Starting phenix.real_space_refine
on Wed Jun  4 23:13:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqr_45820/06_2025/9cqr_45820.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqr_45820/06_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_45820/06_2025/9cqr_45820.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqr_45820/06_2025/9cqr_45820.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqr_45820/06_2025/9cqr_45820.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqr_45820/06_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 4.21, per 1000 atoms: 0.94
  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: 1.32
  Conformation dependent library (CDL) restraints added in 568.0 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: 0.45
  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: 1.57

  Time building geometry restraints manager: 1.55 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:             5.780
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.910
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  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:12.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.170
-------------------------------------------------------------------------------
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  : 0.533 
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: 1.7539
  time to fit residues: 144.6468
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  : 0.570 
-------------------------------------------------------------------------------
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 = 0.3352 r_free = 0.3352 target = 0.128562 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: 4.15 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
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  : 0.485 
Fit side-chains
REVERT: B   17 LYS cc_start: 0.7439 (mtpt) cc_final: 0.7075 (mttt)
REVERT: B   22 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6347 (tt0)
REVERT: B   68 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.6990 (mp)
REVERT: B   90 GLU cc_start: 0.6516 (tp30) cc_final: 0.6169 (mm-30)
REVERT: B   95 LYS cc_start: 0.7628 (tmtt) cc_final: 0.6940 (mptt)
REVERT: B  104 ARG cc_start: 0.7629 (ttp80) cc_final: 0.6726 (mtt90)
REVERT: C   81 SER cc_start: 0.7831 (t) cc_final: 0.7373 (p)
REVERT: D   65 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7881 (mtmm)
REVERT: D   90 GLU cc_start: 0.6903 (tt0) cc_final: 0.5931 (mm-30)
REVERT: D   95 LYS cc_start: 0.7628 (tmtt) cc_final: 0.6803 (mptt)
REVERT: D  101 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7627 (tp30)
REVERT: D  104 ARG cc_start: 0.7538 (ttp-170) cc_final: 0.6562 (mtt90)
REVERT: D  120 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6878 (mptp)
  outliers start: 12
  outliers final: 3
  residues processed: 67
  average time/residue: 2.2945
  time to fit residues: 158.3251
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  : 0.509 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3602 r_free = 0.3602 target = 0.152803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.124308 restraints weight = 4060.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 1.43
r_work: 0.3095 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2936 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.1026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   4614  Z= 0.149
  Angle     :  0.596   6.560   6330  Z= 0.280
  Chirality :  0.042   0.173    692
  Planarity :  0.005   0.046    790
  Dihedral  : 10.420  83.064    624
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.66 %
    Favored  : 83.48 %
  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:  2.70 (0.36), residues: 558
  helix:  2.12 (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 A  58 
 PHE   0.014   0.001   PHE D 118 
 TYR   0.010   0.001   TYR D  35 
 ARG   0.001   0.000   ARG D  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04438 (  347)
  hydrogen bonds       : angle       4.16815 (  990)
  covalent geometry    : bond        0.00382 ( 4610)
  covalent geometry    : angle       0.59619 ( 6330)
  Misc. bond           : bond        0.03706 (    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
  79 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 LYS cc_start: 0.7412 (mtpt) cc_final: 0.7000 (mttt)
REVERT: B   22 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6383 (tt0)
REVERT: B   90 GLU cc_start: 0.6535 (tp30) cc_final: 0.6176 (mm-30)
REVERT: B   95 LYS cc_start: 0.7615 (tmtt) cc_final: 0.6963 (mptt)
REVERT: B  101 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7642 (tp30)
REVERT: B  104 ARG cc_start: 0.7690 (ttp80) cc_final: 0.6810 (mtt90)
REVERT: B  120 LYS cc_start: 0.7842 (tptp) cc_final: 0.7635 (tptp)
REVERT: C    8 THR cc_start: 0.6559 (m) cc_final: 0.6056 (p)
REVERT: D   90 GLU cc_start: 0.6923 (tt0) cc_final: 0.5920 (mm-30)
