Starting phenix.real_space_refine
on Sat May 10 00:59:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqr_45820/05_2025/9cqr_45820.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqr_45820/05_2025/9cqr_45820.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cqr_45820/05_2025/9cqr_45820.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqr_45820/05_2025/9cqr_45820.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqr_45820/05_2025/9cqr_45820.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqr_45820/05_2025/9cqr_45820.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.024
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
     Fe      4      7.16       5
     S      12      5.16       5
     C    2900      2.51       5
     N     760      2.21       5
     O     794      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4470
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1058
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1091
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
    Chain: "C"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1058
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 132}
    Chain: "D"
      Number of atoms: 1091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1091
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.27, per 1000 atoms: 0.96
  Number of scatterers: 4470
  At special positions: 0
  Unit cell: (75.705, 72.765, 66.15, 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)
     Fe      4     26.01
     S      12     16.00
     O     794      8.00
     N     760      7.00
     C    2900      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.28
  Conformation dependent library (CDL) restraints added in 547.3 milliseconds
  

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1052

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 0 sheets defined
      88.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 18
    Processing helix  chain 'A' and resid 20 through 36
    Processing helix  chain 'A' and resid 37 through 43
    Processing helix  chain 'A' and resid 52 through 72
    Processing helix  chain 'A' and resid 75 through 80
    Processing helix  chain 'A' and resid 80 through 89
    Processing helix  chain 'A' and resid 94 through 113
      removed outlier: 3.650A  pdb=" N   PHE A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 138
    Processing helix  chain 'B' and resid 4 through 17
    Processing helix  chain 'B' and resid 19 through 35
      removed outlier: 4.266A  pdb=" N   GLY B  25 " --> pdb=" O   ASP B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 41
    Processing helix  chain 'B' and resid 42 through 46
    Processing helix  chain 'B' and resid 50 through 56
    Processing helix  chain 'B' and resid 57 through 77
    Processing helix  chain 'B' and resid 80 through 85
    Processing helix  chain 'B' and resid 85 through 95
    Processing helix  chain 'B' and resid 99 through 119
      removed outlier: 4.001A  pdb=" N   PHE B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ARG B 104 " --> pdb=" O   PRO B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 122
      No H-bonds generated for 'chain 'B' and resid 120 through 122'
    Processing helix  chain 'B' and resid 123 through 143
    Processing helix  chain 'C' and resid 3 through 18
    Processing helix  chain 'C' and resid 20 through 36
    Processing helix  chain 'C' and resid 37 through 43
    Processing helix  chain 'C' and resid 52 through 72
    Processing helix  chain 'C' and resid 75 through 80
    Processing helix  chain 'C' and resid 80 through 89
    Processing helix  chain 'C' and resid 94 through 113
      removed outlier: 3.639A  pdb=" N   PHE C  98 " --> pdb=" O   ASP C  94 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 138
    Processing helix  chain 'D' and resid 4 through 17
    Processing helix  chain 'D' and resid 19 through 35
      removed outlier: 4.342A  pdb=" N   GLY D  25 " --> pdb=" O   ASP D  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 36 through 41
    Processing helix  chain 'D' and resid 42 through 46
      removed outlier: 3.876A  pdb=" N   GLY D  46 " --> pdb=" O   GLU D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 56
    Processing helix  chain 'D' and resid 57 through 77
    Processing helix  chain 'D' and resid 80 through 85
    Processing helix  chain 'D' and resid 85 through 95
    Processing helix  chain 'D' and resid 99 through 119
      removed outlier: 3.756A  pdb=" N   PHE D 103 " --> pdb=" O   ASP D  99 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ARG D 104 " --> pdb=" O   PRO D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 122
      No H-bonds generated for 'chain 'D' and resid 120 through 122'
    Processing helix  chain 'D' and resid 123 through 143

    347 hydrogen bonds defined for protein.
