Starting phenix.real_space_refine
on Mon Jul 28 14:41:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xnp_33322/07_2025/7xnp_33322.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xnp_33322/07_2025/7xnp_33322.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xnp_33322/07_2025/7xnp_33322.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xnp_33322/07_2025/7xnp_33322.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xnp_33322/07_2025/7xnp_33322.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xnp_33322/07_2025/7xnp_33322.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
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: 5
    Type Number    sf(0)   Gaussians
     P     245      5.49       5
     S      12      5.16       5
     C    6107      2.51       5
     N    2058      2.21       5
     O    2521      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10943
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 800
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 750
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2535
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 2535
          Classifications: {'DNA': 123}
          Link IDs: {'rna3p': 122}
    Chain: "J"
      Number of atoms: 2505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 2505
          Classifications: {'DNA': 123}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 122}
  Time building chain proxies: 6.67, per 1000 atoms: 0.61
  Number of scatterers: 10943
  At special positions: 0
  Unit cell: (97.836, 123.084, 109.408, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      12     16.00
     P     245     15.00
     O    2521      8.00
     N    2058      7.00
     C    6107      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.61
  Conformation dependent library (CDL) restraints added in 670.5 milliseconds
  

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1392

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 9 sheets defined
      72.0% alpha, 2.9% beta
      123 base pairs and 227 stacking pairs defined.
    Time for finding SS restraints: 4.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.580A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.804A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.570A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.437A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.517A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.504A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 121
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.653A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.814A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.624A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.302A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.550A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 34 through 46
      removed outlier: 3.627A  pdb=" N   VAL H  38 " --> pdb=" O   TYR H  34 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 52 through 81
      removed outlier: 3.522A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.098A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.216A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.869A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 6.938A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    395 hydrogen bonds defined for protein.
    1173 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      318 hydrogen bonds
      632 hydrogen bond angles
      0 basepair planarities
      123 basepair parallelities
      227 stacking parallelities
  Total time for adding SS restraints: 3.79

  Time building geometry restraints manager: 3.11 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2006
        1.33 -     1.45: 3792
        1.45 -     1.57: 5324
        1.57 -     1.69: 489
        1.69 -     1.81: 22
  Bond restraints: 11633
  Sorted by residual:
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.480 -0.058 3.00e-02 1.11e+03 3.77e+00
  bond pdb=" C3'  DG I   4 "
       pdb=" O3'  DG I   4 "
    ideal  model  delta    sigma   weight residual
    1.422  1.477 -0.055 3.00e-02 1.11e+03 3.39e+00
  bond pdb=" C3'  DC J  21 "
       pdb=" O3'  DC J  21 "
    ideal  model  delta    sigma   weight residual
    1.422  1.472 -0.050 3.00e-02 1.11e+03 2.82e+00
  bond pdb=" C   LEU E  65 "
       pdb=" N   PRO E  66 "
    ideal  model  delta    sigma   weight residual
    1.335  1.355 -0.019 1.36e-02 5.41e+03 2.04e+00
  bond pdb=" CB  THR H  93 "
       pdb=" CG2 THR H  93 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 2.02e+00
  ... (remaining 11628 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 16036
        1.71 -     3.41: 678
        3.41 -     5.12: 35
        5.12 -     6.82: 6
        6.82 -     8.53: 7
  Bond angle restraints: 16762
  Sorted by residual:
  angle pdb=" N   GLY H 101 "
        pdb=" CA  GLY H 101 "
        pdb=" C   GLY H 101 "
      ideal   model   delta    sigma   weight residual