REVERT: D   95 LYS cc_start: 0.7598 (tmtt) cc_final: 0.6803 (mptt)
REVERT: D  101 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7707 (tp30)
  outliers start: 13
  outliers final: 5
  residues processed: 73
  average time/residue: 1.9169
  time to fit residues: 143.9742
Evaluate side-chains
  65 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 33 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0970
   chunk 37 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A  45 HIS
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.153739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.125382 restraints weight = 4077.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 1.42
r_work: 0.3262 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.1092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4614  Z= 0.134
  Angle     :  0.575   7.074   6330  Z= 0.268
  Chirality :  0.040   0.175    692
  Planarity :  0.005   0.047    790
  Dihedral  : 10.328  82.928    624
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 13.66 %
    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:  2.69 (0.36), residues: 558
  helix:  2.14 (0.25), residues: 440
  sheet:  None (None), residues: 0
  loop :  0.53 (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   0.011   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        0.04043 (  347)
  hydrogen bonds       : angle       4.05782 (  990)
  covalent geometry    : bond        0.00346 ( 4610)
  covalent geometry    : angle       0.57538 ( 6330)
  Misc. bond           : bond        0.02323 (    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: 16
    poor density    : 59
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 LYS cc_start: 0.7387 (mtpt) cc_final: 0.6983 (mttt)
REVERT: B   22 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6469 (tt0)
REVERT: B   90 GLU cc_start: 0.6634 (tp30) cc_final: 0.6366 (mm-30)
REVERT: B   95 LYS cc_start: 0.7663 (tmtt) cc_final: 0.7130 (mptt)
REVERT: B  101 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7879 (tp30)
REVERT: B  104 ARG cc_start: 0.7614 (ttp80) cc_final: 0.6979 (mtt90)
REVERT: C    8 THR cc_start: 0.6795 (m) cc_final: 0.6325 (p)
REVERT: D   90 GLU cc_start: 0.7112 (tt0) cc_final: 0.6256 (mm-30)
REVERT: D   95 LYS cc_start: 0.7666 (tmtt) cc_final: 0.7065 (mptt)
REVERT: D  101 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7856 (tp30)
REVERT: D  120 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7112 (mptp)
  outliers start: 16
  outliers final: 6
  residues processed: 69
  average time/residue: 2.3755
  time to fit residues: 168.9646
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  : 0.521 
-------------------------------------------------------------------------------
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   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
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 45 optimal weight:    0.2980
   chunk 26 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0970
   chunk 54 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 28 optimal weight:    0.1980
   chunk 34 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.3778

-------------------------------------------------------------------------------
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 = 0.3641 r_free = 0.3641 target = 0.156408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.128232 restraints weight = 4120.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 1.42
r_work: 0.3283 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.1189

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= 0.112
  Angle     :  0.544   7.153   6330  Z= 0.250
  Chirality :  0.038   0.145    692
  Planarity :  0.005   0.046    790
  Dihedral  : 10.034  80.193    624
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 14.76 %
    Favored  : 82.60 %
  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:  2.95 (0.36), residues: 558
  helix:  2.27 (0.25), residues: 448
  sheet:  None (None), residues: 0
  loop :  0.74 (0.62), residues: 110

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   0.008   0.001   PHE D 118 
 TYR   0.007   0.001   TYR D  35 
 ARG   0.001   0.000   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03490 (  347)
  hydrogen bonds       : angle       3.88542 (  990)
  covalent geometry    : bond        0.00291 ( 4610)
  covalent geometry    : angle       0.54374 ( 6330)
  Misc. bond           : bond        0.01389 (    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  : 0.538 
Fit side-chains
REVERT: B   90 GLU cc_start: 0.6661 (tp30) cc_final: 0.6379 (mm-30)
REVERT: B   95 LYS cc_start: 0.7659 (tmtt) cc_final: 0.7140 (mptt)
REVERT: B  101 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7842 (tp30)
REVERT: B  104 ARG cc_start: 0.7597 (ttp80) cc_final: 0.6964 (mtt90)
REVERT: C    8 THR cc_start: 0.6697 (m) cc_final: 0.6271 (p)