    990 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: 1.17

  Time building geometry restraints manager: 1.44 seconds

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

  Histogram of bond lengths:
        1.21 -     1.38: 1757
        1.38 -     1.55: 2812
        1.55 -     1.72: 7
        1.72 -     1.89: 18
        1.89 -     2.06: 16
  Bond restraints: 4610
  Sorted by residual:
  bond pdb=" N   THR D 123 "
       pdb=" CA  THR D 123 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.034 8.30e-03 1.45e+04 1.66e+01
  bond pdb=" CA  PRO B 124 "
       pdb=" C   PRO B 124 "
    ideal  model  delta    sigma   weight residual
    1.517  1.547 -0.030 9.30e-03 1.16e+04 1.05e+01
  bond pdb=" N   THR A 137 "
       pdb=" CA  THR A 137 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.21e-02 6.83e+03 8.34e+00
  bond pdb=" N   THR C 137 "
       pdb=" CA  THR C 137 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.21e-02 6.83e+03 8.04e+00
  bond pdb=" N   VAL B  11 "
       pdb=" CA  VAL B  11 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.17e-02 7.31e+03 7.88e+00
  ... (remaining 4605 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 5788
        1.31 -     2.62: 365
        2.62 -     3.92: 136
        3.92 -     5.23: 28
        5.23 -     6.54: 13
  Bond angle restraints: 6330
  Sorted by residual:
  angle pdb=" CA  ASP C   6 "
        pdb=" CB  ASP C   6 "
        pdb=" CG  ASP C   6 "
      ideal   model   delta    sigma   weight residual
     112.60  118.75   -6.15 1.00e+00 1.00e+00 3.79e+01
  angle pdb=" CA  PRO B 124 "
        pdb=" C   PRO B 124 "
        pdb=" N   PRO B 125 "
      ideal   model   delta    sigma   weight residual
     117.93  124.19   -6.26 1.20e+00 6.94e-01 2.72e+01
  angle pdb=" N   PRO B 124 "
        pdb=" CA  PRO B 124 "
        pdb=" C   PRO B 124 "
      ideal   model   delta    sigma   weight residual
     110.70  116.44   -5.74 1.22e+00 6.72e-01 2.21e+01
  angle pdb=" CA  SER A  81 "
        pdb=" C   SER A  81 "
        pdb=" O   SER A  81 "
      ideal   model   delta    sigma   weight residual
     120.55  116.14    4.41 1.06e+00 8.90e-01 1.73e+01
  angle pdb=" CA  SER C  81 "
        pdb=" C   SER C  81 "
        pdb=" O   SER C  81 "
      ideal   model   delta    sigma   weight residual
     120.55  116.15    4.40 1.06e+00 8.90e-01 1.72e+01
  ... (remaining 6325 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.96: 2292
       15.96 -    31.93: 215
       31.93 -    47.89: 73
       47.89 -    63.85: 24
       63.85 -    79.82: 10
  Dihedral angle restraints: 2614
    sinusoidal: 990
      harmonic: 1624
  Sorted by residual:
  dihedral pdb=" C   PHE D 118 "
           pdb=" N   PHE D 118 "
           pdb=" CA  PHE D 118 "
           pdb=" CB  PHE D 118 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.20    8.60     0      2.50e+00 1.60e-01 1.18e+01
  dihedral pdb=" C2D HEM B 201 "
           pdb=" C3D HEM B 201 "
           pdb=" CAD HEM B 201 "
           pdb=" CBD HEM B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -0.00  -79.82   79.82     2      2.00e+01 2.50e-03 1.16e+01
  dihedral pdb=" C2D HEM D 201 "
           pdb=" C3D HEM D 201 "
           pdb=" CAD HEM D 201 "
           pdb=" CBD HEM D 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -79.60   79.60     2      2.00e+01 2.50e-03 1.16e+01
  ... (remaining 2611 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 531
       0.054 -    0.108: 113
       0.108 -    0.162: 38
       0.162 -    0.215: 9
       0.215 -    0.269: 1
  Chirality restraints: 692
  Sorted by residual:
  chirality pdb=" CA  PHE D 122 "
            pdb=" N   PHE D 122 "
            pdb=" C   PHE D 122 "
            pdb=" CB  PHE D 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CA  PHE D 118 "
            pdb=" N   PHE D 118 "
            pdb=" C   PHE D 118 "
            pdb=" CB  PHE D 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.43e-01
  chirality pdb=" CA  ASP C   6 "
            pdb=" N   ASP C   6 "
            pdb=" C   ASP C   6 "
            pdb=" CB  ASP C   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.75e-01
  ... (remaining 689 not shown)

  Planarity restraints: 790
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE D 122 "    0.011 2.00e-02 2.50e+03   2.25e-02 5.05e+00
        pdb=" C   PHE D 122 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   PHE D 122 "    0.014 2.00e-02 2.50e+03
        pdb=" N   THR D 123 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO C  77 "   -0.009 2.00e-02 2.50e+03   1.89e-02 3.59e+00
        pdb=" C   PRO C  77 "    0.033 2.00e-02 2.50e+03
        pdb=" O   PRO C  77 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ASN C  78 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A  77 "    0.009 2.00e-02 2.50e+03   1.82e-02 3.33e+00