     113.18  121.70   -8.52 2.37e+00 1.78e-01 1.29e+01
  angle pdb=" N   GLU H 110 "
        pdb=" CA  GLU H 110 "
        pdb=" CB  GLU H 110 "
      ideal   model   delta    sigma   weight residual
     110.40  116.03   -5.63 1.63e+00 3.76e-01 1.19e+01
  angle pdb=" C3'  DG I   4 "
        pdb=" O3'  DG I   4 "
        pdb=" P    DT I   5 "
      ideal   model   delta    sigma   weight residual
     120.20  124.96   -4.76 1.50e+00 4.44e-01 1.01e+01
  angle pdb=" C3'  DT J -17 "
        pdb=" O3'  DT J -17 "
        pdb=" P    DT J -16 "
      ideal   model   delta    sigma   weight residual
     120.20  124.87   -4.67 1.50e+00 4.44e-01 9.69e+00
  angle pdb=" N   GLY D 101 "
        pdb=" CA  GLY D 101 "
        pdb=" C   GLY D 101 "
      ideal   model   delta    sigma   weight residual
     113.18  120.44   -7.26 2.37e+00 1.78e-01 9.38e+00
  ... (remaining 16757 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.05: 5149
       35.05 -    70.10: 1191
       70.10 -   105.15: 17
      105.15 -   140.20: 1
      140.20 -   175.25: 2
  Dihedral angle restraints: 6360
    sinusoidal: 4201
      harmonic: 2159
  Sorted by residual:
  dihedral pdb=" CA  PRO H 100 "
           pdb=" C   PRO H 100 "
           pdb=" N   GLY H 101 "
           pdb=" CA  GLY H 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.08  -20.92     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   35.25 -175.25     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DC J  21 "
           pdb=" C3'  DC J  21 "
           pdb=" O3'  DC J  21 "
           pdb=" P    DC J  22 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   72.16  147.84     1      3.50e+01 8.16e-04 1.45e+01
  ... (remaining 6357 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1503
       0.051 -    0.101: 337
       0.101 -    0.152: 64
       0.152 -    0.203: 7
       0.203 -    0.254: 2
  Chirality restraints: 1913
  Sorted by residual:
  chirality pdb=" CA  GLU H 110 "
            pdb=" N   GLU H 110 "
            pdb=" C   GLU H 110 "
            pdb=" CB  GLU H 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" P    DC J  22 "
            pdb=" OP1  DC J  22 "
            pdb=" OP2  DC J  22 "
            pdb=" O5'  DC J  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.56   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CB  VAL D 108 "
            pdb=" CA  VAL D 108 "
            pdb=" CG1 VAL D 108 "
            pdb=" CG2 VAL D 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.43e-01
  ... (remaining 1910 not shown)

  Planarity restraints: 1271
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C  79 "   -0.046 5.00e-02 4.00e+02   7.02e-02 7.89e+00
        pdb=" N   PRO C  80 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO C  80 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO C  80 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "    0.044 5.00e-02 4.00e+02   6.64e-02 7.05e+00
        pdb=" N   PRO G  80 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I -26 "    0.031 2.00e-02 2.50e+03   1.60e-02 5.75e+00
        pdb=" N1   DC I -26 "   -0.032 2.00e-02 2.50e+03
        pdb=" C2   DC I -26 "    0.001 2.00e-02 2.50e+03
        pdb=" O2   DC I -26 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3   DC I -26 "    0.003 2.00e-02 2.50e+03
        pdb=" C4   DC I -26 "    0.005 2.00e-02 2.50e+03
        pdb=" N4   DC I -26 "    0.011 2.00e-02 2.50e+03
        pdb=" C5   DC I -26 "   -0.008 2.00e-02 2.50e+03
        pdb=" C6   DC I -26 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1268 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2503
        2.82 -     3.34: 8917
        3.34 -     3.86: 21917
        3.86 -     4.38: 25725
        4.38 -     4.90: 36485
  Nonbonded interactions: 95547
  Sorted by model distance:
  nonbonded pdb=" OG1 THR H  87 "
            pdb=" OE1 GLU H  90 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" N2   DG I -21 "
            pdb=" O2   DC J  21 "
     model   vdw
     2.326 2.496
  nonbonded pdb=" OG1 THR D  87 "
            pdb=" OE1 GLU D  90 "
     model   vdw
     2.371 3.040
  nonbonded pdb=" OH  TYR E  99 "
            pdb=" OE1 GLU E 133 "
     model   vdw
     2.376 3.040
  nonbonded pdb=" NH2 ARG C  88 "
            pdb=" O   VAL C 100 "
     model   vdw
     2.387 3.120
  ... (remaining 95542 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 43 through 133)
  selection = (chain 'E' and resid 43 through 133)
}
ncs_group {
  reference = (chain 'B' and resid 23 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 14 through 117)
}
ncs_group {
  reference = chain 'D'
  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=1.00 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:             0.330
  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:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     29.700
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:11.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  11633  Z= 0.216
