Starting phenix.real_space_refine
on Thu Jun  5 07:16:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ff2_29036/06_2025/8ff2_29036.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ff2_29036/06_2025/8ff2_29036.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ff2_29036/06_2025/8ff2_29036.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ff2_29036/06_2025/8ff2_29036.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ff2_29036/06_2025/8ff2_29036.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ff2_29036/06_2025/8ff2_29036.cif"
  }
  resolution = 2.87
  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=   0.001 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    1840      2.51       5
     N     510      2.21       5
     O     550      1.98       5
     H    2740      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5650
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 565
          Classifications: {'peptide': 38}
          Modifications used: {'NH3': 1}
          Link IDs: {'TRANS': 37}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, K, J
  Time building chain proxies: 3.31, per 1000 atoms: 0.59
  Number of scatterers: 5650
  At special positions: 0
  Unit cell: (70.56, 90.72, 47.04, 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      10     16.00
     O     550      8.00
     N     510      7.00
     C    1840      6.00
     H    2740      1.00
    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: 1.25
  Conformation dependent library (CDL) restraints added in 364.2 milliseconds
  

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  640

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 21.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12
    Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 21
      removed outlier: 6.728A  pdb=" N   GLN A  15 " --> pdb=" O   LYS C  16 " (cutoff:3.500A)
      removed outlier: 8.500A  pdb=" N   VAL C  18 " --> pdb=" O   GLN A  15 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   LEU A  17 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   PHE C  20 " --> pdb=" O   LEU A  17 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   PHE A  19 " --> pdb=" O   PHE C  20 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   GLN C  15 " --> pdb=" O   LYS E  16 " (cutoff:3.500A)
      removed outlier: 8.499A  pdb=" N   VAL E  18 " --> pdb=" O   GLN C  15 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   LEU C  17 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   PHE E  20 " --> pdb=" O   LEU C  17 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   PHE C  19 " --> pdb=" O   PHE E  20 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   GLN E  15 " --> pdb=" O   LYS G  16 " (cutoff:3.500A)
      removed outlier: 8.499A  pdb=" N   VAL G  18 " --> pdb=" O   GLN E  15 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   LEU E  17 " --> pdb=" O   VAL G  18 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   PHE G  20 " --> pdb=" O   LEU E  17 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   PHE E  19 " --> pdb=" O   PHE G  20 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   GLN G  15 " --> pdb=" O   LYS J  16 " (cutoff:3.500A)
      removed outlier: 8.498A  pdb=" N   VAL J  18 " --> pdb=" O   GLN G  15 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   LEU G  17 " --> pdb=" O   VAL J  18 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   PHE J  20 " --> pdb=" O   LEU G  17 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   PHE G  19 " --> pdb=" O   PHE J  20 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 32
    Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 12
    Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 21
      removed outlier: 6.728A  pdb=" N   GLN B  15 " --> pdb=" O   LYS D  16 " (cutoff:3.500A)
      removed outlier: 8.499A  pdb=" N   VAL D  18 " --> pdb=" O   GLN B  15 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   LEU B  17 " --> pdb=" O   VAL D  18 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   PHE D  20 " --> pdb=" O   LEU B  17 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   PHE B  19 " --> pdb=" O   PHE D  20 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   GLN D  15 " --> pdb=" O   LYS F  16 " (cutoff:3.500A)
      removed outlier: 8.498A  pdb=" N   VAL F  18 " --> pdb=" O   GLN D  15 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   LEU D  17 " --> pdb=" O   VAL F  18 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   PHE F  20 " --> pdb=" O   LEU D  17 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   PHE D  19 " --> pdb=" O   PHE F  20 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   GLN F  15 " --> pdb=" O   LYS I  16 " (cutoff:3.500A)
      removed outlier: 8.499A  pdb=" N   VAL I  18 " --> pdb=" O   GLN F  15 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   LEU F  17 " --> pdb=" O   VAL I  18 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   PHE I  20 " --> pdb=" O   LEU F  17 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   PHE F  19 " --> pdb=" O   PHE I  20 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   GLN I  15 " --> pdb=" O   LYS K  16 " (cutoff:3.500A)
      removed outlier: 8.499A  pdb=" N   VAL K  18 " --> pdb=" O   GLN I  15 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   LEU I  17 " --> pdb=" O   VAL K  18 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   PHE K  20 " --> pdb=" O   LEU I  17 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   PHE I  19 " --> pdb=" O   PHE K  20 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 32

    16 hydrogen bonds defined for protein.