        pdb=" C   PRO A  77 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   PRO A  77 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ASN A  78 "    0.011 2.00e-02 2.50e+03
  ... (remaining 787 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 890
        2.79 -     3.31: 4387
        3.31 -     3.84: 7829
        3.84 -     4.37: 9549
        4.37 -     4.90: 15553
  Nonbonded interactions: 38208
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU C  27 "
            pdb=" NE2 HIS C 112 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" OE1 GLU A  27 "
            pdb=" NE2 HIS A 112 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" ND1 HIS A  20 "
            pdb=" OE2 GLU A  23 "
     model   vdw
     2.336 3.120
  nonbonded pdb=" O   PRO A 114 "
            pdb=" NE2 HIS B 116 "
     model   vdw
     2.367 3.120
  nonbonded pdb=" O   PRO C 114 "
            pdb=" NE2 HIS D 116 "
     model   vdw
     2.420 3.120
  ... (remaining 38203 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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:             2.970
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     16.000
  Find NCS groups from input model:        0.150
  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:10.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
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      :  0.006   0.062   4614  Z= 0.386
  Angle     :  0.844   6.538   6330  Z= 0.570
  Chirality :  0.053   0.269    692
  Planarity :  0.005   0.043    790
  Dihedral  : 16.043  79.817   1562
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.20 %
    Favored  : 82.16 %
  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:  3.05 (0.36), residues: 558
  helix:  2.38 (0.25), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.77 (0.62), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C  14 
 HIS   0.004   0.001   HIS B  77 
 PHE   0.030   0.002   PHE D 118 
 TYR   0.010   0.001   TYR D  35 
 ARG   0.002   0.000   ARG D  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12972 (  347)
  hydrogen bonds       : angle       5.06708 (  990)
  covalent geometry    : bond        0.00572 ( 4610)
  covalent geometry    : angle       0.84362 ( 6330)
  Misc. bond           : bond        0.04746 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.478 
Fit side-chains
REVERT: A   81 SER cc_start: 0.7788 (t) cc_final: 0.7539 (p)
REVERT: B   26 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7260 (tt0)
REVERT: B   90 GLU cc_start: 0.6682 (tp30) cc_final: 0.6425 (mm-30)
REVERT: B   95 LYS cc_start: 0.7854 (tmtt) cc_final: 0.7157 (mptt)
REVERT: B  101 GLU cc_start: 0.8238 (tp30) cc_final: 0.7990 (tm-30)
REVERT: B  104 ARG cc_start: 0.7624 (ttp80) cc_final: 0.6927 (mtt90)
REVERT: C    8 THR cc_start: 0.6789 (m) cc_final: 0.6383 (p)
REVERT: C   81 SER cc_start: 0.7848 (t) cc_final: 0.7569 (p)
REVERT: C   90 LYS cc_start: 0.8478 (tttt) cc_final: 0.7702 (mttt)
REVERT: D   90 GLU cc_start: 0.7077 (tt0) cc_final: 0.6243 (mm-30)
REVERT: D   95 LYS cc_start: 0.8031 (tmtt) cc_final: 0.7336 (mttp)
REVERT: D  101 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7844 (tp30)
REVERT: D  104 ARG cc_start: 0.7714 (ttp-170) cc_final: 0.6893 (mtt90)
REVERT: D  120 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.7025 (tptt)
  outliers start: 12
  outliers final: 2
  residues processed: 80
  average time/residue: 1.4422
  time to fit residues: 119.1306
Evaluate side-chains
  69 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  120 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9980
   chunk 23 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 16 optimal weight:    0.1980
   chunk 26 optimal weight:    5.9990
   chunk 32 optimal weight:    0.2980
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 122 HIS
** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.156989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.128577 restraints weight = 4003.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 1.42
r_work: 0.3149 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.0829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4614  Z= 0.123
  Angle     :  0.568   7.038   6330  Z= 0.267
  Chirality :  0.039   0.148    692
  Planarity :  0.005   0.043    790
  Dihedral  : 10.224  79.907    624
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 14.32 %
    Favored  : 83.04 %
  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:  3.03 (0.36), residues: 558
  helix:  2.37 (0.25), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.73 (0.61), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  14 
 HIS   0.003   0.001   HIS A  58 
 PHE   0.009   0.001   PHE D 118 
 TYR   0.008   0.001   TYR B  35 
