Starting phenix.real_space_refine
on Tue Feb 11 03:08:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ozh_13124/02_2025/7ozh_13124.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ozh_13124/02_2025/7ozh_13124.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ozh_13124/02_2025/7ozh_13124.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ozh_13124/02_2025/7ozh_13124.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ozh_13124/02_2025/7ozh_13124.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ozh_13124/02_2025/7ozh_13124.cif"
  }
  resolution = 3.02
  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=   1.002
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: 3
    Type Number    sf(0)   Gaussians
     C    2410      2.51       5
     N     680      2.21       5
     O     800      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3890
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 389
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 389
          Classifications: {'peptide': 58}
          Link IDs: {'TRANS': 57}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, J
  Residues with excluded nonbonded symmetry interactions: 10
    residue:
      pdb=" N   LYS A  45 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS A  45 " occ=0.50
    residue:
      pdb=" N   LYS B  45 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS B  45 " occ=0.50
    residue:
      pdb=" N   LYS C  45 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS C  45 " occ=0.50
    residue:
      pdb=" N   LYS D  45 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS D  45 " occ=0.50
    residue:
      pdb=" N   LYS E  45 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS E  45 " occ=0.50
    residue:
      pdb=" N   LYS F  45 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS F  45 " occ=0.50
    residue:
      pdb=" N   LYS G  45 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS G  45 " occ=0.50
    residue:
      pdb=" N   LYS H  45 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS H  45 " occ=0.50
    residue:
      pdb=" N   LYS I  45 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS I  45 " occ=0.50
    residue:
      pdb=" N   LYS J  45 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS J  45 " occ=0.50
  Time building chain proxies: 1.73, per 1000 atoms: 0.44
  Number of scatterers: 3890
  At special positions: 0
  Unit cell: (116.55, 76.65, 43.05, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     800      8.00
     N     680      7.00
     C    2410      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 547.1 milliseconds
  

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  960

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 22.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 42
      removed outlier: 6.247A  pdb=" N   GLY A  41 " --> pdb=" O   SER C  42 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   GLY C  41 " --> pdb=" O   SER E  42 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   GLY E  41 " --> pdb=" O   SER G  42 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   GLY G  41 " --> pdb=" O   SER I  42 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49
      removed outlier: 6.507A  pdb=" N   VAL A  48 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   VAL C  48 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   VAL E  48 " --> pdb=" O   VAL G  49 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   VAL G  48 " --> pdb=" O   VAL I  49 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66
    Processing sheet with id=AA4, first strand: chain 'A' and resid 70 through 76
      removed outlier: 6.845A  pdb=" N   THR A  75 " --> pdb=" O   VAL C  74 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   ALA C  76 " --> pdb=" O   THR A  75 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   THR C  75 " --> pdb=" O   VAL E  74 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ALA E  76 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   THR E  75 " --> pdb=" O   VAL G  74 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ALA G  76 " --> pdb=" O   THR E  75 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   THR G  75 " --> pdb=" O   VAL I  74 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ALA I  76 " --> pdb=" O   THR G  75 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 87 through 89
      removed outlier: 6.404A  pdb=" N   ILE A  88 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ILE C  88 " --> pdb=" O   ALA E  89 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ILE E  88 " --> pdb=" O   ALA G  89 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ILE G  88 " --> pdb=" O   ALA I  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 41 through 42
      removed outlier: 6.246A  pdb=" N   GLY B  41 " --> pdb=" O   SER D  42 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   GLY D  41 " --> pdb=" O   SER F  42 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   GLY F  41 " --> pdb=" O   SER H  42 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   GLY H  41 " --> pdb=" O   SER J  42 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 48 through 49
      removed outlier: 6.509A  pdb=" N   VAL B  48 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   VAL D  48 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   VAL F  48 " --> pdb=" O   VAL H  49 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   VAL H  48 " --> pdb=" O   VAL J  49 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 66
    Processing sheet with id=AA9, first strand: chain 'B' and resid 70 through 76
      removed outlier: 6.846A  pdb=" N   THR B  75 " --> pdb=" O   VAL D  74 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ALA D  76 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   THR D  75 " --> pdb=" O   VAL F  74 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ALA F  76 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   THR F  75 " --> pdb=" O   VAL H  74 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ALA H  76 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   THR H  75 " --> pdb=" O   VAL J  74 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ALA J  76 " --> pdb=" O   THR H  75 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 87 through 89
      removed outlier: 6.404A  pdb=" N   ILE B  88 " --> pdb=" O   ALA D  89 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ILE D  88 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ILE F  88 " --> pdb=" O   ALA H  89 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ILE H  88 " --> pdb=" O   ALA J  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    56 hydrogen bonds defined for protein.
    168 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: 0.87