    48 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.63

  Time building geometry restraints manager: 1.56 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 2740
        1.03 -     1.22: 0
        1.22 -     1.42: 1360
        1.42 -     1.61: 1590
        1.61 -     1.80: 20
  Bond restraints: 5710
  Sorted by residual:
  bond pdb=" CA  HIS G   6 "
       pdb=" C   HIS G   6 "
    ideal  model  delta    sigma   weight residual
    1.529  1.520  0.009 1.04e-02 9.25e+03 8.17e-01
  bond pdb=" CA  HIS D   6 "
       pdb=" C   HIS D   6 "
    ideal  model  delta    sigma   weight residual
    1.529  1.520  0.009 1.04e-02 9.25e+03 8.09e-01
  bond pdb=" CA  HIS K   6 "
       pdb=" C   HIS K   6 "
    ideal  model  delta    sigma   weight residual
    1.529  1.520  0.009 1.04e-02 9.25e+03 7.98e-01
  bond pdb=" CA  HIS A   6 "
       pdb=" C   HIS A   6 "
    ideal  model  delta    sigma   weight residual
    1.529  1.520  0.009 1.04e-02 9.25e+03 7.70e-01
  bond pdb=" CA  HIS C   6 "
       pdb=" C   HIS C   6 "
    ideal  model  delta    sigma   weight residual
    1.529  1.520  0.009 1.04e-02 9.25e+03 7.51e-01
  ... (remaining 5705 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.48: 7927
        0.48 -     0.96: 1769
        0.96 -     1.44: 446
        1.44 -     1.91: 51
        1.91 -     2.39: 27
  Bond angle restraints: 10220
  Sorted by residual:
  angle pdb=" N   GLY D   9 "
        pdb=" CA  GLY D   9 "
        pdb=" C   GLY D   9 "
      ideal   model   delta    sigma   weight residual
     112.57  110.63    1.94 1.37e+00 5.33e-01 2.00e+00
  angle pdb=" N   GLY B   9 "
        pdb=" CA  GLY B   9 "
        pdb=" C   GLY B   9 "
      ideal   model   delta    sigma   weight residual
     112.57  110.64    1.93 1.37e+00 5.33e-01 1.98e+00
  angle pdb=" N   GLY J   9 "
        pdb=" CA  GLY J   9 "
        pdb=" C   GLY J   9 "
      ideal   model   delta    sigma   weight residual
     112.57  110.67    1.90 1.37e+00 5.33e-01 1.92e+00
  angle pdb=" N   GLY K   9 "
        pdb=" CA  GLY K   9 "
        pdb=" C   GLY K   9 "
      ideal   model   delta    sigma   weight residual
     112.57  110.68    1.89 1.37e+00 5.33e-01 1.90e+00
  angle pdb=" N   GLY I   9 "
        pdb=" CA  GLY I   9 "
        pdb=" C   GLY I   9 "
      ideal   model   delta    sigma   weight residual
     112.57  110.68    1.89 1.37e+00 5.33e-01 1.90e+00
  ... (remaining 10215 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.32: 2300
       11.32 -    22.65: 200
       22.65 -    33.97: 30
       33.97 -    45.29: 60
       45.29 -    56.61: 60
  Dihedral angle restraints: 2650
    sinusoidal: 1350
      harmonic: 1300
  Sorted by residual:
  dihedral pdb=" CA  HIS K  13 "
           pdb=" C   HIS K  13 "
           pdb=" N   HIS K  14 "
           pdb=" CA  HIS K  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.80   20.20     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  HIS I  13 "
           pdb=" C   HIS I  13 "
           pdb=" N   HIS I  14 "
           pdb=" CA  HIS I  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.80   20.20     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  HIS A  13 "
           pdb=" C   HIS A  13 "
           pdb=" N   HIS A  14 "
           pdb=" CA  HIS A  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.81   20.19     0      5.00e+00 4.00e-02 1.63e+01
  ... (remaining 2647 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.023: 214
       0.023 -    0.046: 126
       0.046 -    0.069: 0
       0.069 -    0.092: 10
       0.092 -    0.115: 50
  Chirality restraints: 400
  Sorted by residual:
  chirality pdb=" CA  VAL E  18 "
            pdb=" N   VAL E  18 "
            pdb=" C   VAL E  18 "
            pdb=" CB  VAL E  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.11 2.00e-01 2.50e+01 3.28e-01
  chirality pdb=" CA  VAL D  18 "
            pdb=" N   VAL D  18 "
            pdb=" C   VAL D  18 "
            pdb=" CB  VAL D  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.22e-01
  chirality pdb=" CA  VAL G  18 "
            pdb=" N   VAL G  18 "
            pdb=" C   VAL G  18 "
            pdb=" CB  VAL G  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.22e-01
  ... (remaining 397 not shown)

  Planarity restraints: 900
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A  13 "    0.004 2.00e-02 2.50e+03   3.40e-03 2.60e-01
        pdb=" CG  HIS A  13 "   -0.009 2.00e-02 2.50e+03
        pdb=" ND1 HIS A  13 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 HIS A  13 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 HIS A  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE2 HIS A  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD2 HIS A  13 "    0.000 2.00e-02 2.50e+03
        pdb=" HE1 HIS A  13 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 HIS A  13 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS K  13 "   -0.005 2.00e-02 2.50e+03   3.35e-03 2.52e-01
        pdb=" CG  HIS K  13 "    0.008 2.00e-02 2.50e+03