  Angle     :  0.748   8.527  16762  Z= 0.442
  Chirality :  0.045   0.254   1913
  Planarity :  0.006   0.070   1271
  Dihedral  : 27.194 175.251   4968
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.27), residues: 730
  helix: -0.52 (0.19), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.46 (0.39), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS F  75 
 PHE   0.014   0.002   PHE H  67 
 TYR   0.019   0.002   TYR B  88 
 ARG   0.008   0.000   ARG E  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10344 (  713)
  hydrogen bonds       : angle       4.30712 ( 1805)
  covalent geometry    : bond        0.00469 (11633)
  covalent geometry    : angle       0.74815 (16762)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.846 
Fit side-chains
REVERT: A  118 THR cc_start: 0.8782 (m) cc_final: 0.8542 (m)
REVERT: C   95 LYS cc_start: 0.7302 (mmpt) cc_final: 0.7097 (mtmt)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 1.7582
  time to fit residues: 196.3298
Evaluate side-chains
  91 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 72 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 75 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0770
   chunk 56 optimal weight:    0.9980
   chunk 87 optimal weight:    5.9990
   overall best weight:    0.9942

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
B  93 GLN
C  89 ASN
G  24 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.192516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.160717 restraints weight = 10519.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3775 rms_B_bonded: 0.73
r_work: 0.3538 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3388 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.0990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11633  Z= 0.161
  Angle     :  0.564   7.467  16762  Z= 0.341
  Chirality :  0.035   0.144   1913
  Planarity :  0.004   0.051   1271
  Dihedral  : 30.389 175.038   3504
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  7.92 %
    Favored  : 90.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.29), residues: 730
  helix:  1.15 (0.21), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.37 (0.40), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.011   0.002   PHE A  67 
 TYR   0.015   0.001   TYR G  57 
 ARG   0.007   0.000   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04234 (  713)
  hydrogen bonds       : angle       2.93544 ( 1805)
  covalent geometry    : bond        0.00350 (11633)
  covalent geometry    : angle       0.56408 (16762)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.895 
Fit side-chains
REVERT: C   95 LYS cc_start: 0.7402 (mmpt) cc_final: 0.7071 (mmpt)
REVERT: E   64 LYS cc_start: 0.8376 (mptm) cc_final: 0.8100 (mptt)
REVERT: E   76 GLN cc_start: 0.7900 (tt0) cc_final: 0.7506 (pt0)
REVERT: G   92 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7823 (mt-10)
REVERT: H   68 GLU cc_start: 0.7730 (tp30) cc_final: 0.7523 (tm-30)
  outliers start: 8
  outliers final: 4
  residues processed: 103
  average time/residue: 1.6659
  time to fit residues: 181.6257
Evaluate side-chains
  100 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain H residue   44 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 77 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 19 optimal weight:    5.9990
   chunk 95 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9990
   chunk 94 optimal weight:   10.0000
   chunk 82 optimal weight:    7.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
C  89 ASN
D  92 GLN
D 106 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.188680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.156470 restraints weight = 10474.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 0.67
r_work: 0.3527 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.1219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  11633  Z= 0.216
  Angle     :  0.609   8.260  16762  Z= 0.363
  Chirality :  0.038   0.142   1913
  Planarity :  0.005   0.049   1271
  Dihedral  : 30.626 173.021   3504
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  :  9.05 %
    Favored  : 88.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.29), residues: 730
  helix:  1.57 (0.21), residues: 539
  sheet:  None (None), residues: 0
  loop : -0.38 (0.39), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  46 
 PHE   0.012   0.002   PHE F  61 
 TYR   0.014   0.002   TYR D  37 
 ARG   0.007   0.001   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04774 (  713)
  hydrogen bonds       : angle       2.94634 ( 1805)
  covalent geometry    : bond        0.00490 (11633)
  covalent geometry    : angle       0.60911 (16762)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
REVERT: C   77 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6840 (tpt-90)
REVERT: C   95 LYS cc_start: 0.7367 (mmpt) cc_final: 0.7053 (mmpt)
REVERT: D   90 GLU cc_start: 0.7212 (mp0) cc_final: 0.7005 (mp0)