 ARG   0.002   0.000   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03812 (  347)
  hydrogen bonds       : angle       4.20496 (  990)
  covalent geometry    : bond        0.00311 ( 4610)
  covalent geometry    : angle       0.56762 ( 6330)
  Misc. bond           : bond        0.01487 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.501 
Fit side-chains
REVERT: B   17 LYS cc_start: 0.7444 (mtpt) cc_final: 0.7079 (mttt)
REVERT: B   22 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6349 (tt0)
REVERT: B   68 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.6990 (mp)
REVERT: B   90 GLU cc_start: 0.6520 (tp30) cc_final: 0.6174 (mm-30)
REVERT: B   95 LYS cc_start: 0.7633 (tmtt) cc_final: 0.6946 (mptt)
REVERT: B  104 ARG cc_start: 0.7631 (ttp80) cc_final: 0.6732 (mtt90)
REVERT: C   81 SER cc_start: 0.7832 (t) cc_final: 0.7374 (p)
REVERT: D   65 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7883 (mtmm)
REVERT: D   90 GLU cc_start: 0.6907 (tt0) cc_final: 0.5938 (mm-30)
REVERT: D   95 LYS cc_start: 0.7633 (tmtt) cc_final: 0.6809 (mptt)
REVERT: D  101 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7630 (tp30)
REVERT: D  104 ARG cc_start: 0.7543 (ttp-170) cc_final: 0.6568 (mtt90)
REVERT: D  120 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6877 (mptp)
  outliers start: 12
  outliers final: 3
  residues processed: 67
  average time/residue: 1.6742
  time to fit residues: 115.4748
Evaluate side-chains
  63 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   65 LYS
Chi-restraints excluded: chain D residue  120 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 117 HIS ** 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 = 0.3612 r_free = 0.3612 target = 0.153751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.125236 restraints weight = 4049.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 1.43
r_work: 0.3224 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.0989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4614  Z= 0.140
  Angle     :  0.584   6.788   6330  Z= 0.273
  Chirality :  0.041   0.171    692
  Planarity :  0.005   0.046    790
  Dihedral  : 10.321  81.487    624
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.88 %
    Favored  : 83.26 %
  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:  2.76 (0.36), residues: 558
  helix:  2.16 (0.25), residues: 440
  sheet:  None (None), residues: 0
  loop :  0.67 (0.61), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  14 
 HIS   0.004   0.001   HIS C  58 
 PHE   0.012   0.001   PHE D 118 
 TYR   0.009   0.001   TYR D  35 
 ARG   0.001   0.000   ARG D  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04228 (  347)
  hydrogen bonds       : angle       4.12183 (  990)
  covalent geometry    : bond        0.00358 ( 4610)
  covalent geometry    : angle       0.58378 ( 6330)
  Misc. bond           : bond        0.03071 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 LYS cc_start: 0.7287 (mtpt) cc_final: 0.6864 (mttt)
REVERT: B   22 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6234 (tt0)
REVERT: B   90 GLU cc_start: 0.6347 (tp30) cc_final: 0.6015 (mm-30)
REVERT: B   95 LYS cc_start: 0.7580 (tmtt) cc_final: 0.6954 (mptt)
REVERT: B  101 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7645 (tp30)
REVERT: B  104 ARG cc_start: 0.7462 (ttp80) cc_final: 0.6633 (mtt90)
REVERT: C    8 THR cc_start: 0.6389 (m) cc_final: 0.5885 (p)
REVERT: D   90 GLU cc_start: 0.6776 (tt0) cc_final: 0.5831 (mm-30)
REVERT: D   95 LYS cc_start: 0.7571 (tmtt) cc_final: 0.6820 (mptt)
REVERT: D  101 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7576 (tp30)
REVERT: D  120 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6906 (mptp)
  outliers start: 13
  outliers final: 5
  residues processed: 69
  average time/residue: 1.6103
  time to fit residues: 114.4877
Evaluate side-chains
  63 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  120 LYS
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0670
   chunk 18 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  45 HIS
** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.154495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.126407 restraints weight = 4059.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.41
r_work: 0.3237 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.1081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4614  Z= 0.125
  Angle     :  0.563   7.395   6330  Z= 0.261
  Chirality :  0.039   0.170    692
  Planarity :  0.005   0.046    790
  Dihedral  : 10.188  80.761    624
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 13.44 %
    Favored  : 82.82 %
  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:  2.79 (0.36), residues: 558
  helix:  2.21 (0.25), residues: 440