        pdb=" ND1 HIS K  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS K  13 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 HIS K  13 "    0.001 2.00e-02 2.50e+03
        pdb=" NE2 HIS K  13 "    0.000 2.00e-02 2.50e+03
        pdb=" HD2 HIS K  13 "    0.000 2.00e-02 2.50e+03
        pdb=" HE1 HIS K  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE2 HIS K  13 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS G  13 "    0.004 2.00e-02 2.50e+03   3.28e-03 2.43e-01
        pdb=" CG  HIS G  13 "   -0.008 2.00e-02 2.50e+03
        pdb=" ND1 HIS G  13 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 HIS G  13 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 HIS G  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE2 HIS G  13 "   -0.000 2.00e-02 2.50e+03
        pdb=" HD2 HIS G  13 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE1 HIS G  13 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 HIS G  13 "    0.001 2.00e-02 2.50e+03
  ... (remaining 897 not shown)

  Histogram of nonbonded interaction distances:
        1.82 -     2.37: 2123
        2.37 -     2.93: 12418
        2.93 -     3.49: 13179
        3.49 -     4.04: 20019
        4.04 -     4.60: 28533
  Nonbonded interactions: 76272
  Sorted by model distance:
  nonbonded pdb="HE22 GLN A  15 "
            pdb=" O   VAL D  36 "
     model   vdw
     1.818 2.450
  nonbonded pdb="HE22 GLN E  15 "
            pdb=" O   VAL I  36 "
     model   vdw
     1.818 2.450
  nonbonded pdb="HE22 GLN B  15 "
            pdb=" O   VAL E  36 "
     model   vdw
     1.818 2.450
  nonbonded pdb="HE22 GLN G  15 "
            pdb=" O   VAL K  36 "
     model   vdw
     1.818 2.450
  nonbonded pdb="HE22 GLN F  15 "
            pdb=" O   VAL J  36 "
     model   vdw
     1.818 2.450
  ... (remaining 76267 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: 0.03
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 'K'
  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=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:             6.620
  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:             0.090
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.610
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
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   0.017   2970  Z= 0.208
  Angle     :  0.429   1.979   3970  Z= 0.265
  Chirality :  0.044   0.115    400
  Planarity :  0.002   0.009    530
  Dihedral  : 10.635  42.562   1020
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -2.01 (0.35), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.52 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A  13 
 PHE   0.006   0.001   PHE D  19 
 TYR   0.001   0.001   TYR K  10 
 ARG   0.001   0.000   ARG B   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.31639 (   16)
  hydrogen bonds       : angle      10.37197 (   48)
  covalent geometry    : bond        0.00469 ( 2970)
  covalent geometry    : angle       0.42867 ( 3970)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.8313 (mtt-85) cc_final: 0.6486 (mmp-170)
REVERT: A   27 ASN cc_start: 0.8497 (m-40) cc_final: 0.8264 (m110)
REVERT: B    3 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7504 (tp30)
REVERT: B    5 ARG cc_start: 0.8454 (mtt-85) cc_final: 0.6673 (mmp-170)
REVERT: C    5 ARG cc_start: 0.8231 (mtt-85) cc_final: 0.7657 (mtp85)
REVERT: C    7 ASP cc_start: 0.8358 (m-30) cc_final: 0.8157 (m-30)
REVERT: C   27 ASN cc_start: 0.8597 (m-40) cc_final: 0.8370 (m-40)
REVERT: D   11 GLU cc_start: 0.8388 (pt0) cc_final: 0.8003 (pt0)
REVERT: F    5 ARG cc_start: 0.8475 (mtt-85) cc_final: 0.8087 (tpp80)
REVERT: F   13 HIS cc_start: 0.7885 (m90) cc_final: 0.7644 (m-70)
REVERT: G   28 LYS cc_start: 0.8975 (tttt) cc_final: 0.8657 (tttm)
REVERT: I    8 SER cc_start: 0.8898 (m) cc_final: 0.8548 (m)
REVERT: I   11 GLU cc_start: 0.8275 (pt0) cc_final: 0.7988 (pt0)
REVERT: I   28 LYS cc_start: 0.9122 (tttt) cc_final: 0.8849 (tttm)
REVERT: J    5 ARG cc_start: 0.8292 (mtt-85) cc_final: 0.5872 (ppt170)
REVERT: J   28 LYS cc_start: 0.9081 (tttt) cc_final: 0.8160 (tppt)
REVERT: K    5 ARG cc_start: 0.8604 (mtt-85) cc_final: 0.6282 (pmt170)
REVERT: K   11 GLU cc_start: 0.8203 (pt0) cc_final: 0.7920 (pt0)
REVERT: K   28 LYS cc_start: 0.8996 (tttt) cc_final: 0.8220 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 2.1317
  time to fit residues: 277.8459
Evaluate side-chains
  108 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 27 optimal weight:    0.3980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** C  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  15 GLN
** G  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  15 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.096317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.088598 restraints weight = 14120.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 2.47
r_work: 0.3518 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3406 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.3020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   2970  Z= 0.247
  Angle     :  0.548   3.551   3970  Z= 0.318