REVERT: D   90 GLU cc_start: 0.7160 (tt0) cc_final: 0.6220 (mm-30)
REVERT: D   95 LYS cc_start: 0.7662 (tmtt) cc_final: 0.7101 (mptt)
REVERT: D  101 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7815 (tp30)
REVERT: D  104 ARG cc_start: 0.7620 (ttp-170) cc_final: 0.6823 (mtt90)
REVERT: D  120 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7048 (mptp)
  outliers start: 12
  outliers final: 4
  residues processed: 72
  average time/residue: 2.3681
  time to fit residues: 175.5584
Evaluate side-chains
  64 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
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   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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 4 optimal weight:    0.0670
   chunk 7 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    0.2980
   chunk 55 optimal weight:    0.7980
   chunk 28 optimal weight:    0.4980
   chunk 22 optimal weight:    0.0980
   chunk 32 optimal weight:    0.4980
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.2918

-------------------------------------------------------------------------------
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 = 0.3640 r_free = 0.3640 target = 0.156849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.128972 restraints weight = 4055.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 1.40
r_work: 0.3167 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4614  Z= 0.106
  Angle     :  0.531   6.809   6330  Z= 0.243
  Chirality :  0.037   0.130    692
  Planarity :  0.005   0.045    790
  Dihedral  :  9.809  80.669    624
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.64 %
    Favored  : 81.94 %
  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:  3.07 (0.36), residues: 558
  helix:  2.35 (0.25), residues: 448
  sheet:  None (None), residues: 0
  loop :  0.76 (0.62), residues: 110

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 A 128 
 TYR   0.007   0.001   TYR B  35 
 ARG   0.002   0.000   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03286 (  347)
  hydrogen bonds       : angle       3.80762 (  990)
  covalent geometry    : bond        0.00275 ( 4610)
  covalent geometry    : angle       0.53145 ( 6330)
  Misc. bond           : bond        0.01485 (    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
  71 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.435 
Fit side-chains
REVERT: B   26 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7260 (tt0)
REVERT: B   90 GLU cc_start: 0.6547 (tp30) cc_final: 0.6192 (mm-30)
REVERT: B   95 LYS cc_start: 0.7577 (tmtt) cc_final: 0.6996 (mptt)
REVERT: B  101 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7736 (tp30)
REVERT: B  104 ARG cc_start: 0.7637 (ttp80) cc_final: 0.6817 (mtt90)
REVERT: C    3 SER cc_start: 0.7059 (OUTLIER) cc_final: 0.6603 (p)
REVERT: C    8 THR cc_start: 0.6405 (m) cc_final: 0.5993 (p)
REVERT: D   17 LYS cc_start: 0.7446 (mtmt) cc_final: 0.6929 (mtpt)
REVERT: D   65 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7862 (mtmm)
REVERT: D   90 GLU cc_start: 0.7041 (tt0) cc_final: 0.5935 (mm-30)
REVERT: D   95 LYS cc_start: 0.7621 (tmtt) cc_final: 0.6928 (mptt)
REVERT: D  101 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7700 (tp30)
REVERT: D  104 ARG cc_start: 0.7576 (ttp-170) cc_final: 0.6673 (mtt90)
REVERT: D  120 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7000 (mptp)
  outliers start: 11
  outliers final: 3
  residues processed: 65
  average time/residue: 1.6120
  time to fit residues: 107.8238
Evaluate side-chains
  64 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain D residue   65 LYS
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:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   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 = 0.3609 r_free = 0.3609 target = 0.153195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.124955 restraints weight = 4098.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 1.43
r_work: 0.3249 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.1283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   4614  Z= 0.139
  Angle     :  0.573   6.167   6330  Z= 0.267
  Chirality :  0.041   0.161    692
  Planarity :  0.005   0.047    790
  Dihedral  :  9.902  81.966    620
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 15.86 %
    Favored  : 81.06 %
  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        0.04117 (  347)
  hydrogen bonds       : angle       3.98604 (  990)
  covalent geometry    : bond        0.00360 ( 4610)
  covalent geometry    : angle       0.57330 ( 6330)
  Misc. bond           : bond        0.03406 (    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
  76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.429 
Fit side-chains
REVERT: B   17 LYS cc_start: 0.7314 (mtpt) cc_final: 0.6899 (mttt)