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.20 -     1.28: 690
        1.28 -     1.35: 630
        1.35 -     1.43: 269
        1.43 -     1.51: 1434
        1.51 -     1.58: 877
  Bond restraints: 3900
  Sorted by residual:
  bond pdb=" CA  LYS D  45 "
       pdb=" CB  LYS D  45 "
    ideal  model  delta    sigma   weight residual
    1.535  1.446  0.089 2.02e-02 2.45e+03 1.95e+01
  bond pdb=" CA  LYS H  45 "
       pdb=" CB  LYS H  45 "
    ideal  model  delta    sigma   weight residual
    1.535  1.446  0.089 2.02e-02 2.45e+03 1.94e+01
  bond pdb=" CA  LYS E  45 "
       pdb=" CB  LYS E  45 "
    ideal  model  delta    sigma   weight residual
    1.535  1.446  0.089 2.02e-02 2.45e+03 1.93e+01
  bond pdb=" CA  LYS J  45 "
       pdb=" CB  LYS J  45 "
    ideal  model  delta    sigma   weight residual
    1.535  1.446  0.089 2.02e-02 2.45e+03 1.93e+01
  bond pdb=" CA  LYS G  45 "
       pdb=" CB  LYS G  45 "
    ideal  model  delta    sigma   weight residual
    1.535  1.446  0.089 2.02e-02 2.45e+03 1.93e+01
  ... (remaining 3895 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 3878
        1.27 -     2.54: 1007
        2.54 -     3.81: 285
        3.81 -     5.07: 80
        5.07 -     6.34: 40
  Bond angle restraints: 5290
  Sorted by residual:
  angle pdb=" C   VAL A  52 "
        pdb=" CA  VAL A  52 "
        pdb=" CB  VAL A  52 "
      ideal   model   delta    sigma   weight residual
     111.19  105.91    5.28 1.39e+00 5.18e-01 1.44e+01
  angle pdb=" C   VAL F  52 "
        pdb=" CA  VAL F  52 "
        pdb=" CB  VAL F  52 "
      ideal   model   delta    sigma   weight residual
     111.19  105.93    5.26 1.39e+00 5.18e-01 1.43e+01
  angle pdb=" C   VAL E  52 "
        pdb=" CA  VAL E  52 "
        pdb=" CB  VAL E  52 "
      ideal   model   delta    sigma   weight residual
     111.19  105.94    5.25 1.39e+00 5.18e-01 1.43e+01
  angle pdb=" C   VAL H  52 "
        pdb=" CA  VAL H  52 "
        pdb=" CB  VAL H  52 "
      ideal   model   delta    sigma   weight residual
     111.19  105.94    5.25 1.39e+00 5.18e-01 1.43e+01
  angle pdb=" C   VAL J  52 "
        pdb=" CA  VAL J  52 "
        pdb=" CB  VAL J  52 "
      ideal   model   delta    sigma   weight residual
     111.19  105.94    5.25 1.39e+00 5.18e-01 1.43e+01
  ... (remaining 5285 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     6.25: 1741
        6.25 -    12.49: 419
       12.49 -    18.73: 60
       18.73 -    24.98: 20
       24.98 -    31.22: 10
  Dihedral angle restraints: 2250
    sinusoidal: 710
      harmonic: 1540
  Sorted by residual:
  dihedral pdb=" CA  GLU F  61 "
           pdb=" C   GLU F  61 "
           pdb=" N   GLN F  62 "
           pdb=" CA  GLN F  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.13   18.87     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  GLU G  61 "
           pdb=" C   GLU G  61 "
           pdb=" N   GLN G  62 "
           pdb=" CA  GLN G  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.15   18.85     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  GLU H  61 "
           pdb=" C   GLU H  61 "
           pdb=" N   GLN H  62 "
           pdb=" CA  GLN H  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.15   18.85     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 2247 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 260
       0.045 -    0.089: 241
       0.089 -    0.134: 99
       0.134 -    0.178: 71
       0.178 -    0.222: 39
  Chirality restraints: 710
  Sorted by residual:
  chirality pdb=" CB  VAL H  49 "
            pdb=" CA  VAL H  49 "
            pdb=" CG1 VAL H  49 "
            pdb=" CG2 VAL H  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CB  VAL C  49 "
            pdb=" CA  VAL C  49 "
            pdb=" CG1 VAL C  49 "
            pdb=" CG2 VAL C  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CB  VAL G  49 "
            pdb=" CA  VAL G  49 "
            pdb=" CG1 VAL G  49 "
            pdb=" CG2 VAL G  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 707 not shown)

