Starting phenix.real_space_refine
on Wed Sep 17 04:46:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqr_45820/09_2025/9cqr_45820.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqr_45820/09_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_45820/09_2025/9cqr_45820.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqr_45820/09_2025/9cqr_45820.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqr_45820/09_2025/9cqr_45820.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqr_45820/09_2025/9cqr_45820.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.14, per 1000 atoms: 0.26
  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: 0.42
  Conformation dependent library (CDL) restraints added in 109.6 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.10
  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: 0.65

  Time building geometry restraints manager: 0.56 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: 0.00
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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.730
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.440
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG D  40 
 TYR   0.010   0.001   TYR D  35 
 PHE   0.030   0.002   PHE D 118 
 TRP   0.011   0.002   TRP C  14 
 HIS   0.004   0.001   HIS B  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 ( 4610)
  covalent geometry    : angle       0.84362 ( 6330)
  hydrogen bonds       : bond        0.12972 (  347)
  hydrogen bonds       : angle       5.06708 (  990)
  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  : 0.107 
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: 0.6482
  time to fit residues: 53.4720
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  : 0.162 
-------------------------------------------------------------------------------
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 54 optimal weight:    0.2980
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0970
   chunk 32 optimal weight:    0.0010
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.3384

-------------------------------------------------------------------------------
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 = 0.3659 r_free = 0.3659 target = 0.157891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.129349 restraints weight = 4057.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 1.42
r_work: 0.3307 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3172 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.0874

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= 0.117
  Angle     :  0.558   7.181   6330  Z= 0.260
  Chirality :  0.038   0.152    692
  Planarity :  0.005   0.042    790
  Dihedral  : 10.121  80.319    624
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.32 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.08 (0.36), residues: 558
  helix:  2.40 (0.25), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.79 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  92 
 TYR   0.007   0.001   TYR D  35 
 PHE   0.008   0.001   PHE D 118 
 TRP   0.011   0.001   TRP C  14 
 HIS   0.003   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 4610)
  covalent geometry    : angle       0.55839 ( 6330)
  hydrogen bonds       : bond        0.03574 (  347)
  hydrogen bonds       : angle       4.15242 (  990)
  Misc. bond           : bond        0.01193 (    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
  72 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.183 
Fit side-chains
REVERT: B   17 LYS cc_start: 0.7466 (mtpt) cc_final: 0.7160 (mtmm)
REVERT: B   22 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6495 (tt0)
REVERT: B   68 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7172 (mp)
REVERT: B   90 GLU cc_start: 0.6695 (tp30) cc_final: 0.6407 (mm-30)
REVERT: B   95 LYS cc_start: 0.7703 (tmtt) cc_final: 0.7130 (mptt)
REVERT: B  104 ARG cc_start: 0.7576 (ttp80) cc_final: 0.6896 (mtt90)
REVERT: C   81 SER cc_start: 0.7939 (t) cc_final: 0.7551 (p)
REVERT: D   65 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8034 (mtmm)
REVERT: D   90 GLU cc_start: 0.7075 (tt0) cc_final: 0.6261 (mm-30)
REVERT: D   95 LYS cc_start: 0.7732 (tmtt) cc_final: 0.7023 (mptt)
REVERT: D  101 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7761 (tp30)
REVERT: D  104 ARG cc_start: 0.7566 (ttp-170) cc_final: 0.6803 (mtt90)
REVERT: D  120 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6869 (mptp)
  outliers start: 11
  outliers final: 3
  residues processed: 67
  average time/residue: 0.7568
  time to fit residues: 52.0713
Evaluate side-chains
  62 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
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 43 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9980
   chunk 30 optimal weight:    0.3980
   chunk 33 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 47 optimal weight:    0.5980
   chunk 46 optimal weight:    0.3980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3618 r_free = 0.3618 target = 0.154842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.126515 restraints weight = 4055.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 1.41
r_work: 0.3137 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.0939