REVERT: B   22 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6575 (tt0)
REVERT: B   90 GLU cc_start: 0.6705 (tp30) cc_final: 0.6446 (mm-30)
REVERT: B   95 LYS cc_start: 0.7694 (tmtt) cc_final: 0.7191 (mptt)
REVERT: B  101 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7884 (tp30)
REVERT: B  104 ARG cc_start: 0.7662 (ttp80) cc_final: 0.7029 (mtt90)
REVERT: C    3 SER cc_start: 0.7293 (OUTLIER) cc_final: 0.6806 (p)
REVERT: C    8 THR cc_start: 0.6873 (m) cc_final: 0.6389 (p)
REVERT: D   90 GLU cc_start: 0.7192 (tt0) cc_final: 0.6290 (mm-30)
REVERT: D   95 LYS cc_start: 0.7736 (tmtt) cc_final: 0.7165 (mptt)
REVERT: D  101 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7874 (tp30)
REVERT: D  104 ARG cc_start: 0.7676 (ttp-170) cc_final: 0.6899 (mtt90)
  outliers start: 14
  outliers final: 5
  residues processed: 69
  average time/residue: 1.5483
  time to fit residues: 109.9968
Evaluate side-chains
  69 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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:    0.8980
   chunk 37 optimal weight:    0.4980
   chunk 0 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 18 optimal weight:    0.4980
   chunk 16 optimal weight:    0.0970
   overall best weight:    0.4778

-------------------------------------------------------------------------------
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 = 0.3631 r_free = 0.3631 target = 0.155203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.127406 restraints weight = 4036.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 1.40
r_work: 0.3286 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.1299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4614  Z= 0.121
  Angle     :  0.553   6.538   6330  Z= 0.256
  Chirality :  0.039   0.144    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.811  80.892    620
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 16.08 %
    Favored  : 81.28 %
  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:  2.21 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop :  0.63 (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 C  58 
 PHE   0.008   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        0.03734 (  347)
  hydrogen bonds       : angle       3.92039 (  990)
  covalent geometry    : bond        0.00315 ( 4610)
  covalent geometry    : angle       0.55338 ( 6330)
  Misc. bond           : bond        0.01973 (    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
  70 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
REVERT: B   26 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7247 (tt0)
REVERT: B   90 GLU cc_start: 0.6629 (tp30) cc_final: 0.6363 (mm-30)
REVERT: B   95 LYS cc_start: 0.7656 (tmtt) cc_final: 0.7157 (mptt)
REVERT: B  101 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7839 (tp30)
REVERT: B  104 ARG cc_start: 0.7583 (ttp80) cc_final: 0.6941 (mtt90)
REVERT: C    3 SER cc_start: 0.7215 (OUTLIER) cc_final: 0.6761 (p)
REVERT: C    8 THR cc_start: 0.6769 (m) cc_final: 0.6318 (p)
REVERT: D   90 GLU cc_start: 0.7158 (tt0) cc_final: 0.6240 (mm-30)
REVERT: D   95 LYS cc_start: 0.7728 (tmtt) cc_final: 0.7168 (mptt)
REVERT: D  101 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7841 (tp30)
REVERT: D  120 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7128 (mptp)
  outliers start: 12
  outliers final: 4
  residues processed: 64
  average time/residue: 1.5612
  time to fit residues: 102.9415
Evaluate side-chains
  66 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0870
   chunk 47 optimal weight:    0.0980
   chunk 33 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.4758

-------------------------------------------------------------------------------
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 = 0.3626 r_free = 0.3626 target = 0.155000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.126919 restraints weight = 4083.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 1.43
r_work: 0.3282 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.1331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4614  Z= 0.121
  Angle     :  0.551   6.362   6330  Z= 0.255
  Chirality :  0.039   0.141    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.796  81.065    620
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 16.52 %
    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 (0.25), residues: 450
  sheet:  None (None), residues: 0
  loop :  0.64 (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 C  58 
 PHE   0.008   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        0.03726 (  347)
  hydrogen bonds       : angle       3.91403 (  990)
  covalent geometry    : bond        0.00315 ( 4610)
  covalent geometry    : angle       0.55122 ( 6330)
  Misc. bond           : bond        0.02217 (    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
  71 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 LYS cc_start: 0.7325 (mtpt) cc_final: 0.6906 (mttt)