  sheet:  None (None), residues: 0
  loop :  0.57 (0.60), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  14 
 HIS   0.003   0.001   HIS C  58 
 PHE   0.010   0.001   PHE D 118 
 TYR   0.008   0.001   TYR D  35 
 ARG   0.001   0.000   ARG D  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03826 (  347)
  hydrogen bonds       : angle       3.99277 (  990)
  covalent geometry    : bond        0.00324 ( 4610)
  covalent geometry    : angle       0.56345 ( 6330)
  Misc. bond           : bond        0.01885 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 LYS cc_start: 0.7287 (mtpt) cc_final: 0.6894 (mttt)
REVERT: B   22 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6454 (tt0)
REVERT: B   90 GLU cc_start: 0.6662 (tp30) cc_final: 0.6351 (mm-30)
REVERT: B   95 LYS cc_start: 0.7621 (tmtt) cc_final: 0.7156 (mptt)
REVERT: B  101 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7854 (tp30)
REVERT: B  104 ARG cc_start: 0.7596 (ttp80) cc_final: 0.6945 (mtt90)
REVERT: C    8 THR cc_start: 0.6703 (m) cc_final: 0.6246 (p)
REVERT: D   90 GLU cc_start: 0.7048 (tt0) cc_final: 0.6176 (mm-30)
REVERT: D   95 LYS cc_start: 0.7664 (tmtt) cc_final: 0.7076 (mptt)
REVERT: D  101 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7864 (tp30)
REVERT: D  120 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7098 (mptp)
  outliers start: 17
  outliers final: 6
  residues processed: 68
  average time/residue: 1.4749
  time to fit residues: 103.4016
Evaluate side-chains
  67 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain C residue   23 GLU
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  120 LYS
Chi-restraints excluded: chain D residue  121 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 11 optimal weight:    0.0870
   chunk 27 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0970
   chunk 26 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 54 optimal weight:    0.3980
   chunk 15 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    0.3556

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

Flipped N/Q/H residues before XYZ refinement:
** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 117 HIS ** 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 = 0.3628 r_free = 0.3628 target = 0.155836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.127705 restraints weight = 4113.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 1.40
r_work: 0.3303 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.1176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4614  Z= 0.111
  Angle     :  0.542   7.299   6330  Z= 0.248
  Chirality :  0.038   0.147    692
  Planarity :  0.005   0.045    790
  Dihedral  :  9.957  80.084    624
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.20 %
    Favored  : 82.16 %
  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:  2.91 (0.36), residues: 558
  helix:  2.34 (0.25), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.46 (0.59), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  14 
 HIS   0.003   0.001   HIS B 116 
 PHE   0.007   0.001   PHE D 118 
 TYR   0.007   0.001   TYR B  35 
 ARG   0.001   0.000   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03448 (  347)
  hydrogen bonds       : angle       3.86345 (  990)
  covalent geometry    : bond        0.00289 ( 4610)
  covalent geometry    : angle       0.54180 ( 6330)
  Misc. bond           : bond        0.01414 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.675 
Fit side-chains
REVERT: B   22 GLU cc_start: 0.6847 (mt-10) cc_final: 0.6309 (tt0)
REVERT: B   90 GLU cc_start: 0.6428 (tp30) cc_final: 0.6128 (mm-30)
REVERT: B   95 LYS cc_start: 0.7570 (tmtt) cc_final: 0.6996 (mptt)
REVERT: B  101 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7691 (tp30)
REVERT: B  104 ARG cc_start: 0.7468 (ttp80) cc_final: 0.6727 (mtt90)
REVERT: C    8 THR cc_start: 0.6473 (m) cc_final: 0.6041 (p)
REVERT: D   90 GLU cc_start: 0.6982 (tt0) cc_final: 0.5993 (mm-30)
REVERT: D   95 LYS cc_start: 0.7582 (tmtt) cc_final: 0.6955 (mptt)
REVERT: D  101 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7673 (tp30)
REVERT: D  104 ARG cc_start: 0.7483 (ttp-170) cc_final: 0.6554 (mtt90)
REVERT: D  120 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6942 (mptp)
  outliers start: 12
  outliers final: 3
  residues processed: 71
  average time/residue: 1.6475
  time to fit residues: 120.7015
Evaluate side-chains
  65 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  120 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 4 optimal weight:    0.0870
   chunk 7 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 8 optimal weight:    6.9990
   chunk 16 optimal weight:    0.0980