  Planarity restraints: 660
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B  81 "   -0.014 2.00e-02 2.50e+03   2.78e-02 7.75e+00
        pdb=" C   THR B  81 "    0.048 2.00e-02 2.50e+03
        pdb=" O   THR B  81 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   VAL B  82 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C  81 "    0.014 2.00e-02 2.50e+03   2.78e-02 7.74e+00
        pdb=" C   THR C  81 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   THR C  81 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL C  82 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR I  81 "    0.014 2.00e-02 2.50e+03   2.78e-02 7.73e+00
        pdb=" C   THR I  81 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   THR I  81 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL I  82 "    0.016 2.00e-02 2.50e+03
  ... (remaining 657 not shown)

  Histogram of nonbonded interaction distances:
        2.55 -     3.02: 2504
        3.02 -     3.49: 4006
        3.49 -     3.96: 5893
        3.96 -     4.43: 6914
        4.43 -     4.90: 13870
  Nonbonded interactions: 33187
  Sorted by model distance:
  nonbonded pdb=" N   VAL A  82 "
            pdb=" O   THR C  81 "
     model   vdw
     2.546 3.120
  nonbonded pdb=" N   VAL C  82 "
            pdb=" O   THR E  81 "
     model   vdw
     2.546 3.120
  nonbonded pdb=" N   VAL E  82 "
            pdb=" O   THR G  81 "
     model   vdw
     2.547 3.120
  nonbonded pdb=" N   VAL B  82 "
            pdb=" O   THR D  81 "
     model   vdw
     2.547 3.120
  nonbonded pdb=" N   VAL H  82 "
            pdb=" O   THR J  81 "
     model   vdw
     2.547 3.120
  ... (remaining 33182 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'J'
}

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=0.50 max=1.00 mean=0.99
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:             2.000
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     12.760
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5861
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      :  0.024   0.101   3900  Z= 1.627
  Angle     :  1.403   6.343   5290  Z= 0.831
  Chirality :  0.088   0.222    710
  Planarity :  0.008   0.028    660
  Dihedral  :  7.442  31.218   1290
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.78 (0.26), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.20), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.005   HIS B  50 
 TYR   0.027   0.011   TYR C  39 