  Chirality :  0.051   0.153    400
  Planarity :  0.002   0.011    530
  Dihedral  :  6.426  21.002    390
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 16.55 %
    Favored  : 82.07 %
  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: -2.11 (0.34), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.60 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS I  13 
 PHE   0.006   0.001   PHE J  19 
 TYR   0.013   0.001   TYR I  10 
 ARG   0.001   0.000   ARG A   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09908 (   16)
  hydrogen bonds       : angle       6.26073 (   48)
  covalent geometry    : bond        0.00533 ( 2970)
  covalent geometry    : angle       0.54840 ( 3970)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 115
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.8371 (mtt-85) cc_final: 0.6767 (mmp-170)
REVERT: A   28 LYS cc_start: 0.9277 (tttt) cc_final: 0.9006 (tttp)
REVERT: B    3 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7934 (tp30)
REVERT: B    5 ARG cc_start: 0.8650 (mtt-85) cc_final: 0.7142 (mmp-170)
REVERT: C    5 ARG cc_start: 0.8354 (mtt-85) cc_final: 0.8044 (mtp85)
REVERT: D   11 GLU cc_start: 0.8286 (pt0) cc_final: 0.8003 (pt0)
REVERT: F    5 ARG cc_start: 0.8597 (mtt-85) cc_final: 0.8354 (tpp80)
REVERT: G    1 ASP cc_start: 0.7196 (p0) cc_final: 0.6801 (p0)
REVERT: I    1 ASP cc_start: 0.7770 (p0) cc_final: 0.7490 (p0)
REVERT: I    8 SER cc_start: 0.8860 (m) cc_final: 0.8253 (m)
REVERT: I   11 GLU cc_start: 0.8456 (pt0) cc_final: 0.8006 (pt0)
REVERT: I   28 LYS cc_start: 0.9230 (tttt) cc_final: 0.8958 (tttp)
REVERT: J    5 ARG cc_start: 0.8513 (mtt-85) cc_final: 0.6187 (ppt170)
REVERT: J    8 SER cc_start: 0.9106 (m) cc_final: 0.8886 (t)
REVERT: J   10 TYR cc_start: 0.8515 (t80) cc_final: 0.8306 (t80)
REVERT: J   11 GLU cc_start: 0.8267 (pt0) cc_final: 0.7814 (mm-30)
REVERT: J   28 LYS cc_start: 0.9232 (tttt) cc_final: 0.8352 (tppt)
REVERT: K    5 ARG cc_start: 0.8725 (mtt-85) cc_final: 0.6596 (pmt170)
REVERT: K   28 LYS cc_start: 0.9151 (tttt) cc_final: 0.8410 (tppt)
  outliers start: 4
  outliers final: 1
  residues processed: 115
  average time/residue: 2.5880
  time to fit residues: 304.9026
Evaluate side-chains
  108 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 28 optimal weight:    0.2980
   chunk 21 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 19 optimal weight:    0.2980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
** D  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  15 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.094158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.086642 restraints weight = 15065.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.49
r_work: 0.3536 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3416 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   2970  Z= 0.195
  Angle     :  0.478   3.475   3970  Z= 0.279
  Chirality :  0.050   0.136    400
  Planarity :  0.002   0.017    530
  Dihedral  :  6.098  20.136    390
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 19.66 %
    Favored  : 77.93 %
  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 (0.33), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.68 (0.25), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS C  13 
 PHE   0.003   0.001   PHE I   4 
 TYR   0.011   0.001   TYR G  10 
 ARG   0.001   0.000   ARG G   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09398 (   16)
  hydrogen bonds       : angle       6.10661 (   48)
  covalent geometry    : bond        0.00422 ( 2970)
  covalent geometry    : angle       0.47835 ( 3970)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.8300 (mtt-85) cc_final: 0.6726 (mmp-170)
REVERT: A   28 LYS cc_start: 0.9287 (tttt) cc_final: 0.9046 (tttp)
REVERT: B    5 ARG cc_start: 0.8517 (mtt-85) cc_final: 0.7076 (mmp-170)
REVERT: C    5 ARG cc_start: 0.8353 (mtt-85) cc_final: 0.8026 (mtp85)
REVERT: D   11 GLU cc_start: 0.8255 (pt0) cc_final: 0.7953 (pt0)
REVERT: E    1 ASP cc_start: 0.7668 (p0) cc_final: 0.7466 (p0)
REVERT: E   28 LYS cc_start: 0.9091 (ttpt) cc_final: 0.8810 (ttpt)
REVERT: I    1 ASP cc_start: 0.8009 (p0) cc_final: 0.7638 (p0)
REVERT: I    8 SER cc_start: 0.8848 (m) cc_final: 0.8142 (m)
REVERT: I   11 GLU cc_start: 0.8381 (pt0) cc_final: 0.7971 (pt0)
REVERT: I   28 LYS cc_start: 0.9260 (tttt) cc_final: 0.8974 (tttm)
REVERT: J    5 ARG cc_start: 0.8431 (mtt-85) cc_final: 0.6150 (ppt170)
REVERT: J   10 TYR cc_start: 0.8562 (t80) cc_final: 0.8300 (t80)
REVERT: J   11 GLU cc_start: 0.8234 (pt0) cc_final: 0.7873 (mm-30)
REVERT: J   28 LYS cc_start: 0.9283 (tttt) cc_final: 0.8431 (tppt)
REVERT: K    5 ARG cc_start: 0.8600 (mtt-85) cc_final: 0.6546 (pmt170)
REVERT: K   28 LYS cc_start: 0.9143 (tttt) cc_final: 0.8394 (tppt)
  outliers start: 7
  outliers final: 5
  residues processed: 107
  average time/residue: 2.3155
  time to fit residues: 253.9062
Evaluate side-chains
  109 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain E residue   26 SER
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain K residue   26 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 4 optimal weight:    0.3980