REVERT: D  105 LYS cc_start: 0.6789 (mttt) cc_final: 0.6565 (mmtp)
REVERT: E   64 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8069 (mptt)
REVERT: E   76 GLN cc_start: 0.7801 (tt0) cc_final: 0.7426 (pt0)
REVERT: E  120 MET cc_start: 0.7968 (mtt) cc_final: 0.7574 (mtt)
REVERT: F   77 LYS cc_start: 0.8421 (mttp) cc_final: 0.8152 (mttp)
REVERT: F   91 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7793 (ttmm)
REVERT: G   64 GLU cc_start: 0.7477 (tp30) cc_final: 0.7254 (tp30)
REVERT: G   92 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7787 (mt-10)
REVERT: H   68 GLU cc_start: 0.7849 (tp30) cc_final: 0.7627 (tm-30)
REVERT: H   90 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6138 (mp0)
  outliers start: 16
  outliers final: 8
  residues processed: 110
  average time/residue: 1.7740
  time to fit residues: 205.8664
Evaluate side-chains
  113 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain C residue   32 ARG
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0050
   chunk 49 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   overall best weight:    1.3398

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
C  89 ASN
D  92 GLN
E 125 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.189301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.158623 restraints weight = 10441.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 0.74
r_work: 0.3528 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3378 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.1241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11633  Z= 0.183
  Angle     :  0.590   8.110  16762  Z= 0.355
  Chirality :  0.037   0.140   1913
  Planarity :  0.004   0.047   1271
  Dihedral  : 30.621 173.105   3504
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 10.18 %
    Favored  : 86.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.29), residues: 730
  helix:  1.76 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.39 (0.40), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D 106 
 PHE   0.012   0.002   PHE F  61 
 TYR   0.015   0.001   TYR G  57 
 ARG   0.006   0.000   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04577 (  713)
  hydrogen bonds       : angle       2.89251 ( 1805)
  covalent geometry    : bond        0.00405 (11633)
  covalent geometry    : angle       0.59026 (16762)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
REVERT: C   77 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6766 (tpt-90)
REVERT: C   95 LYS cc_start: 0.7331 (mmpt) cc_final: 0.7010 (mmpt)
REVERT: D   90 GLU cc_start: 0.7259 (mp0) cc_final: 0.7008 (mp0)
REVERT: D  105 LYS cc_start: 0.6814 (mttt) cc_final: 0.6559 (mmtp)
REVERT: E   64 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8063 (mptt)
REVERT: E   76 GLN cc_start: 0.7819 (tt0) cc_final: 0.7419 (pt0)
REVERT: E  120 MET cc_start: 0.7949 (mtt) cc_final: 0.7537 (mtt)
REVERT: F   77 LYS cc_start: 0.8449 (mttp) cc_final: 0.8194 (mttp)
REVERT: F   91 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7790 (ttmm)
REVERT: G   64 GLU cc_start: 0.7512 (tp30) cc_final: 0.7289 (tp30)
REVERT: G   92 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7812 (mt-10)
REVERT: H   68 GLU cc_start: 0.7850 (tp30) cc_final: 0.7630 (tm-30)
REVERT: H   90 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6218 (mp0)
  outliers start: 18
  outliers final: 10
  residues processed: 108
  average time/residue: 1.7935
  time to fit residues: 204.8124
Evaluate side-chains
  115 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain C residue   32 ARG
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 29 optimal weight:    8.9990
   chunk 21 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 92 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 68 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
A  76 GLN
A  93 GLN
B  75 HIS
C  89 ASN
D  92 GLN
E 125 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.186158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.153531 restraints weight = 10471.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 0.68
r_work: 0.3476 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3332 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  11633  Z= 0.272
  Angle     :  0.671   8.621  16762  Z= 0.394
  Chirality :  0.042   0.151   1913
  Planarity :  0.006   0.051   1271
  Dihedral  : 30.945 171.752   3504
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  :  9.85 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.29), residues: 730
  helix:  1.51 (0.21), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.58 (0.39), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS D 106 
 PHE   0.014   0.003   PHE F  61 
 TYR   0.015   0.002   TYR G  57 
 ARG   0.007   0.001   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05366 (  713)
  hydrogen bonds       : angle       3.06855 ( 1805)
  covalent geometry    : bond        0.00625 (11633)
  covalent geometry    : angle       0.67053 (16762)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