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.440 
Fit side-chains
REVERT: A   80 LYS cc_start: 0.7607 (tttt) cc_final: 0.7045 (pttm)
REVERT: B   80 LYS cc_start: 0.7372 (tttt) cc_final: 0.6660 (tmmt)
REVERT: C   65 ASN cc_start: 0.6524 (m-40) cc_final: 0.6315 (m-40)
REVERT: E   65 ASN cc_start: 0.6603 (m-40) cc_final: 0.6356 (m-40)
REVERT: F   65 ASN cc_start: 0.6373 (m-40) cc_final: 0.5989 (m-40)
REVERT: G   57 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6108 (mp0)
REVERT: G   65 ASN cc_start: 0.6459 (m-40) cc_final: 0.6230 (m110)
REVERT: I   50 HIS cc_start: 0.6096 (m-70) cc_final: 0.5799 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1305
  time to fit residues: 16.5655
Evaluate side-chains
  82 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4951 r_free = 0.4951 target = 0.238416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4724 r_free = 0.4724 target = 0.214113 restraints weight = 5619.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.4730 rms_B_bonded: 3.64
r_work: 0.4632 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.4632
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4631
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4631 r_free = 0.4631    target_work(ls_wunit_k1) = 0.206         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4608 r_free = 0.4608    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4608
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6633
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.038   3900  Z= 0.460
  Angle     :  0.832   5.385   5290  Z= 0.476
  Chirality :  0.053   0.191    710
  Planarity :  0.003   0.014    660
  Dihedral  :  6.586  22.028    580
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 16.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.29 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  :  6.41 %
    Favored  : 90.51 %
  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: -2.03 (0.31), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.54 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS H  50 
 TYR   0.013   0.003   TYR J  39 

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 LYS cc_start: 0.7582 (tttt) cc_final: 0.6978 (pttp)
REVERT: B   80 LYS cc_start: 0.7538 (tttt) cc_final: 0.6759 (pttm)
REVERT: E   80 LYS cc_start: 0.7431 (tttt) cc_final: 0.6886 (tttp)
  outliers start: 12
  outliers final: 10
  residues processed: 122
  average time/residue: 0.1538
  time to fit residues: 23.1930
Evaluate side-chains
  102 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain E residue   50 HIS
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain H residue   50 HIS
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain I residue   70 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 42 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 47 optimal weight:    0.0470
   chunk 6 optimal weight:    6.9990
   chunk 48 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 39 optimal weight:    9.9990
   chunk 46 optimal weight:    2.9990
   chunk 7 optimal weight:   10.0000
   overall best weight:    1.3884

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4996 r_free = 0.4996 target = 0.237502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4773 r_free = 0.4773 target = 0.214183 restraints weight = 5471.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.4781 rms_B_bonded: 3.44
r_work: 0.4687 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.4687
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4666
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4666 r_free = 0.4666    target_work(ls_wunit_k1) = 0.205         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4663 r_free = 0.4663    target_work(ls_wunit_k1) = 0.204         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4663
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6501
moved from start:          0.4118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3900  Z= 0.191
  Angle     :  0.592   4.744   5290  Z= 0.351
  Chirality :  0.051   0.170    710
  Planarity :  0.002   0.012    660
  Dihedral  :  5.651  17.709    580
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 11.28 %
    Favored  : 84.36 %
  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: -2.04 (0.29), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.55 (0.22), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  50 
 TYR   0.009   0.001   TYR G  39 

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.387 
Fit side-chains
REVERT: A   80 LYS cc_start: 0.7442 (tttt) cc_final: 0.6732 (pttp)
REVERT: B   80 LYS cc_start: 0.7386 (tttt) cc_final: 0.6577 (pttm)
REVERT: C   88 ILE cc_start: 0.6896 (pt) cc_final: 0.6664 (pt)
  outliers start: 17
  outliers final: 13
  residues processed: 115
  average time/residue: 0.1199
  time to fit residues: 17.8749
Evaluate side-chains
  110 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   50 HIS
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain H residue   50 HIS
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain J residue   44 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 6 optimal weight:    0.0170
   chunk 13 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 15 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9990
   chunk 33 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   overall best weight:    3.0026