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     :  0.562   6.979   6330  Z= 0.261
  Chirality :  0.039   0.153    692
  Planarity :  0.005   0.044    790
  Dihedral  : 10.141  79.623    624
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 13.88 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.93 (0.36), residues: 558
  helix:  2.30 (0.25), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.68 (0.60), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  40 
 TYR   0.008   0.001   TYR B  35 
 PHE   0.010   0.001   PHE D 118 
 TRP   0.010   0.001   TRP C  14 
 HIS   0.003   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4610)
  covalent geometry    : angle       0.56229 ( 6330)
  hydrogen bonds       : bond        0.03860 (  347)
  hydrogen bonds       : angle       4.03477 (  990)
  Misc. bond           : bond        0.02142 (    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
  74 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.176 
Fit side-chains
REVERT: B   17 LYS cc_start: 0.7298 (mtpt) cc_final: 0.6932 (mttt)
REVERT: B   22 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6417 (tt0)
REVERT: B   90 GLU cc_start: 0.6547 (tp30) cc_final: 0.6188 (mm-30)
REVERT: B   95 LYS cc_start: 0.7597 (tmtt) cc_final: 0.6997 (mptt)
REVERT: B  101 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7742 (tp30)
REVERT: B  104 ARG cc_start: 0.7658 (ttp80) cc_final: 0.6825 (mtt90)
REVERT: C    8 THR cc_start: 0.6491 (m) cc_final: 0.6007 (p)
REVERT: D   90 GLU cc_start: 0.6965 (tt0) cc_final: 0.5996 (mm-30)
REVERT: D   95 LYS cc_start: 0.7632 (tmtt) cc_final: 0.6872 (mptt)
REVERT: D  101 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7743 (tp30)
REVERT: D  104 ARG cc_start: 0.7619 (ttp-170) cc_final: 0.6697 (mtt90)
REVERT: D  120 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6991 (tptt)
  outliers start: 14
  outliers final: 5
  residues processed: 68
  average time/residue: 0.7771
  time to fit residues: 54.3043
Evaluate side-chains
  62 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
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 53 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0770
   chunk 16 optimal weight:    0.0980
   chunk 13 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.4338

-------------------------------------------------------------------------------
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 = 0.3635 r_free = 0.3635 target = 0.156012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.127554 restraints weight = 4063.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.44
r_work: 0.3303 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.1067

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= 0.116
  Angle     :  0.550   7.112   6330  Z= 0.253
  Chirality :  0.039   0.159    692
  Planarity :  0.005   0.045    790
  Dihedral  :  9.991  79.771    624
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 14.10 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.89 (0.36), residues: 558
  helix:  2.30 (0.25), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.54 (0.58), residues: 120

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 4610)
  covalent geometry    : angle       0.54993 ( 6330)
  hydrogen bonds       : bond        0.03602 (  347)
  hydrogen bonds       : angle       3.92622 (  990)
  Misc. bond           : bond        0.01677 (    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
  73 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.112 
Fit side-chains
REVERT: B   17 LYS cc_start: 0.7256 (mtpt) cc_final: 0.6887 (mttt)
REVERT: B   22 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6556 (tt0)
REVERT: B   90 GLU cc_start: 0.6680 (tp30) cc_final: 0.6387 (mm-30)
REVERT: B   95 LYS cc_start: 0.7712 (tmtt) cc_final: 0.7241 (mttp)
REVERT: B  101 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7869 (tp30)
REVERT: B  104 ARG cc_start: 0.7609 (ttp80) cc_final: 0.6988 (mtt90)
REVERT: C    8 THR cc_start: 0.6689 (m) cc_final: 0.6245 (p)
REVERT: D   90 GLU cc_start: 0.7109 (tt0) cc_final: 0.6272 (mm-30)
REVERT: D   95 LYS cc_start: 0.7710 (tmtt) cc_final: 0.7090 (mptt)
REVERT: D  101 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7837 (tp30)
REVERT: D  104 ARG cc_start: 0.7623 (ttp-170) cc_final: 0.6829 (mtt90)
REVERT: D  120 LYS cc_start: 0.7375 (OUTLIER) cc_final: 0.6963 (mptp)
  outliers start: 14
  outliers final: 3
  residues processed: 68
  average time/residue: 0.7402
  time to fit residues: 51.6331
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  : 0.154 
-------------------------------------------------------------------------------
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  101 GLU
Chi-restraints excluded: chain D residue  120 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 21 optimal weight:    0.2980
   chunk 52 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   chunk 23 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.152722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.124253 restraints weight = 4093.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 1.42
r_work: 0.3261 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.1102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   4614  Z= 0.143
  Angle     :  0.580   6.291   6330  Z= 0.270
  Chirality :  0.041   0.168    692
  Planarity :  0.005   0.046    790
  Dihedral  : 10.113  81.581    622
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.05
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.75 (0.36), residues: 558
  helix:  2.10 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop :  0.78 (0.62), residues: 108