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
** D  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  15 GLN
** I  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.093270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.085603 restraints weight = 15281.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 2.52
r_work: 0.3529 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3405 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.3878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.030   2970  Z= 0.268
  Angle     :  0.516   3.802   3970  Z= 0.303
  Chirality :  0.050   0.147    400
  Planarity :  0.002   0.020    530
  Dihedral  :  6.299  20.616    390
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 21.03 %
    Favored  : 76.55 %
  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: -2.45 (0.33), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.86 (0.25), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C  13 
 PHE   0.005   0.001   PHE E  19 
 TYR   0.008   0.001   TYR D  10 
 ARG   0.002   0.000   ARG F   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09468 (   16)
  hydrogen bonds       : angle       6.03174 (   48)
  covalent geometry    : bond        0.00588 ( 2970)
  covalent geometry    : angle       0.51574 ( 3970)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 GLU cc_start: 0.5185 (tp30) cc_final: 0.3007 (tp30)
REVERT: A    5 ARG cc_start: 0.8291 (mtt-85) cc_final: 0.6676 (mmp-170)
REVERT: A   28 LYS cc_start: 0.9311 (tttt) cc_final: 0.9068 (tttp)
REVERT: B    5 ARG cc_start: 0.8533 (mtt-85) cc_final: 0.7157 (mmp-170)
REVERT: C    5 ARG cc_start: 0.8326 (mtt-85) cc_final: 0.8054 (mtp85)
REVERT: E    1 ASP cc_start: 0.7831 (p0) cc_final: 0.7608 (p0)
REVERT: E   28 LYS cc_start: 0.9062 (ttpt) cc_final: 0.8779 (ttpt)
REVERT: F   23 ASP cc_start: 0.7797 (m-30) cc_final: 0.7589 (m-30)
REVERT: I    1 ASP cc_start: 0.8125 (p0) cc_final: 0.7759 (p0)
REVERT: I    8 SER cc_start: 0.8855 (m) cc_final: 0.8061 (m)
REVERT: I   11 GLU cc_start: 0.8323 (pt0) cc_final: 0.7907 (pt0)
REVERT: I   28 LYS cc_start: 0.9287 (tttt) cc_final: 0.9010 (tttp)
REVERT: J    5 ARG cc_start: 0.8495 (mtt-85) cc_final: 0.6173 (ppt170)
REVERT: J   28 LYS cc_start: 0.9284 (tttt) cc_final: 0.8412 (tppt)
REVERT: K    5 ARG cc_start: 0.8629 (mtt-85) cc_final: 0.6561 (pmt170)
REVERT: K   28 LYS cc_start: 0.9147 (tttt) cc_final: 0.8359 (tppt)
  outliers start: 7
  outliers final: 5
  residues processed: 109
  average time/residue: 2.2722
  time to fit residues: 253.8711
Evaluate side-chains
  111 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 106
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain E residue   26 SER
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain K residue   26 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 22 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
** E  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  15 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.095551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.087709 restraints weight = 14778.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 2.43
r_work: 0.3552 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3439 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.4157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   2970  Z= 0.234
  Angle     :  0.535   4.401   3970  Z= 0.309
  Chirality :  0.050   0.141    400
  Planarity :  0.002   0.014    530
  Dihedral  :  6.189  19.718    390
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 25.17 %
    Favored  : 72.07 %
  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: -2.61 (0.33), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.25), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D  13 
 PHE   0.005   0.001   PHE I   4 
 TYR   0.013   0.002   TYR I  10 
 ARG   0.001   0.000   ARG A   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08989 (   16)
  hydrogen bonds       : angle       6.00138 (   48)
  covalent geometry    : bond        0.00516 ( 2970)
  covalent geometry    : angle       0.53501 ( 3970)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.8294 (mtt-85) cc_final: 0.6755 (mmp-170)
REVERT: A   28 LYS cc_start: 0.9286 (tttt) cc_final: 0.9045 (tttp)
REVERT: B    5 ARG cc_start: 0.8475 (mtt-85) cc_final: 0.7116 (mmp-170)
REVERT: C    5 ARG cc_start: 0.8305 (mtt-85) cc_final: 0.8068 (mtp85)
REVERT: E    8 SER cc_start: 0.8942 (m) cc_final: 0.8358 (t)
REVERT: E   28 LYS cc_start: 0.9103 (ttpt) cc_final: 0.8870 (ttpt)
REVERT: F   11 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7758 (pt0)
REVERT: F   23 ASP cc_start: 0.7838 (m-30) cc_final: 0.7618 (m-30)
REVERT: I    1 ASP cc_start: 0.8112 (p0) cc_final: 0.7758 (p0)
REVERT: I   28 LYS cc_start: 0.9276 (tttt) cc_final: 0.8997 (tttp)
REVERT: J    5 ARG cc_start: 0.8413 (mtt-85) cc_final: 0.6195 (ppt170)
REVERT: J   28 LYS cc_start: 0.9304 (tttt) cc_final: 0.8432 (tppt)
REVERT: K    5 ARG cc_start: 0.8629 (mtt-85) cc_final: 0.6693 (pmt170)