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4891 r_free = 0.4891 target = 0.226256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4663 r_free = 0.4663 target = 0.203294 restraints weight = 5626.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.4657 rms_B_bonded: 3.56
r_work: 0.4566 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.4566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6585
moved from start:          0.4881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3900  Z= 0.307
  Angle     :  0.648   4.981   5290  Z= 0.382
  Chirality :  0.051   0.171    710
  Planarity :  0.003   0.012    660
  Dihedral  :  5.728  16.035    580
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.04 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 13.33 %
    Favored  : 80.51 %
  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: -2.09 (0.30), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.59 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS H  50 
 TYR   0.010   0.002   TYR D  39 

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 LYS cc_start: 0.7445 (tttt) cc_final: 0.6756 (pttp)
REVERT: B   80 LYS cc_start: 0.7307 (tttt) cc_final: 0.6778 (pttp)
REVERT: E   80 LYS cc_start: 0.7380 (tttt) cc_final: 0.6596 (tppt)
REVERT: F   80 LYS cc_start: 0.7020 (tttt) cc_final: 0.6230 (tptt)
  outliers start: 24
  outliers final: 21
  residues processed: 110
  average time/residue: 0.1131
  time to fit residues: 16.4263
Evaluate side-chains
  113 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   50 HIS
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   55 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain H residue   50 HIS
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   48 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   chunk 32 optimal weight:    9.9990
   chunk 10 optimal weight:    2.9990
   chunk 36 optimal weight:   10.0000
   chunk 33 optimal weight:    9.9990
   chunk 37 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4862 r_free = 0.4862 target = 0.222518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4636 r_free = 0.4636 target = 0.199852 restraints weight = 5754.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.4632 rms_B_bonded: 3.62
r_work: 0.4543 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.4543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6647
moved from start:          0.5462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   3900  Z= 0.319
  Angle     :  0.627   5.023   5290  Z= 0.370
  Chirality :  0.051   0.170    710
  Planarity :  0.002   0.013    660
  Dihedral  :  5.777  15.498    580
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 15.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  7.18 %
    Allowed  : 16.41 %
    Favored  : 76.41 %
  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: -2.09 (0.31), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.58 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS F  50 
 TYR   0.012   0.002   TYR F  39 

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 106
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 LYS cc_start: 0.7530 (tttt) cc_final: 0.6868 (pttp)
REVERT: B   80 LYS cc_start: 0.7407 (tttt) cc_final: 0.6904 (pttp)
  outliers start: 28
  outliers final: 21
  residues processed: 117
  average time/residue: 0.1111
  time to fit residues: 17.2355
Evaluate side-chains
  118 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   50 HIS
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   50 HIS
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   48 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 4 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 40 optimal weight:    9.9990
   chunk 17 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4723 r_free = 0.4723 target = 0.208486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.187660 restraints weight = 5677.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.4506 rms_B_bonded: 3.41
r_work: 0.4410 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.4410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6860
moved from start:          0.6317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.061   3900  Z= 0.546
  Angle     :  0.807   5.605   5290  Z= 0.467
  Chirality :  0.055   0.210    710
  Planarity :  0.004   0.017    660
  Dihedral  :  6.527  17.358    580
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 21.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.07 %
    Favored  : 88.93 %
  Rotamer:
    Outliers : 10.26 %
    Allowed  : 15.13 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.26 (0.31), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.71 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS H  50 
 TYR   0.019   0.003   TYR F  39 