REVERT: B   52 GLU cc_start: 0.7500 (tp30) cc_final: 0.7075 (mp0)
REVERT: C   95 LYS cc_start: 0.7581 (mmpt) cc_final: 0.7357 (mmpt)
REVERT: D   90 GLU cc_start: 0.7260 (mp0) cc_final: 0.6999 (mp0)
REVERT: D  105 LYS cc_start: 0.6844 (mttt) cc_final: 0.6562 (mmtp)
REVERT: F   91 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7865 (ttmm)
REVERT: F   92 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7169 (ttp80)
REVERT: G   92 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7820 (mt-10)
REVERT: H   90 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6047 (mp0)
  outliers start: 23
  outliers final: 11
  residues processed: 117
  average time/residue: 1.7885
  time to fit residues: 220.6570
Evaluate side-chains
  112 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   32 ARG
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 58 optimal weight:    3.9990
   chunk 88 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 79 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0870
   chunk 76 optimal weight:    4.9990
   overall best weight:    2.6166

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
C  89 ASN
D  92 GLN
E 125 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.186727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.153788 restraints weight = 10497.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 0.68
r_work: 0.3496 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3354 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  11633  Z= 0.250
  Angle     :  0.647   8.537  16762  Z= 0.382
  Chirality :  0.040   0.153   1913
  Planarity :  0.005   0.048   1271
  Dihedral  : 30.884 172.735   3504
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 11.47 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.29), residues: 730
  helix:  1.59 (0.21), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.63 (0.39), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS D 106 
 PHE   0.014   0.002   PHE F  61 
 TYR   0.015   0.002   TYR G  57 
 ARG   0.009   0.001   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05075 (  713)
  hydrogen bonds       : angle       2.99060 ( 1805)
  covalent geometry    : bond        0.00573 (11633)
  covalent geometry    : angle       0.64654 (16762)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
REVERT: B   52 GLU cc_start: 0.7389 (tp30) cc_final: 0.6996 (mp0)
REVERT: C   95 LYS cc_start: 0.7607 (mmpt) cc_final: 0.7371 (mmpt)
REVERT: D   90 GLU cc_start: 0.7244 (mp0) cc_final: 0.6978 (mp0)
REVERT: E   64 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8081 (mptt)
REVERT: E   90 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7990 (mmm)
REVERT: E  120 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7831 (mtt)
REVERT: F   77 LYS cc_start: 0.8439 (mttp) cc_final: 0.8185 (mttp)
REVERT: F   91 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7847 (ttmm)
REVERT: G   92 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7791 (mt-10)
REVERT: H   90 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6544 (mp0)
  outliers start: 22
  outliers final: 15
  residues processed: 109
  average time/residue: 1.7856
  time to fit residues: 205.1133
Evaluate side-chains
  116 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   32 ARG
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   83 ARG
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   90 MET
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue  110 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 60 optimal weight:    0.5980
   chunk 72 optimal weight:   10.0000
   chunk 33 optimal weight:    0.5980
   chunk 92 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 52 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 85 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    2.8386

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
C  89 ASN
D  92 GLN
E 125 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.186219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.153606 restraints weight = 10618.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 0.65
r_work: 0.3487 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3342 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  11633  Z= 0.264
  Angle     :  0.665   8.731  16762  Z= 0.392
  Chirality :  0.041   0.152   1913
  Planarity :  0.005   0.048   1271
  Dihedral  : 30.941 172.532   3504
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 11.95 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.29), residues: 730
  helix:  1.53 (0.21), residues: 539
  sheet:  None (None), residues: 0
  loop : -0.64 (0.39), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS D 106 
 PHE   0.015   0.002   PHE F  61 
 TYR   0.017   0.002   TYR G  57 
 ARG   0.008   0.001   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05330 (  713)
  hydrogen bonds       : angle       3.04537 ( 1805)
  covalent geometry    : bond        0.00609 (11633)