REVERT: B   22 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6544 (tt0)
REVERT: B   26 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7368 (tt0)
REVERT: B   90 GLU cc_start: 0.6701 (tp30) cc_final: 0.6437 (mm-30)
REVERT: B   95 LYS cc_start: 0.7634 (tmtt) cc_final: 0.7172 (mptt)
REVERT: B  101 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7865 (tp30)
REVERT: B  104 ARG cc_start: 0.7612 (ttp80) cc_final: 0.6986 (mtt90)
REVERT: C    3 SER cc_start: 0.7232 (OUTLIER) cc_final: 0.6796 (p)
REVERT: C    8 THR cc_start: 0.6847 (m) cc_final: 0.6404 (p)
REVERT: D   68 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7207 (mp)
REVERT: D   90 GLU cc_start: 0.7212 (tt0) cc_final: 0.6271 (mm-30)
REVERT: D   95 LYS cc_start: 0.7743 (tmtt) cc_final: 0.7228 (mttp)
REVERT: D  101 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7854 (tp30)
REVERT: D  120 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7108 (mptp)
  outliers start: 12
  outliers final: 4
  residues processed: 66
  average time/residue: 1.5972
  time to fit residues: 108.5512
Evaluate side-chains
  68 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   68 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:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3593 r_free = 0.3593 target = 0.151743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.123618 restraints weight = 4091.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 1.42
r_work: 0.3244 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.1355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   4614  Z= 0.157
  Angle     :  0.597   5.927   6330  Z= 0.281
  Chirality :  0.042   0.176    692
  Planarity :  0.005   0.047    790
  Dihedral  : 10.085  86.123    620
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.74 %
    Favored  : 81.06 %
  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 (0.36), residues: 558
  helix:  2.04 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop :  0.55 (0.62), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C  14 
 HIS   0.004   0.001   HIS A  58 
 PHE   0.011   0.001   PHE D 118 
 TYR   0.009   0.001   TYR D  35 
 ARG   0.001   0.000   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04461 (  347)
  hydrogen bonds       : angle       4.07950 (  990)
  covalent geometry    : bond        0.00407 ( 4610)
  covalent geometry    : angle       0.59744 ( 6330)
  Misc. bond           : bond        0.04074 (    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
  70 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.467 
Fit side-chains
REVERT: B   22 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6552 (tt0)
REVERT: B   90 GLU cc_start: 0.6657 (tp30) cc_final: 0.6415 (mm-30)
REVERT: B   95 LYS cc_start: 0.7683 (tmtt) cc_final: 0.7170 (mptt)
REVERT: B  101 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7802 (tp30)
REVERT: B  104 ARG cc_start: 0.7662 (ttp80) cc_final: 0.7002 (mtt90)
REVERT: C    3 SER cc_start: 0.7306 (OUTLIER) cc_final: 0.6795 (p)
REVERT: C    8 THR cc_start: 0.6852 (m) cc_final: 0.6361 (p)
REVERT: D   90 GLU cc_start: 0.7159 (tt0) cc_final: 0.6279 (mm-30)
REVERT: D   95 LYS cc_start: 0.7739 (tmtt) cc_final: 0.7177 (mptt)
REVERT: D  101 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7863 (tp30)
REVERT: D  104 ARG cc_start: 0.7662 (ttp-170) cc_final: 0.6877 (mtt90)
REVERT: D  120 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7125 (mptp)
  outliers start: 10
  outliers final: 3
  residues processed: 65
  average time/residue: 1.6355
  time to fit residues: 109.4229
Evaluate side-chains
  66 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3609 r_free = 0.3609 target = 0.152036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.124283 restraints weight = 4089.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 1.41
r_work: 0.3195 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   4614  Z= 0.159
  Angle     :  0.603   6.609   6330  Z= 0.283
  Chirality :  0.043   0.189    692
  Planarity :  0.005   0.047    790
  Dihedral  : 10.252  89.798    620
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.30 %
    Favored  : 81.28 %
  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:  2.53 (0.36), residues: 558
  helix:  1.98 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop :  0.53 (0.62), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   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   0.002   0.000   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04516 (  347)
  hydrogen bonds       : angle       4.11597 (  990)
  covalent geometry    : bond        0.00411 ( 4610)
  covalent geometry    : angle       0.60307 ( 6330)
  Misc. bond           : bond        0.03779 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4111.17 seconds
wall clock time: 72 minutes 22.08 seconds (4342.08 seconds total)