1 THR H  53 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" O   TYR F  32 "
            pdb=" OG1 THR F  53 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   PRO L   7 "
            pdb=" OG1 THR L 105 "
     model   vdw
     2.293 3.040
  ... (remaining 50673 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' and (resid 446 through 473 or resid 475 through 501 or resid 503 thro \ 
ugh 597))
  selection = (chain 'B' and (resid 446 through 473 or resid 475 through 501 or resid 503 thro \ 
ugh 597))
}
ncs_group {
  reference = chain 'E'
  selection = chain 'L'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'H'
}

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=0.32 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:             6.090
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.810
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
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   0.186   6090  Z= 0.376
  Angle     :  0.682  10.000   8330  Z= 0.374
  Chirality :  0.045   0.142    918
  Planarity :  0.020   0.393   1060
  Dihedral  : 14.719  82.147   2106
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 10.73 %
    Favored  : 88.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.24 (0.31), residues: 774
  helix:  None (None), residues: 0
  sheet:  0.79 (0.29), residues: 328
  loop : -0.93 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 449 
 TYR   0.015   0.002   TYR F  60 
 PHE   0.010   0.002   PHE F  64 
 TRP   0.025   0.002   TRP A 561 
 HIS   0.010   0.002   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00667 ( 6086)
  covalent geometry    : angle       0.66203 ( 8322)
  SS BOND              : bond        0.11370 (    4)
  SS BOND              : angle       5.31110 (    8)
  hydrogen bonds       : bond        0.21472 (   82)
  hydrogen bonds       : angle       8.60555 (  204)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 139
  time to evaluate  : 0.216 
Fit side-chains
REVERT: H  112 MET cc_start: 0.7867 (mpp) cc_final: 0.7031 (mpp)
REVERT: B  476 MET cc_start: 0.7733 (mtt) cc_final: 0.7425 (mtm)
REVERT: F   48 MET cc_start: 0.8408 (mtm) cc_final: 0.8207 (mtp)
REVERT: F   73 ASP cc_start: 0.7664 (t0) cc_final: 0.7348 (t70)
  outliers start: 2
  outliers final: 1
  residues processed: 141
  average time/residue: 0.2623
  time to fit residues: 40.7196
Evaluate side-chains
  116 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  572 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.1980
   chunk 5 optimal weight:    0.0870
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.3980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0980
   overall best weight:    0.2758

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

Flipped N/Q/H residues before XYZ refinement:
A 507 GLN
L  16 GLN
L  38 GLN
H 117 ASN
B 473 GLN
B 491 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.146096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.127069 restraints weight = 25142.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 3.42
r_work: 0.3504 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3501
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3501 r_free = 0.3501    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3501 r_free = 0.3501    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3501
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.1463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6090  Z= 0.124
  Angle     :  0.533   6.337   8330  Z= 0.279
  Chirality :  0.043   0.167    918
  Planarity :  0.005   0.053   1060
  Dihedral  :  5.349  39.770    852
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 17.67 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.30), residues: 774
  helix:  None (None), residues: 0
  sheet:  0.63 (0.28), residues: 324
  loop : -0.73 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  55 
 TYR   0.009   0.001   TYR B 546 
 PHE   0.008   0.001   PHE H  64 
 TRP   0.011   0.001   TRP A 561 
 HIS   0.003   0.001   HIS A 520 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6086)
  covalent geometry    : angle       0.53306 ( 8322)
  SS BOND              : bond        0.00094 (    4)
  SS BOND              : angle       0.54482 (    8)
  hydrogen bonds       : bond        0.03550 (   82)
  hydrogen bonds       : angle       5.38863 (  204)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.281 
Fit side-chains
REVERT: B  476 MET cc_start: 0.7637 (mtt) cc_final: 0.7400 (mtm)
REVERT: E   49 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7556 (mp)
REVERT: F   50 SER cc_start: 0.8492 (m) cc_final: 0.8266 (t)
REVERT: F   73 ASP cc_start: 0.7817 (t0) cc_final: 0.7415 (t70)
  outliers start: 16
  outliers final: 11
  residues processed: 117
  average time/residue: 0.2861
  time to fit residues: 36.6087
Evaluate side-chains
  125 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   35 VAL
Chi-restraints excluded: chain H residue   50 SER
Chi-restraints excluded: chain H residue  110 HIS
Chi-restraints excluded: chain B residue  553 THR
Chi-restraints excluded: chain B residue  554 ASP
Chi-restraints excluded: chain B residue  572 ILE
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   95 SER
Chi-restraints excluded: chain F residue   71 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 49 optimal weight:    0.4980
   chunk 37 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 62 optimal weight:    0.5980
   chunk 63 optimal weight:    0.7980