   chunk 55 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 117 HIS ** 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 = 0.3608 r_free = 0.3608 target = 0.153899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.125863 restraints weight = 4062.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 1.39
r_work: 0.3280 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.1196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4614  Z= 0.123
  Angle     :  0.555   6.667   6330  Z= 0.257
  Chirality :  0.039   0.155    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.918  80.307    622
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 14.32 %
    Favored  : 82.16 %
  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 (0.36), residues: 558
  helix:  2.19 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop :  0.73 (0.62), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  14 
 HIS   0.003   0.001   HIS A  58 
 PHE   0.009   0.001   PHE D 118 
 TYR   0.008   0.001   TYR D  35 
 ARG   0.001   0.000   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03769 (  347)
  hydrogen bonds       : angle       3.91975 (  990)
  covalent geometry    : bond        0.00322 ( 4610)
  covalent geometry    : angle       0.55533 ( 6330)
  Misc. bond           : bond        0.02255 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 LYS cc_start: 0.7236 (mtpt) cc_final: 0.6809 (mttt)
REVERT: B   22 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6550 (tt0)
REVERT: B   90 GLU cc_start: 0.6645 (tp30) cc_final: 0.6366 (mm-30)
REVERT: B   95 LYS cc_start: 0.7655 (tmtt) cc_final: 0.7121 (mptt)
REVERT: B  101 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7848 (tp30)
REVERT: B  104 ARG cc_start: 0.7599 (ttp80) cc_final: 0.6946 (mtt90)
REVERT: C    3 SER cc_start: 0.7291 (OUTLIER) cc_final: 0.6778 (p)
REVERT: C    8 THR cc_start: 0.6738 (m) cc_final: 0.6284 (p)
REVERT: D   90 GLU cc_start: 0.7142 (tt0) cc_final: 0.6230 (mm-30)
REVERT: D   95 LYS cc_start: 0.7716 (tmtt) cc_final: 0.7122 (mptt)
REVERT: D  101 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7846 (tp30)
REVERT: D  120 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7032 (mptp)
  outliers start: 16
  outliers final: 6
  residues processed: 72
  average time/residue: 1.5401
  time to fit residues: 114.2863
Evaluate side-chains
  69 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue    2 LEU
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  120 LYS
Chi-restraints excluded: chain D residue  121 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 45 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0370
   chunk 30 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 117 HIS ** 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 = 0.3615 r_free = 0.3615 target = 0.154009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.126171 restraints weight = 4105.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 1.38
r_work: 0.3227 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.1226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4614  Z= 0.128
  Angle     :  0.559   6.612   6330  Z= 0.259
  Chirality :  0.040   0.157    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.959  81.262    622
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.20 %
    Favored  : 81.50 %
  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:  2.82 (0.36), residues: 558
  helix:  2.17 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop :  0.68 (0.62), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  14 
 HIS   0.003   0.001   HIS C  58 
 PHE   0.010   0.001   PHE D 118 
 TYR   0.008   0.001   TYR B  35 
 ARG   0.001   0.000   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03869 (  347)
  hydrogen bonds       : angle       3.94628 (  990)
  covalent geometry    : bond        0.00334 ( 4610)
  covalent geometry    : angle       0.55925 ( 6330)
  Misc. bond           : bond        0.02430 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 LYS cc_start: 0.7032 (mtpt) cc_final: 0.6557 (mttt)
REVERT: B   22 GLU cc_start: 0.6648 (mt-10) cc_final: 0.6090 (tt0)
REVERT: B   90 GLU cc_start: 0.6173 (tp30) cc_final: 0.5856 (mm-30)
REVERT: B   95 LYS cc_start: 0.7442 (tmtt) cc_final: 0.6834 (mptt)
REVERT: B  101 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7492 (tp30)
REVERT: B  104 ARG cc_start: 0.7358 (ttp80) cc_final: 0.6452 (mtt90)
REVERT: C    3 SER cc_start: 0.6944 (OUTLIER) cc_final: 0.6391 (p)
REVERT: C    8 THR cc_start: 0.6300 (m) cc_final: 0.5832 (p)
REVERT: D   90 GLU cc_start: 0.6741 (tt0) cc_final: 0.5690 (mm-30)
REVERT: D   95 LYS cc_start: 0.7519 (tmtt) cc_final: 0.6814 (mptt)
REVERT: D  101 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7526 (tp30)
REVERT: D  120 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6868 (mptp)
  outliers start: 15
  outliers final: 5