  covalent geometry    : angle       0.66532 (16762)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7779 (tt0)
REVERT: B   52 GLU cc_start: 0.7421 (tp30) cc_final: 0.6985 (mp0)
REVERT: C   95 LYS cc_start: 0.7563 (mmpt) cc_final: 0.6749 (mtmt)
REVERT: D   90 GLU cc_start: 0.7255 (mp0) cc_final: 0.6990 (mp0)
REVERT: F   91 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7858 (ttmm)
REVERT: F   92 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7260 (ttp80)
REVERT: G   92 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7794 (mt-10)
REVERT: H   90 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6056 (mp0)
  outliers start: 27
  outliers final: 19
  residues processed: 109
  average time/residue: 1.8929
  time to fit residues: 217.3875
Evaluate side-chains
  118 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   32 ARG
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   83 ARG
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   90 MET
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   45 VAL
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue  110 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 72 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 59 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 33 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
C  89 ASN
D  92 GLN
E 125 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.187024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.154985 restraints weight = 10506.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3725 rms_B_bonded: 0.61
r_work: 0.3519 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  11633  Z= 0.209
  Angle     :  0.640   8.516  16762  Z= 0.380
  Chirality :  0.039   0.147   1913
  Planarity :  0.005   0.046   1271
  Dihedral  : 30.935 172.773   3504
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 12.28 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.29), residues: 730
  helix:  1.62 (0.21), residues: 539
  sheet:  None (None), residues: 0
  loop : -0.60 (0.39), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS D 106 
 PHE   0.014   0.002   PHE F  61 
 TYR   0.020   0.002   TYR G  57 
 ARG   0.008   0.001   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05160 (  713)
  hydrogen bonds       : angle       3.00031 ( 1805)
  covalent geometry    : bond        0.00466 (11633)
  covalent geometry    : angle       0.63976 (16762)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7740 (tt0)
REVERT: B   52 GLU cc_start: 0.7344 (tp30) cc_final: 0.6935 (mp0)
REVERT: C   95 LYS cc_start: 0.7562 (mmpt) cc_final: 0.6759 (mtmt)
REVERT: D   90 GLU cc_start: 0.7213 (mp0) cc_final: 0.6938 (mp0)
REVERT: F   77 LYS cc_start: 0.8414 (mttp) cc_final: 0.8169 (mttp)
REVERT: F   91 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7832 (ttmm)
REVERT: F   92 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7211 (ttp80)
REVERT: G   92 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7757 (mt-10)
REVERT: H   90 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6013 (mp0)
  outliers start: 26
  outliers final: 19
  residues processed: 104
  average time/residue: 2.4374
  time to fit residues: 266.6140
Evaluate side-chains
  118 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 1.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   32 ARG
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   83 ARG
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   90 MET
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   45 VAL
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue  110 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 60 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0270
   chunk 16 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
C  89 ASN
E 125 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.188772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.156877 restraints weight = 10536.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 0.74
r_work: 0.3505 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3362 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.1680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11633  Z= 0.159
  Angle     :  0.604   8.130  16762  Z= 0.365
  Chirality :  0.037   0.296   1913
  Planarity :  0.004   0.044   1271
  Dihedral  : 30.915 172.920   3504
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 12.76 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.30), residues: 730
  helix:  1.89 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.50 (0.41), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  75 
 PHE   0.012   0.002   PHE F  61 
 TYR   0.023   0.002   TYR G  57 
 ARG   0.007   0.001   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04659 (  713)
  hydrogen bonds       : angle       2.89586 ( 1805)
  covalent geometry    : bond        0.00335 (11633)
  covalent geometry    : angle       0.60428 (16762)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