   chunk 54 optimal weight:    0.2980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 473 GLN
B 491 ASN
E  28 ASN
** F 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.142914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.122932 restraints weight = 32234.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 3.86
r_work: 0.3438 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3434
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3434 r_free = 0.3434    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3434 r_free = 0.3434    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3434
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   6090  Z= 0.197
  Angle     :  0.600   6.831   8330  Z= 0.313
  Chirality :  0.045   0.176    918
  Planarity :  0.005   0.059   1060
  Dihedral  :  5.764  45.563    852
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 15.93 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.34 (0.30), residues: 774
  helix:  None (None), residues: 0
  sheet:  0.42 (0.28), residues: 348
  loop : -0.77 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 449 
 TYR   0.012   0.002   TYR B 546 
 PHE   0.011   0.002   PHE H  64 
 TRP   0.010   0.002   TRP A 561 
 HIS   0.006   0.001   HIS E  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 6086)
  covalent geometry    : angle       0.60041 ( 8322)
  SS BOND              : bond        0.00138 (    4)
  SS BOND              : angle       0.50735 (    8)
  hydrogen bonds       : bond        0.03317 (   82)
  hydrogen bonds       : angle       5.28139 (  204)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 119
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
REVERT: A  497 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7063 (pmm-80)
REVERT: H  112 MET cc_start: 0.7760 (mpp) cc_final: 0.7095 (mpp)
REVERT: B  455 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7610 (mtt180)
REVERT: B  476 MET cc_start: 0.7791 (mtt) cc_final: 0.7518 (mtm)
REVERT: E   49 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7589 (mp)
REVERT: F   73 ASP cc_start: 0.7871 (t0) cc_final: 0.7435 (t70)
  outliers start: 27
  outliers final: 18
  residues processed: 127
  average time/residue: 0.3208
  time to fit residues: 44.1424
Evaluate side-chains
  136 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  456 SER
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  497 ARG
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   35 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  110 HIS
Chi-restraints excluded: chain B residue  468 GLU
Chi-restraints excluded: chain B residue  553 THR
Chi-restraints excluded: chain B residue  554 ASP
Chi-restraints excluded: chain B residue  572 ILE
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   95 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain F residue  110 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 75 optimal weight:    0.5980
   chunk 49 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9990
   chunk 62 optimal weight:    0.5980
   chunk 68 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 47 optimal weight:    0.2980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 491 ASN
** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 473 GLN
B 491 ASN
F   6 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.142794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.123629 restraints weight = 27050.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 3.50
r_work: 0.3466 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3463
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3463 r_free = 0.3463    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3463 r_free = 0.3463    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3463
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   6090  Z= 0.195
  Angle     :  0.597   6.769   8330  Z= 0.312
  Chirality :  0.045   0.170    918
  Planarity :  0.005   0.059   1060
  Dihedral  :  5.860  51.689    852
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 15.46 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.30), residues: 774
  helix:  None (None), residues: 0
  sheet:  0.35 (0.28), residues: 348
  loop : -0.85 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 449 
 TYR   0.014   0.002   TYR F  60 
 PHE   0.010   0.002   PHE H  64 
 TRP   0.014   0.002   TRP B 483 
 HIS   0.004   0.001   HIS A 520 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 6086)
  covalent geometry    : angle       0.59701 ( 8322)
  SS BOND              : bond        0.00129 (    4)
  SS BOND              : angle       0.50670 (    8)
  hydrogen bonds       : bond        0.03076 (   82)
  hydrogen bonds       : angle       5.13183 (  204)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 120
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A  497 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7037 (pmm-80)
REVERT: H  112 MET cc_start: 0.7694 (mpp) cc_final: 0.7181 (mpp)
REVERT: B  455 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7572 (mtt180)
REVERT: B  476 MET cc_start: 0.7786 (mtt) cc_final: 0.7542 (mtm)
REVERT: B  530 LEU cc_start: 0.5604 (OUTLIER) cc_final: 0.5002 (pt)
REVERT: E   49 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7543 (mp)
  outliers start: 30
  outliers final: 22
  residues processed: 131
  average time/residue: 0.3153
  time to fit residues: 44.8107
Evaluate side-chains
  141 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  456 SER
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  497 ARG
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   35 VAL