REVERT: K   28 LYS cc_start: 0.9153 (tttt) cc_final: 0.8408 (tppt)
  outliers start: 8
  outliers final: 8
  residues processed: 109
  average time/residue: 2.2142
  time to fit residues: 247.4258
Evaluate side-chains
  114 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain C residue    3 GLU
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain E residue   26 SER
Chi-restraints excluded: chain F residue   11 GLU
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain K residue   26 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0970
   chunk 22 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
** E  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  15 GLN
G  15 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.095449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.087390 restraints weight = 14847.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 2.56
r_work: 0.3572 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3452 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.4266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2970  Z= 0.196
  Angle     :  0.535   4.614   3970  Z= 0.308
  Chirality :  0.050   0.140    400
  Planarity :  0.002   0.015    530
  Dihedral  :  6.015  19.280    390
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 27.24 %
    Favored  : 69.31 %
  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: -2.65 (0.33), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.01 (0.25), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D  13 
 PHE   0.006   0.001   PHE A   4 
 TYR   0.012   0.002   TYR I  10 
 ARG   0.002   0.000   ARG C   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08419 (   16)
  hydrogen bonds       : angle       6.04724 (   48)
  covalent geometry    : bond        0.00432 ( 2970)
  covalent geometry    : angle       0.53504 ( 3970)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.8228 (mtt-85) cc_final: 0.6664 (mmp-170)
REVERT: A   28 LYS cc_start: 0.9279 (tttt) cc_final: 0.9028 (tttp)
REVERT: B    5 ARG cc_start: 0.8438 (mtt-85) cc_final: 0.6814 (mmp-170)
REVERT: C    5 ARG cc_start: 0.8256 (mtt-85) cc_final: 0.8025 (mtp85)
REVERT: E    8 SER cc_start: 0.8905 (m) cc_final: 0.8317 (t)
REVERT: E   28 LYS cc_start: 0.9078 (ttpt) cc_final: 0.8844 (ttpt)
REVERT: F   11 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7696 (pt0)
REVERT: I    1 ASP cc_start: 0.8119 (p0) cc_final: 0.7777 (p0)
REVERT: I   28 LYS cc_start: 0.9263 (tttt) cc_final: 0.8975 (tttm)
REVERT: J    5 ARG cc_start: 0.8495 (mtt-85) cc_final: 0.6154 (ppt170)
REVERT: J   28 LYS cc_start: 0.9311 (tttt) cc_final: 0.8401 (tppt)
REVERT: K    5 ARG cc_start: 0.8625 (mtt-85) cc_final: 0.6635 (pmt170)
REVERT: K   28 LYS cc_start: 0.9160 (tttt) cc_final: 0.8404 (tppt)
  outliers start: 10
  outliers final: 6
  residues processed: 108
  average time/residue: 2.8763
  time to fit residues: 320.7173
Evaluate side-chains
  114 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain D residue    8 SER
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain E residue   26 SER
Chi-restraints excluded: chain F residue   11 GLU
Chi-restraints excluded: chain F residue   26 SER
Chi-restraints excluded: chain K residue   26 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 0 optimal weight:    0.0980
   chunk 28 optimal weight:    0.2980
   chunk 8 optimal weight:    0.0970
   chunk 15 optimal weight:    0.8980
   chunk 25 optimal weight:    0.4980
   chunk 19 optimal weight:    0.0980
   overall best weight:    0.2178

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
B  15 GLN
** E  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  15 GLN
G  15 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.098183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.089947 restraints weight = 14736.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 2.61
r_work: 0.3601 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3481 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.4454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2970  Z= 0.117
  Angle     :  0.506   5.444   3970  Z= 0.286
  Chirality :  0.051   0.138    400
  Planarity :  0.002   0.018    530
  Dihedral  :  5.576  18.143    390
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 29.66 %
    Favored  : 68.62 %
  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: -2.43 (0.33), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.84 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D  13 
 PHE   0.005   0.001   PHE I   4 
 TYR   0.012   0.002   TYR G  10 
 ARG   0.001   0.000   ARG B   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06981 (   16)
  hydrogen bonds       : angle       6.00527 (   48)
  covalent geometry    : bond        0.00263 ( 2970)
  covalent geometry    : angle       0.50569 ( 3970)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.8185 (mtt-85) cc_final: 0.6650 (mmp-170)
REVERT: A   28 LYS cc_start: 0.9257 (tttt) cc_final: 0.9017 (tttp)
REVERT: B    5 ARG cc_start: 0.8467 (mtt-85) cc_final: 0.6920 (mmp-170)