REVERT: B   52 GLU cc_start: 0.7403 (tp30) cc_final: 0.6955 (mp0)
REVERT: C   95 LYS cc_start: 0.7550 (mmpt) cc_final: 0.6740 (mtmt)
REVERT: D   57 SER cc_start: 0.7883 (m) cc_final: 0.7609 (m)
REVERT: D   90 GLU cc_start: 0.7244 (mp0) cc_final: 0.6983 (mp0)
REVERT: E   64 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8045 (mptt)
REVERT: E  120 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7358 (mtt)
REVERT: F   77 LYS cc_start: 0.8437 (mttp) cc_final: 0.8200 (mttp)
REVERT: F   91 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7831 (ttmm)
REVERT: F   92 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7139 (ttp80)
REVERT: G   92 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7808 (mt-10)
REVERT: H   90 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6093 (mp0)
  outliers start: 23
  outliers final: 12
  residues processed: 109
  average time/residue: 1.8257
  time to fit residues: 209.5797
Evaluate side-chains
  117 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain C residue   32 ARG
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   45 VAL
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue  110 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 53 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   chunk 76 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
C  89 ASN
D  92 GLN
E 125 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.188848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.157124 restraints weight = 10414.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 0.61
r_work: 0.3544 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3406 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11633  Z= 0.173
  Angle     :  0.604   8.121  16762  Z= 0.363
  Chirality :  0.037   0.142   1913
  Planarity :  0.004   0.045   1271
  Dihedral  : 30.884 172.275   3504
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 14.54 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.30), residues: 730
  helix:  1.93 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.49 (0.41), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  75 
 PHE   0.012   0.002   PHE F  61 
 TYR   0.019   0.001   TYR G  57 
 ARG   0.008   0.000   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04591 (  713)
  hydrogen bonds       : angle       2.86704 ( 1805)
  covalent geometry    : bond        0.00380 (11633)
  covalent geometry    : angle       0.60391 (16762)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
REVERT: B   52 GLU cc_start: 0.7356 (tp30) cc_final: 0.6941 (mp0)
REVERT: C   95 LYS cc_start: 0.7524 (mmpt) cc_final: 0.6723 (mtmt)
REVERT: D   57 SER cc_start: 0.7892 (m) cc_final: 0.7607 (m)
REVERT: D   90 GLU cc_start: 0.7185 (mp0) cc_final: 0.6929 (mp0)
REVERT: E   64 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8027 (mptt)
REVERT: F   77 LYS cc_start: 0.8426 (mttp) cc_final: 0.8190 (mttp)
REVERT: F   91 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7818 (ttmm)
REVERT: G   92 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7766 (mt-10)
REVERT: H   90 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6161 (mp0)
  outliers start: 16
  outliers final: 10
  residues processed: 103
  average time/residue: 1.7986
  time to fit residues: 195.5571
Evaluate side-chains
  110 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain C residue   32 ARG
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   45 VAL
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue  110 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 32 optimal weight:    7.9990
   chunk 12 optimal weight:    0.5980
   chunk 73 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 68 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
C  89 ASN
D  92 GLN
E 125 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.189344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.157737 restraints weight = 10448.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 0.74
r_work: 0.3513 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3372 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11633  Z= 0.158
  Angle     :  0.591   7.618  16762  Z= 0.358
  Chirality :  0.036   0.146   1913
  Planarity :  0.004   0.046   1271
  Dihedral  : 30.871 172.433   3504
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 13.73 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.30), residues: 730
  helix:  1.98 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.45 (0.41), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS B  75 
 PHE   0.012   0.001   PHE F  61 
 TYR   0.021   0.001   TYR G  57 
 ARG   0.009   0.000   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04520 (  713)
  hydrogen bonds       : angle       2.84700 ( 1805)
  covalent geometry    : bond        0.00334 (11633)
  covalent geometry    : angle       0.59078 (16762)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7825.61 seconds
wall clock time: 135 minutes 59.09 seconds (8159.09 seconds total)