Chi-restraints excluded: chain H residue   50 SER
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  110 HIS
Chi-restraints excluded: chain B residue  468 GLU
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  553 THR
Chi-restraints excluded: chain B residue  554 ASP
Chi-restraints excluded: chain B residue  572 ILE
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   95 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain F residue  110 HIS
Chi-restraints excluded: chain F residue  117 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 54 optimal weight:    0.0010
   chunk 2 optimal weight:    0.6980
   chunk 67 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 5 optimal weight:    0.4980
   chunk 42 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 507 GLN
L  28 ASN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 473 GLN
B 491 ASN
F   6 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.143291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.122972 restraints weight = 34294.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 4.03
r_work: 0.3434 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3430
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3430 r_free = 0.3430    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3430 r_free = 0.3430    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3430
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6090  Z= 0.168
  Angle     :  0.573   6.374   8330  Z= 0.297
  Chirality :  0.044   0.162    918
  Planarity :  0.005   0.057   1060
  Dihedral  :  5.776  54.420    852
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 18.14 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.48 (0.30), residues: 774
  helix:  None (None), residues: 0
  sheet:  0.31 (0.28), residues: 348
  loop : -0.85 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 449 
 TYR   0.012   0.002   TYR F  60 
 PHE   0.009   0.002   PHE L 101 
 TRP   0.013   0.002   TRP B 561 
 HIS   0.006   0.001   HIS E  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 6086)
  covalent geometry    : angle       0.57263 ( 8322)
  SS BOND              : bond        0.00135 (    4)
  SS BOND              : angle       0.50050 (    8)
  hydrogen bonds       : bond        0.02826 (   82)
  hydrogen bonds       : angle       4.95122 (  204)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 118
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A  497 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7091 (pmm-80)
REVERT: H   19 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8189 (ttpp)
REVERT: B  455 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7622 (mtt180)
REVERT: B  530 LEU cc_start: 0.5609 (OUTLIER) cc_final: 0.4978 (pt)
REVERT: E   49 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7586 (mp)
REVERT: F   19 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8065 (ttpp)
  outliers start: 29
  outliers final: 23
  residues processed: 130
  average time/residue: 0.3348
  time to fit residues: 46.9803
Evaluate side-chains
  145 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 117
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  456 SER
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  497 ARG
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   28 ASN
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   19 LYS
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   35 VAL
Chi-restraints excluded: chain H residue   50 SER
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  110 HIS
Chi-restraints excluded: chain B residue  468 GLU
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  553 THR
Chi-restraints excluded: chain B residue  554 ASP
Chi-restraints excluded: chain B residue  572 ILE
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   95 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   19 LYS
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain F residue  110 HIS
Chi-restraints excluded: chain F residue  117 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 46 optimal weight:    0.0980
   chunk 60 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 53 optimal weight:    0.1980
   chunk 19 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
L  28 ASN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 473 GLN
B 491 ASN
F   6 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.142820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.123321 restraints weight = 29564.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 3.67
r_work: 0.3454 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3452
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3452 r_free = 0.3452    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3452 r_free = 0.3452    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3452
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6090  Z= 0.183
  Angle     :  0.586   6.429   8330  Z= 0.304
  Chirality :  0.045   0.164    918
  Planarity :  0.005   0.058   1060
  Dihedral  :  5.865  56.249    852
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 17.51 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.30), residues: 774
  helix:  None (None), residues: 0
  sheet:  0.28 (0.28), residues: 348
  loop : -0.88 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 449 
 TYR   0.011   0.002   TYR L  87 
 PHE   0.009   0.002   PHE L 101 
 TRP   0.017   0.002   TRP B 561 
 HIS   0.005   0.001   HIS E  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 6086)