REVERT: E    8 SER cc_start: 0.8875 (m) cc_final: 0.8228 (t)
REVERT: E   11 GLU cc_start: 0.8231 (pt0) cc_final: 0.7755 (pt0)
REVERT: E   28 LYS cc_start: 0.9100 (ttpt) cc_final: 0.8890 (ttpt)
REVERT: F    8 SER cc_start: 0.8484 (m) cc_final: 0.8116 (t)
REVERT: F   15 GLN cc_start: 0.8372 (pt0) cc_final: 0.8162 (pt0)
REVERT: I    1 ASP cc_start: 0.8198 (p0) cc_final: 0.7805 (p0)
REVERT: I   28 LYS cc_start: 0.9242 (tttt) cc_final: 0.8957 (tttp)
REVERT: J    5 ARG cc_start: 0.8397 (mtt-85) cc_final: 0.6144 (ppt170)
REVERT: J   10 TYR cc_start: 0.8541 (t80) cc_final: 0.8276 (t80)
REVERT: J   28 LYS cc_start: 0.9307 (tttt) cc_final: 0.8401 (tppt)
REVERT: K    5 ARG cc_start: 0.8617 (mtt-85) cc_final: 0.6566 (pmt170)
REVERT: K    8 SER cc_start: 0.8310 (m) cc_final: 0.7791 (t)
REVERT: K   28 LYS cc_start: 0.9164 (tttt) cc_final: 0.8410 (tppt)
  outliers start: 5
  outliers final: 3
  residues processed: 108
  average time/residue: 2.3185
  time to fit residues: 256.8105
Evaluate side-chains
  107 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 104
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain F residue   11 GLU
Chi-restraints excluded: chain K residue   26 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 1 optimal weight:    0.1980
   chunk 9 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  15 GLN
** I  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.096003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.087706 restraints weight = 14823.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 2.62
r_work: 0.3580 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3460 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.4569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   2970  Z= 0.220
  Angle     :  0.533   5.664   3970  Z= 0.306
  Chirality :  0.050   0.141    400
  Planarity :  0.002   0.016    530
  Dihedral  :  5.912  19.082    390
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 30.69 %
    Favored  : 67.59 %
  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: -2.60 (0.34), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS G  13 
 PHE   0.010   0.001   PHE I   4 
 TYR   0.012   0.001   TYR G  10 
 ARG   0.002   0.000   ARG D   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08516 (   16)
  hydrogen bonds       : angle       6.00495 (   48)
  covalent geometry    : bond        0.00487 ( 2970)
  covalent geometry    : angle       0.53279 ( 3970)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.8330 (mtt-85) cc_final: 0.6785 (mmp-170)
REVERT: A   28 LYS cc_start: 0.9316 (tttt) cc_final: 0.9077 (tttp)
REVERT: B    5 ARG cc_start: 0.8536 (mtt-85) cc_final: 0.7036 (mmp-170)
REVERT: D   28 LYS cc_start: 0.9117 (tttp) cc_final: 0.8742 (ttpp)
REVERT: E    3 GLU cc_start: 0.8138 (tt0) cc_final: 0.7519 (tm-30)
REVERT: E    8 SER cc_start: 0.8830 (m) cc_final: 0.8334 (t)
REVERT: E   28 LYS cc_start: 0.9090 (ttpt) cc_final: 0.8876 (ttpt)
REVERT: F   11 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7740 (pt0)
REVERT: G   23 ASP cc_start: 0.7948 (m-30) cc_final: 0.7562 (m-30)
REVERT: I    1 ASP cc_start: 0.8218 (p0) cc_final: 0.7841 (p0)
REVERT: I   28 LYS cc_start: 0.9275 (tttt) cc_final: 0.8989 (tttm)
REVERT: J    5 ARG cc_start: 0.8452 (mtt-85) cc_final: 0.6262 (ppt170)
REVERT: J   28 LYS cc_start: 0.9356 (tttt) cc_final: 0.8471 (tppt)
REVERT: K    5 ARG cc_start: 0.8660 (mtt-85) cc_final: 0.6669 (pmt170)
REVERT: K   28 LYS cc_start: 0.9169 (tttt) cc_final: 0.8437 (tppt)
  outliers start: 5
  outliers final: 3
  residues processed: 105
  average time/residue: 2.2052
  time to fit residues: 237.5439
Evaluate side-chains
  109 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain F residue   11 GLU
Chi-restraints excluded: chain K residue   26 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
B  15 GLN
F  15 GLN
G  15 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.094676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.086743 restraints weight = 15048.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 2.57
r_work: 0.3568 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3450 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.4624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   2970  Z= 0.282
  Angle     :  0.590   6.226   3970  Z= 0.341
  Chirality :  0.050   0.142    400
  Planarity :  0.002   0.021    530
  Dihedral  :  6.193  19.662    390
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 32.41 %
    Favored  : 65.86 %
  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: -2.84 (0.33), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.16 (0.25), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS G  13 
 PHE   0.010   0.001   PHE I   4 
 TYR   0.014   0.001   TYR I  10 
 ARG   0.002   0.000   ARG D   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09153 (   16)
  hydrogen bonds       : angle       6.08019 (   48)
  covalent geometry    : bond        0.00624 ( 2970)
  covalent geometry    : angle       0.58952 ( 3970)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.9300 (tttt) cc_final: 0.9047 (tttp)