  residues processed: 68
  average time/residue: 1.5793
  time to fit residues: 110.6548
Evaluate side-chains
  69 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain C residue    2 LEU
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  120 LYS
Chi-restraints excluded: chain D residue  121 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 37 optimal weight:    0.4980
   chunk 0 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0030
   chunk 27 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.4790

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

Flipped N/Q/H residues before XYZ refinement:
** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 117 HIS ** 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 = 0.3628 r_free = 0.3628 target = 0.154773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.126873 restraints weight = 4020.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 1.39
r_work: 0.3254 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4614  Z= 0.120
  Angle     :  0.550   6.604   6330  Z= 0.255
  Chirality :  0.039   0.145    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.889  80.828    622
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.30 %
    Favored  : 80.84 %
  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:  2.88 (0.36), residues: 558
  helix:  2.22 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop :  0.69 (0.62), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  14 
 HIS   0.003   0.001   HIS B 116 
 PHE   0.009   0.001   PHE D 118 
 TYR   0.007   0.001   TYR D  35 
 ARG   0.002   0.000   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03702 (  347)
  hydrogen bonds       : angle       3.91112 (  990)
  covalent geometry    : bond        0.00314 ( 4610)
  covalent geometry    : angle       0.55003 ( 6330)
  Misc. bond           : bond        0.02073 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
REVERT: B   26 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7286 (tt0)
REVERT: B   90 GLU cc_start: 0.6649 (tp30) cc_final: 0.6398 (mm-30)
REVERT: B   95 LYS cc_start: 0.7638 (tmtt) cc_final: 0.7180 (mptt)
REVERT: B  101 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7834 (tp30)
REVERT: B  104 ARG cc_start: 0.7582 (ttp80) cc_final: 0.6947 (mtt90)
REVERT: C    3 SER cc_start: 0.7184 (OUTLIER) cc_final: 0.6716 (p)
REVERT: C    8 THR cc_start: 0.6719 (m) cc_final: 0.6266 (p)
REVERT: D   90 GLU cc_start: 0.7132 (tt0) cc_final: 0.6200 (mm-30)
REVERT: D   95 LYS cc_start: 0.7694 (tmtt) cc_final: 0.7142 (mptt)
REVERT: D  101 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7866 (tp30)
REVERT: D  120 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6996 (mptp)
  outliers start: 13
  outliers final: 6
  residues processed: 66
  average time/residue: 1.5321
  time to fit residues: 104.2316
Evaluate side-chains
  68 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue    2 LEU
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  120 LYS
Chi-restraints excluded: chain D residue  121 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0870
   chunk 39 optimal weight:    0.0870
   chunk 47 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 19 optimal weight:    0.3980
   chunk 1 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 117 HIS ** 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 = 0.3622 r_free = 0.3622 target = 0.153688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.126620 restraints weight = 4080.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 1.34
r_work: 0.3228 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4614  Z= 0.135
  Angle     :  0.568   6.242   6330  Z= 0.265
  Chirality :  0.040   0.158    692
  Planarity :  0.005   0.047    790
  Dihedral  : 10.031  83.284    622
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.30 %
    Favored  : 80.62 %
  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:  2.78 (0.36), residues: 558
  helix:  2.15 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop :  0.66 (0.62), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  14 
 HIS   0.004   0.001   HIS C  58 
 PHE   0.010   0.001   PHE D 118 
 TYR   0.008   0.001   TYR D  35 
 ARG   0.002   0.000   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04040 (  347)
  hydrogen bonds       : angle       3.98526 (  990)
  covalent geometry    : bond        0.00352 ( 4610)
  covalent geometry    : angle       0.56752 ( 6330)
  Misc. bond           : bond        0.03040 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
REVERT: B   90 GLU cc_start: 0.6647 (tp30) cc_final: 0.6351 (mm-30)
REVERT: B   95 LYS cc_start: 0.7635 (tmtt) cc_final: 0.7152 (mptt)
REVERT: B  101 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7827 (tp30)