  covalent geometry    : angle       0.58631 ( 8322)
  SS BOND              : bond        0.00152 (    4)
  SS BOND              : angle       0.55769 (    8)
  hydrogen bonds       : bond        0.02836 (   82)
  hydrogen bonds       : angle       4.96683 (  204)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 120
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A  497 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7072 (pmm-80)
REVERT: H   19 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8193 (ttpp)
REVERT: B  455 ARG cc_start: 0.7800 (mtm-85) cc_final: 0.7584 (mtt180)
REVERT: B  530 LEU cc_start: 0.5609 (OUTLIER) cc_final: 0.5005 (pt)
REVERT: E   49 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7553 (mp)
REVERT: F   19 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8032 (ttpp)
  outliers start: 36
  outliers final: 23
  residues processed: 134
  average time/residue: 0.3306
  time to fit residues: 47.8411
Evaluate side-chains
  147 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 119
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  456 SER
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  497 ARG
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   28 ASN
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   19 LYS
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   35 VAL
Chi-restraints excluded: chain H residue   50 SER
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  110 HIS
Chi-restraints excluded: chain B residue  468 GLU
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  553 THR
Chi-restraints excluded: chain B residue  572 ILE
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   95 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   19 LYS
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain F residue  110 HIS
Chi-restraints excluded: chain F residue  117 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 72 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0050
   chunk 39 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
A 507 GLN
L  28 ASN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 473 GLN
B 491 ASN
F   6 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.142741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.122956 restraints weight = 30924.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 3.79
r_work: 0.3444 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3439
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3439
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6090  Z= 0.189
  Angle     :  0.594   6.468   8330  Z= 0.308
  Chirality :  0.045   0.164    918
  Planarity :  0.005   0.058   1060
  Dihedral  :  5.936  57.981    852
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 17.82 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.57 (0.30), residues: 774
  helix:  None (None), residues: 0
  sheet:  0.25 (0.28), residues: 348
  loop : -0.91 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 449 
 TYR   0.012   0.002   TYR L  87 
 PHE   0.009   0.002   PHE L 101 
 TRP   0.018   0.002   TRP B 561 
 HIS   0.004   0.001   HIS E  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 6086)
  covalent geometry    : angle       0.59368 ( 8322)
  SS BOND              : bond        0.00149 (    4)
  SS BOND              : angle       0.59081 (    8)
  hydrogen bonds       : bond        0.02900 (   82)
  hydrogen bonds       : angle       5.02000 (  204)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 123
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  497 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7092 (pmm-80)
REVERT: H   19 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8183 (ttpp)
REVERT: B  455 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7598 (mtt180)
REVERT: B  530 LEU cc_start: 0.5657 (OUTLIER) cc_final: 0.5045 (pt)
REVERT: E   49 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7607 (mp)
REVERT: F   19 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8057 (ttpp)
  outliers start: 34
  outliers final: 25
  residues processed: 137
  average time/residue: 0.3211
  time to fit residues: 47.4978
Evaluate side-chains
  151 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 121
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  456 SER
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  497 ARG
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   28 ASN
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   19 LYS
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   35 VAL
Chi-restraints excluded: chain H residue   50 SER
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  110 HIS
Chi-restraints excluded: chain B residue  456 SER
Chi-restraints excluded: chain B residue  468 GLU
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  553 THR
Chi-restraints excluded: chain B residue  554 ASP
Chi-restraints excluded: chain B residue  572 ILE
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   95 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   19 LYS
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain F residue  110 HIS
Chi-restraints excluded: chain F residue  117 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0870
   chunk 1 optimal weight:    0.1980
   chunk 51 optimal weight:    0.3980
   chunk 25 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
L  28 ASN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 473 GLN
B 491 ASN