REVERT: E    3 GLU cc_start: 0.8250 (tt0) cc_final: 0.7574 (tm-30)
REVERT: E    8 SER cc_start: 0.8911 (m) cc_final: 0.8404 (t)
REVERT: E   28 LYS cc_start: 0.9101 (ttpt) cc_final: 0.8871 (ttpt)
REVERT: F    8 SER cc_start: 0.8593 (m) cc_final: 0.8238 (t)
REVERT: G   23 ASP cc_start: 0.7942 (m-30) cc_final: 0.7581 (m-30)
REVERT: I    1 ASP cc_start: 0.8274 (p0) cc_final: 0.7877 (p0)
REVERT: I   28 LYS cc_start: 0.9251 (tttt) cc_final: 0.8954 (tttp)
REVERT: J    5 ARG cc_start: 0.8408 (mtt-85) cc_final: 0.6192 (ppt170)
REVERT: J   28 LYS cc_start: 0.9322 (tttt) cc_final: 0.8408 (tppt)
REVERT: K    5 ARG cc_start: 0.8676 (mtt-85) cc_final: 0.6607 (pmt170)
REVERT: K   28 LYS cc_start: 0.9135 (tttt) cc_final: 0.8355 (tppt)
  outliers start: 5
  outliers final: 5
  residues processed: 104
  average time/residue: 2.1668
  time to fit residues: 231.5262
Evaluate side-chains
  110 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain F residue   11 GLU
Chi-restraints excluded: chain K residue   26 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 3 optimal weight:    0.3980
   chunk 29 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0670
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
B  15 GLN
F  15 GLN
G  15 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.096003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.087588 restraints weight = 15162.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 2.66
r_work: 0.3593 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3470 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.4695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   2970  Z= 0.212
  Angle     :  0.593   6.225   3970  Z= 0.337
  Chirality :  0.050   0.136    400
  Planarity :  0.002   0.015    530
  Dihedral  :  6.030  19.201    390
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 32.76 %
    Favored  : 65.52 %
  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: -2.85 (0.33), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.16 (0.25), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS G  13 
 PHE   0.008   0.001   PHE I   4 
 TYR   0.013   0.001   TYR I  10 
 ARG   0.002   0.000   ARG D   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08470 (   16)
  hydrogen bonds       : angle       6.07580 (   48)
  covalent geometry    : bond        0.00470 ( 2970)
  covalent geometry    : angle       0.59257 ( 3970)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.9319 (tttt) cc_final: 0.9077 (tttp)
REVERT: B    5 ARG cc_start: 0.8511 (mtt-85) cc_final: 0.6990 (mmp-170)
REVERT: E    3 GLU cc_start: 0.8249 (tt0) cc_final: 0.7547 (tm-30)
REVERT: E    8 SER cc_start: 0.8887 (m) cc_final: 0.8338 (t)
REVERT: E   28 LYS cc_start: 0.9128 (ttpt) cc_final: 0.8900 (ttpt)
REVERT: F    8 SER cc_start: 0.8568 (m) cc_final: 0.8204 (t)
REVERT: G   23 ASP cc_start: 0.7970 (m-30) cc_final: 0.7618 (m-30)
REVERT: I    1 ASP cc_start: 0.8253 (p0) cc_final: 0.7841 (p0)
REVERT: I   28 LYS cc_start: 0.9261 (tttt) cc_final: 0.8968 (tttm)
REVERT: J    5 ARG cc_start: 0.8479 (mtt-85) cc_final: 0.6233 (ppt170)
REVERT: J   28 LYS cc_start: 0.9344 (tttt) cc_final: 0.8447 (tppt)
REVERT: K    5 ARG cc_start: 0.8674 (mtt-85) cc_final: 0.6615 (pmt170)
REVERT: K   28 LYS cc_start: 0.9158 (tttt) cc_final: 0.8409 (tppt)
  outliers start: 5
  outliers final: 5
  residues processed: 104
  average time/residue: 2.3949
  time to fit residues: 256.4914
Evaluate side-chains
  107 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 MET
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain F residue   11 GLU
Chi-restraints excluded: chain K residue   26 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 14 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
B  15 GLN
F  15 GLN
G  15 GLN
** I  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.095671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.087188 restraints weight = 14998.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 2.66
r_work: 0.3579 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3456 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.4665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   2970  Z= 0.224
  Angle     :  0.591   5.763   3970  Z= 0.337
  Chirality :  0.050   0.140    400
  Planarity :  0.002   0.020    530
  Dihedral  :  6.076  19.670    390
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 33.10 %
    Favored  : 64.83 %
  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: -2.94 (0.33), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.23 (0.25), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS G  13 
 PHE   0.008   0.001   PHE A   4 
 TYR   0.013   0.001   TYR J  10 
 ARG   0.001   0.000   ARG J   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08359 (   16)
  hydrogen bonds       : angle       6.07762 (   48)
  covalent geometry    : bond        0.00494 ( 2970)
  covalent geometry    : angle       0.59057 ( 3970)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7723.27 seconds
wall clock time: 134 minutes 20.83 seconds (8060.83 seconds total)