REVERT: B  104 ARG cc_start: 0.7600 (ttp80) cc_final: 0.6938 (mtt90)
REVERT: C    3 SER cc_start: 0.7199 (OUTLIER) cc_final: 0.6705 (p)
REVERT: C    8 THR cc_start: 0.6748 (m) cc_final: 0.6257 (p)
REVERT: D   90 GLU cc_start: 0.7087 (tt0) cc_final: 0.6155 (mm-30)
REVERT: D   95 LYS cc_start: 0.7713 (tmtt) cc_final: 0.7136 (mptt)
REVERT: D  101 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7861 (tp30)
REVERT: D  120 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7028 (mptp)
  outliers start: 14
  outliers final: 5
  residues processed: 69
  average time/residue: 1.5132
  time to fit residues: 107.6893
Evaluate side-chains
  69 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain C residue    2 LEU
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  120 LYS
Chi-restraints excluded: chain D residue  121 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0040
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 117 HIS ** 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 = 0.3605 r_free = 0.3605 target = 0.153153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.125363 restraints weight = 4081.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 1.39
r_work: 0.3260 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4614  Z= 0.137
  Angle     :  0.571   6.300   6330  Z= 0.267
  Chirality :  0.040   0.159    692
  Planarity :  0.005   0.047    790
  Dihedral  : 10.086  84.547    622
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.18 %
    Favored  : 80.62 %
  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:  2.75 (0.36), residues: 558
  helix:  2.12 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop :  0.65 (0.62), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  14 
 HIS   0.004   0.001   HIS C  58 
 PHE   0.011   0.001   PHE D 118 
 TYR   0.008   0.001   TYR D  35 
 ARG   0.001   0.000   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04074 (  347)
  hydrogen bonds       : angle       4.00675 (  990)
  covalent geometry    : bond        0.00355 ( 4610)
  covalent geometry    : angle       0.57054 ( 6330)
  Misc. bond           : bond        0.02876 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
REVERT: B   26 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7156 (tt0)
REVERT: B   90 GLU cc_start: 0.6478 (tp30) cc_final: 0.6177 (mm-30)
REVERT: B   95 LYS cc_start: 0.7594 (tmtt) cc_final: 0.7048 (mptt)
REVERT: B  101 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7729 (tp30)
REVERT: B  104 ARG cc_start: 0.7542 (ttp80) cc_final: 0.6777 (mtt90)
REVERT: C    3 SER cc_start: 0.7170 (OUTLIER) cc_final: 0.6637 (p)
REVERT: C    8 THR cc_start: 0.6623 (m) cc_final: 0.6137 (p)
REVERT: D   90 GLU cc_start: 0.7015 (tt0) cc_final: 0.6044 (mm-30)
REVERT: D   95 LYS cc_start: 0.7672 (tmtt) cc_final: 0.7057 (mptt)
REVERT: D  101 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7738 (tp30)
REVERT: D  120 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6971 (mptp)
  outliers start: 10
  outliers final: 5
  residues processed: 63
  average time/residue: 1.7138
  time to fit residues: 111.1462
Evaluate side-chains
  67 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain C residue    2 LEU
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  120 LYS
Chi-restraints excluded: chain D residue  121 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 53 optimal weight:    0.3980
   chunk 16 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 117 HIS ** 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 = 0.3600 r_free = 0.3600 target = 0.152390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.124616 restraints weight = 4105.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 1.39
r_work: 0.3254 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   4614  Z= 0.147
  Angle     :  0.584   6.156   6330  Z= 0.275
  Chirality :  0.041   0.169    692
  Planarity :  0.005   0.047    790
  Dihedral  : 10.222  87.388    622
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.74 %
    Favored  : 80.40 %
  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:  2.67 (0.36), residues: 558
  helix:  2.07 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop :  0.65 (0.62), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  14 
 HIS   0.004   0.001   HIS C  58 
 PHE   0.011   0.001   PHE D 118 
 TYR   0.008   0.001   TYR D  35 
 ARG   0.001   0.000   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04289 (  347)
  hydrogen bonds       : angle       4.05724 (  990)
  covalent geometry    : bond        0.00381 ( 4610)
  covalent geometry    : angle       0.58412 ( 6330)
  Misc. bond           : bond        0.03368 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3769.59 seconds
wall clock time: 65 minutes 40.11 seconds (3940.11 seconds total)