F   6 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.143555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.124785 restraints weight = 25299.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 3.38
r_work: 0.3489 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3482
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3482 r_free = 0.3482    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3482 r_free = 0.3482    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3482
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   6090  Z= 0.151
  Angle     :  0.559   6.241   8330  Z= 0.290
  Chirality :  0.044   0.162    918
  Planarity :  0.005   0.056   1060
  Dihedral  :  5.786  57.870    852
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  5.52 %
    Allowed  : 18.30 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.30), residues: 774
  helix:  None (None), residues: 0
  sheet:  0.34 (0.28), residues: 344
  loop : -0.93 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 449 
 TYR   0.011   0.002   TYR F  60 
 PHE   0.008   0.002   PHE L 101 
 TRP   0.021   0.002   TRP B 561 
 HIS   0.004   0.001   HIS E  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 6086)
  covalent geometry    : angle       0.55940 ( 8322)
  SS BOND              : bond        0.00140 (    4)
  SS BOND              : angle       0.49787 (    8)
  hydrogen bonds       : bond        0.02681 (   82)
  hydrogen bonds       : angle       4.89311 (  204)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 123
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  497 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7028 (pmm-80)
REVERT: H   19 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8160 (ttpp)
REVERT: B  455 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.7551 (mtt180)
REVERT: B  530 LEU cc_start: 0.5572 (OUTLIER) cc_final: 0.4986 (pt)
REVERT: E   49 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7575 (mp)
REVERT: F   19 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8001 (ttpp)
  outliers start: 33
  outliers final: 24
  residues processed: 138
  average time/residue: 0.3108
  time to fit residues: 46.3216
Evaluate side-chains
  151 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 122
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  456 SER
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  497 ARG
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   19 LYS
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   35 VAL
Chi-restraints excluded: chain H residue   50 SER
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  110 HIS
Chi-restraints excluded: chain B residue  456 SER
Chi-restraints excluded: chain B residue  468 GLU
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  553 THR
Chi-restraints excluded: chain B residue  554 ASP
Chi-restraints excluded: chain B residue  572 ILE
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   95 SER
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   19 LYS
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain F residue  110 HIS
Chi-restraints excluded: chain F residue  117 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 67 optimal weight:    0.5980
   chunk 24 optimal weight:    0.4980
   chunk 46 optimal weight:    0.1980
   chunk 15 optimal weight:    0.4980
   chunk 71 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0670
   overall best weight:    0.3718

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 473 GLN
B 491 ASN
F   6 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.143775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.123468 restraints weight = 38571.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 4.76
r_work: 0.3430 rms_B_bonded: 4.65 restraints_weight: 0.5000
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3423
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3423 r_free = 0.3423    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3423 r_free = 0.3423    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3423
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6090  Z= 0.140
  Angle     :  0.552   6.191   8330  Z= 0.285
  Chirality :  0.043   0.160    918
  Planarity :  0.005   0.060   1060
  Dihedral  :  5.633  57.072    852
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 18.30 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.51 (0.30), residues: 774
  helix:  None (None), residues: 0
  sheet:  0.27 (0.28), residues: 348
  loop : -0.85 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  67 
 TYR   0.011   0.001   TYR B 546 
 PHE   0.008   0.001   PHE L 101 
 TRP   0.023   0.002   TRP B 561 
 HIS   0.004   0.001   HIS E  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6086)
  covalent geometry    : angle       0.55228 ( 8322)
  SS BOND              : bond        0.00167 (    4)
  SS BOND              : angle       0.49458 (    8)
  hydrogen bonds       : bond        0.02608 (   82)
  hydrogen bonds       : angle       4.76949 (  204)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 120
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A  497 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7102 (pmm-80)
REVERT: B  455 ARG cc_start: 0.7845 (mtm-85) cc_final: 0.7629 (mtt180)
REVERT: B  530 LEU cc_start: 0.5563 (OUTLIER) cc_final: 0.4915 (pt)
REVERT: E   49 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7581 (mp)
REVERT: F   19 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8049 (ttpp)
  outliers start: 30
  outliers final: 21
  residues processed: 133
  average time/residue: 0.3328
  time to fit residues: 47.6886
Evaluate side-chains