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 4610)
  covalent geometry    : angle       0.58030 ( 6330)
  hydrogen bonds       : bond        0.04200 (  347)
  hydrogen bonds       : angle       4.04425 (  990)
  Misc. bond           : bond        0.03369 (    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
  79 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.170 
Fit side-chains
REVERT: B   17 LYS cc_start: 0.7370 (mtpt) cc_final: 0.6961 (mttt)
REVERT: B   22 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6574 (tt0)
REVERT: B   90 GLU cc_start: 0.6679 (tp30) cc_final: 0.6382 (mm-30)
REVERT: B   95 LYS cc_start: 0.7736 (tmtt) cc_final: 0.7245 (mttp)
REVERT: B  101 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7893 (tp30)
REVERT: B  104 ARG cc_start: 0.7646 (ttp80) cc_final: 0.7000 (mtt90)
REVERT: C    8 THR cc_start: 0.6834 (m) cc_final: 0.6340 (p)
REVERT: D   68 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7203 (mp)
REVERT: D   90 GLU cc_start: 0.7105 (tt0) cc_final: 0.6249 (mm-30)
REVERT: D   95 LYS cc_start: 0.7686 (tmtt) cc_final: 0.7089 (mptt)
REVERT: D  101 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7855 (tp30)
REVERT: D  104 ARG cc_start: 0.7662 (ttp-170) cc_final: 0.6872 (mpt90)
REVERT: D  120 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7110 (mptp)
  outliers start: 17
  outliers final: 8
  residues processed: 71
  average time/residue: 0.7634
  time to fit residues: 55.7831
Evaluate side-chains
  69 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
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 B residue  121 GLU
Chi-restraints excluded: chain C residue    2 LEU
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain D residue   14 LEU
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
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 50 optimal weight:    4.9990
   chunk 32 optimal weight:    0.4980
   chunk 22 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 28 optimal weight:    0.4980
   chunk 26 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3612 r_free = 0.3612 target = 0.153688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.125439 restraints weight = 4145.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 1.42
r_work: 0.3264 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.1166

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= 0.131
  Angle     :  0.566   6.892   6330  Z= 0.262
  Chirality :  0.040   0.175    692
  Planarity :  0.005   0.047    790
  Dihedral  : 10.052  81.936    622
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 14.10 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.75 (0.36), residues: 558
  helix:  2.12 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop :  0.71 (0.62), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  92 
 TYR   0.008   0.001   TYR D  35 
 PHE   0.010   0.001   PHE D 118 
 TRP   0.011   0.001   TRP C  14 
 HIS   0.003   0.001   HIS C  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 4610)
  covalent geometry    : angle       0.56611 ( 6330)
  hydrogen bonds       : bond        0.03929 (  347)
  hydrogen bonds       : angle       3.98172 (  990)
  Misc. bond           : bond        0.02425 (    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
  75 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 LYS cc_start: 0.7247 (mtpt) cc_final: 0.6826 (mttt)
REVERT: B   22 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6547 (tt0)
REVERT: B   90 GLU cc_start: 0.6646 (tp30) cc_final: 0.6339 (mm-30)
REVERT: B   95 LYS cc_start: 0.7716 (tmtt) cc_final: 0.7235 (mttp)
REVERT: B  101 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7865 (tp30)
REVERT: B  104 ARG cc_start: 0.7617 (ttp80) cc_final: 0.6958 (mtt90)
REVERT: C    8 THR cc_start: 0.6795 (m) cc_final: 0.6319 (p)
REVERT: D   90 GLU cc_start: 0.7097 (tt0) cc_final: 0.6240 (mm-30)
REVERT: D   95 LYS cc_start: 0.7664 (tmtt) cc_final: 0.7080 (mptt)
REVERT: D  101 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7842 (tp30)
REVERT: D  120 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7099 (mptp)
  outliers start: 17
  outliers final: 7
  residues processed: 67
  average time/residue: 0.7609
  time to fit residues: 52.4504
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  : 0.172 
-------------------------------------------------------------------------------
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    2 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 23 optimal weight:    8.9990
   chunk 52 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3599 r_free = 0.3599 target = 0.152376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.124046 restraints weight = 4160.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 1.44
r_work: 0.3263 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.1210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4614  Z= 0.143
  Angle     :  0.578   6.347   6330  Z= 0.270
  Chirality :  0.041   0.181    692
  Planarity :  0.005   0.047    790
  Dihedral  : 10.178  85.027    622
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 14.76 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.67 (0.36), residues: 558
  helix:  2.06 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop :  0.67 (0.63), residues: 108