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 98
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 LYS cc_start: 0.7610 (tttt) cc_final: 0.7094 (pttp)
REVERT: B   80 LYS cc_start: 0.7518 (tttt) cc_final: 0.7158 (pttp)
REVERT: G   50 HIS cc_start: 0.7736 (OUTLIER) cc_final: 0.7519 (m-70)
REVERT: J   80 LYS cc_start: 0.7487 (tttt) cc_final: 0.6852 (tptt)
REVERT: J   88 ILE cc_start: 0.6940 (pt) cc_final: 0.6455 (pt)
  outliers start: 40
  outliers final: 29
  residues processed: 121
  average time/residue: 0.1102
  time to fit residues: 17.5795
Evaluate side-chains
  119 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 89
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   50 HIS
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   70 VAL
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   50 HIS
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   55 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   50 HIS
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain I residue   38 LEU
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   48 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 8 optimal weight:    0.0870
   chunk 32 optimal weight:    9.9990
   chunk 6 optimal weight:    0.0000
   chunk 2 optimal weight:    9.9990
   chunk 46 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.5766

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4944 r_free = 0.4944 target = 0.229171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4741 r_free = 0.4741 target = 0.207217 restraints weight = 5369.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.4721 rms_B_bonded: 3.36
r_work: 0.4627 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.4627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6709
moved from start:          0.6383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3900  Z= 0.147
  Angle     :  0.525   4.603   5290  Z= 0.315
  Chirality :  0.051   0.153    710
  Planarity :  0.002   0.010    660
  Dihedral  :  5.465  16.932    580
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 21.79 %
    Favored  : 72.56 %
  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: -2.25 (0.30), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.70 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  50 
 TYR   0.006   0.001   TYR G  39 

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 0.435 
Fit side-chains
REVERT: A   80 LYS cc_start: 0.7535 (tttt) cc_final: 0.7074 (pttp)
REVERT: B   80 LYS cc_start: 0.7353 (tttt) cc_final: 0.6917 (pttp)
REVERT: G   80 LYS cc_start: 0.8029 (mttt) cc_final: 0.6776 (ttmt)
  outliers start: 22
  outliers final: 18
  residues processed: 119
  average time/residue: 0.1049
  time to fit residues: 16.7178
Evaluate side-chains
  118 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   50 HIS
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   50 HIS
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain J residue   44 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 24 optimal weight:    6.9990
   chunk 30 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 14 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 46 optimal weight:    8.9990
   chunk 19 optimal weight:   20.0000
   chunk 8 optimal weight:    5.9990
   chunk 17 optimal weight:    8.9990
   overall best weight:    4.0786

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4796 r_free = 0.4796 target = 0.214896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.193189 restraints weight = 5434.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.4573 rms_B_bonded: 3.38
r_work: 0.4478 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.4478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6897
moved from start:          0.6670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   3900  Z= 0.359
  Angle     :  0.651   5.026   5290  Z= 0.382
  Chirality :  0.052   0.191    710
  Planarity :  0.003   0.013    660
  Dihedral  :  5.706  17.769    580
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 18.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.64 %
    Favored  : 90.36 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 21.54 %
    Favored  : 71.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.22 (0.31), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.69 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS F  50 
 TYR   0.013   0.002   TYR F  39 

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 0.356 
Fit side-chains
REVERT: A   80 LYS cc_start: 0.7512 (tttt) cc_final: 0.7107 (pttp)
REVERT: B   80 LYS cc_start: 0.7453 (tttt) cc_final: 0.7074 (pttp)
REVERT: D   80 LYS cc_start: 0.7456 (tttt) cc_final: 0.7185 (mttm)
  outliers start: 27
  outliers final: 24
  residues processed: 114
  average time/residue: 0.1082
  time to fit residues: 16.3659
Evaluate side-chains
  118 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   49 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   55 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   50 HIS
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   50 HIS
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   48 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 39 optimal weight:   20.0000
   chunk 45 optimal weight:    0.8980
   chunk 7 optimal weight:   10.0000
   chunk 35 optimal weight:    0.8980
   chunk 12 optimal weight:    8.9990
   chunk 46 optimal weight:    0.6980
   chunk 30 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4928 r_free = 0.4928 target = 0.227751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4724 r_free = 0.4724 target = 0.204805 restraints weight = 5180.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.4711 rms_B_bonded: 3.34
r_work: 0.4617 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.4617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6742
moved from start:          0.6759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   3900  Z= 0.161
  Angle     :  0.507   4.919   5290  Z= 0.304
  Chirality :  0.050   0.154    710
  Planarity :  0.002   0.011    660
  Dihedral  :  5.104  16.390    580
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 22.56 %
    Favored  : 71.79 %
  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: -2.22 (0.30), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.68 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  50 
 TYR   0.007   0.001   TYR G  39 