  145 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  456 SER
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  497 ARG
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   35 VAL
Chi-restraints excluded: chain H residue   50 SER
Chi-restraints excluded: chain H residue   64 PHE
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  110 HIS
Chi-restraints excluded: chain B residue  456 SER
Chi-restraints excluded: chain B residue  468 GLU
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  553 THR
Chi-restraints excluded: chain B residue  572 ILE
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   95 SER
Chi-restraints excluded: chain F residue   19 LYS
Chi-restraints excluded: chain F residue  110 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 57 optimal weight:    0.8980
   chunk 0 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0470
   chunk 38 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0980
   chunk 19 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 473 GLN
B 491 ASN
F   6 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.142848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.123689 restraints weight = 27377.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 3.51
r_work: 0.3462 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3469
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3469
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6090  Z= 0.176
  Angle     :  0.584   6.397   8330  Z= 0.302
  Chirality :  0.044   0.163    918
  Planarity :  0.005   0.063   1060
  Dihedral  :  5.850  59.431    852
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 18.93 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.57 (0.30), residues: 774
  helix:  None (None), residues: 0
  sheet:  0.23 (0.28), residues: 348
  loop : -0.88 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  67 
 TYR   0.012   0.002   TYR B 546 
 PHE   0.009   0.002   PHE L 101 
 TRP   0.025   0.002   TRP B 561 
 HIS   0.004   0.001   HIS E  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 6086)
  covalent geometry    : angle       0.58355 ( 8322)
  SS BOND              : bond        0.00147 (    4)
  SS BOND              : angle       0.53096 (    8)
  hydrogen bonds       : bond        0.02797 (   82)
  hydrogen bonds       : angle       4.91430 (  204)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 119
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A  461 TRP cc_start: 0.7748 (t-100) cc_final: 0.7503 (t-100)
REVERT: A  497 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7073 (pmm-80)
REVERT: B  455 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7585 (mtt180)
REVERT: B  530 LEU cc_start: 0.5602 (OUTLIER) cc_final: 0.4991 (pt)
REVERT: E   49 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7599 (mp)
REVERT: F   19 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7977 (ttpp)
  outliers start: 27
  outliers final: 22
  residues processed: 133
  average time/residue: 0.3272
  time to fit residues: 47.0199
Evaluate side-chains
  143 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  456 SER
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  497 ARG
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   35 VAL
Chi-restraints excluded: chain H residue   50 SER
Chi-restraints excluded: chain H residue   64 PHE
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  110 HIS
Chi-restraints excluded: chain B residue  456 SER
Chi-restraints excluded: chain B residue  468 GLU
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  553 THR
Chi-restraints excluded: chain B residue  572 ILE
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   95 SER
Chi-restraints excluded: chain F residue   19 LYS
Chi-restraints excluded: chain F residue   51 ILE
Chi-restraints excluded: chain F residue  110 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 46 optimal weight:    0.4980
   chunk 10 optimal weight:    0.7980
   chunk 28 optimal weight:    0.4980
   chunk 54 optimal weight:    6.9990
   chunk 14 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 473 GLN
B 491 ASN
F   6 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.142299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.122670 restraints weight = 30107.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 3.71
r_work: 0.3442 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3439
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3439
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   6090  Z= 0.200
  Angle     :  0.607   6.599   8330  Z= 0.314
  Chirality :  0.045   0.164    918
  Planarity :  0.005   0.064   1060
  Dihedral  :  6.016  61.708    852
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 18.77 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.30), residues: 774
  helix:  None (None), residues: 0
  sheet:  0.21 (0.28), residues: 348
  loop : -0.91 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 449 
 TYR   0.014   0.002   TYR B 546 
 PHE   0.008   0.002   PHE L 101 
 TRP   0.026   0.002   TRP A 561 
 HIS   0.004   0.001   HIS E  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 6086)
  covalent geometry    : angle       0.60687 ( 8322)
  SS BOND              : bond        0.00156 (    4)
  SS BOND              : angle       0.57914 (    8)
  hydrogen bonds       : bond        0.02920 (   82)
  hydrogen bonds       : angle       5.01382 (  204)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2566.62 seconds
wall clock time: 44 minutes 35.46 seconds (2675.46 seconds total)