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 LYS cc_start: 0.7506 (tttt) cc_final: 0.7050 (pttp)
REVERT: B   80 LYS cc_start: 0.7258 (tttt) cc_final: 0.6982 (pttp)
REVERT: D   80 LYS cc_start: 0.7299 (tttt) cc_final: 0.6894 (mttt)
REVERT: J   50 HIS cc_start: 0.6894 (m-70) cc_final: 0.6020 (p90)
  outliers start: 22
  outliers final: 21
  residues processed: 116
  average time/residue: 0.1245
  time to fit residues: 19.2035
Evaluate side-chains
  128 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   50 HIS
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   50 HIS
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   50 HIS
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain J residue   44 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 3 optimal weight:    6.9990
   chunk 27 optimal weight:   20.0000
   chunk 45 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 41 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   chunk 18 optimal weight:    7.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    2.5184

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4879 r_free = 0.4879 target = 0.222474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4673 r_free = 0.4673 target = 0.199983 restraints weight = 5369.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.4650 rms_B_bonded: 3.31
r_work: 0.4553 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.4553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6818
moved from start:          0.6876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3900  Z= 0.254
  Angle     :  0.571   7.545   5290  Z= 0.334
  Chirality :  0.051   0.169    710
  Planarity :  0.002   0.011    660
  Dihedral  :  5.167  18.635    580
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 15.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 23.59 %
    Favored  : 70.77 %
  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: -2.19 (0.31), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.66 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H  50 
 TYR   0.009   0.001   TYR I  39 

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 LYS cc_start: 0.7510 (tttt) cc_final: 0.7059 (pttp)
REVERT: B   80 LYS cc_start: 0.7373 (tttt) cc_final: 0.7098 (pttp)
REVERT: D   80 LYS cc_start: 0.7300 (tttt) cc_final: 0.6953 (mttt)
REVERT: E   60 LYS cc_start: 0.3677 (mtpp) cc_final: 0.3331 (ttmm)
  outliers start: 22
  outliers final: 21
  residues processed: 118
  average time/residue: 0.1154
  time to fit residues: 17.8944
Evaluate side-chains
  128 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   50 HIS
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   50 HIS
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   50 HIS
Chi-restraints excluded: chain G residue   70 VAL
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   50 HIS
Chi-restraints excluded: chain H residue   70 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain J residue   44 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 39 optimal weight:   20.0000
   chunk 24 optimal weight:   20.0000
   chunk 25 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:   20.0000
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4905 r_free = 0.4905 target = 0.224705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4694 r_free = 0.4694 target = 0.201766 restraints weight = 5238.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.4680 rms_B_bonded: 3.38
r_work: 0.4579 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.4579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6769
moved from start:          0.6959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3900  Z= 0.206
  Angle     :  0.537   6.105   5290  Z= 0.316
  Chirality :  0.050   0.156    710
  Planarity :  0.002   0.011    660
  Dihedral  :  5.094  18.773    580
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 23.33 %
    Favored  : 70.51 %
  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: -2.22 (0.31), residues: 560
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.69 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS H  50 
 TYR   0.007   0.001   TYR J  39 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2255.43 seconds
wall clock time: 41 minutes 4.59 seconds (2464.59 seconds total)