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 4610)
  covalent geometry    : angle       0.57849 ( 6330)
  hydrogen bonds       : bond        0.04210 (  347)
  hydrogen bonds       : angle       4.03359 (  990)
  Misc. bond           : bond        0.03166 (    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  : 0.177 
Fit side-chains
REVERT: B   17 LYS cc_start: 0.7349 (mtpt) cc_final: 0.6909 (mttt)
REVERT: B   22 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6597 (tt0)
REVERT: B   68 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7177 (mp)
REVERT: B   90 GLU cc_start: 0.6677 (tp30) cc_final: 0.6384 (mm-30)
REVERT: B   95 LYS cc_start: 0.7707 (tmtt) cc_final: 0.7230 (mttp)
REVERT: B  101 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7877 (tp30)
REVERT: B  104 ARG cc_start: 0.7640 (ttp80) cc_final: 0.6976 (mtt90)
REVERT: C    8 THR cc_start: 0.6841 (m) cc_final: 0.6346 (p)
REVERT: D   90 GLU cc_start: 0.7139 (tt0) cc_final: 0.6271 (mm-30)
REVERT: D   95 LYS cc_start: 0.7698 (tmtt) cc_final: 0.7101 (mptt)
REVERT: D  101 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7857 (tp30)
REVERT: D  104 ARG cc_start: 0.7657 (ttp-170) cc_final: 0.6865 (mtt90)
REVERT: D  120 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7143 (mptp)
  outliers start: 15
  outliers final: 8
  residues processed: 70
  average time/residue: 0.7501
  time to fit residues: 53.9247
Evaluate side-chains
  72 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
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 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
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 8 optimal weight:    0.4980
   chunk 49 optimal weight:    0.6980
   chunk 55 optimal weight:    0.0970
   chunk 19 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0370
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.4456

-------------------------------------------------------------------------------
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 = 0.3637 r_free = 0.3637 target = 0.155276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.126909 restraints weight = 4095.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 1.46
r_work: 0.3236 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.1243

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= 0.118
  Angle     :  0.551   6.814   6330  Z= 0.254
  Chirality :  0.039   0.146    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.974  82.843    622
  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 :  3.30 %
    Allowed  : 14.98 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.86 (0.36), residues: 558
  helix:  2.19 (0.25), residues: 450
  sheet:  None (None), residues: 0
  loop :  0.73 (0.63), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  92 
 TYR   0.007   0.001   TYR D  35 
 PHE   0.009   0.001   PHE D 118 
 TRP   0.012   0.001   TRP C  14 
 HIS   0.003   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 4610)
  covalent geometry    : angle       0.55080 ( 6330)
  hydrogen bonds       : bond        0.03667 (  347)
  hydrogen bonds       : angle       3.91969 (  990)
  Misc. bond           : bond        0.01693 (    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
  76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: B   22 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6529 (tt0)
REVERT: B   65 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7911 (mtmm)
REVERT: B   90 GLU cc_start: 0.6747 (tp30) cc_final: 0.6485 (mm-30)
REVERT: B   95 LYS cc_start: 0.7651 (tmtt) cc_final: 0.7200 (mptt)
REVERT: B  101 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7889 (tp30)
REVERT: B  104 ARG cc_start: 0.7625 (ttp80) cc_final: 0.7020 (mtt90)
REVERT: C    3 SER cc_start: 0.7246 (OUTLIER) cc_final: 0.6767 (p)
REVERT: C    8 THR cc_start: 0.6780 (m) cc_final: 0.6324 (p)
REVERT: D   90 GLU cc_start: 0.7171 (tt0) cc_final: 0.6248 (mm-30)
REVERT: D   95 LYS cc_start: 0.7706 (tmtt) cc_final: 0.7157 (mptt)
REVERT: D  101 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7911 (tp30)
REVERT: D  120 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7077 (mptp)
  outliers start: 15
  outliers final: 4
  residues processed: 70
  average time/residue: 0.7979
  time to fit residues: 57.3697
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  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue  101 GLU
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 38 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   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 = 0.3620 r_free = 0.3620 target = 0.153198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.124840 restraints weight = 4065.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 1.45
r_work: 0.3219 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3086 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.1269

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= 0.146
  Angle     :  0.580   6.228   6330  Z= 0.271
  Chirality :  0.041   0.172    692
  Planarity :  0.005   0.047    790
  Dihedral  : 10.193  86.193    622
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 16.08 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.65 (0.36), residues: 558
  helix:  2.05 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop :  0.64 (0.62), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  92 
 TYR   0.008   0.001   TYR B  35 
 PHE   0.011   0.001   PHE D 118 
 TRP   0.010   0.001   TRP C  14 
 HIS   0.004   0.001   HIS C  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 4610)
  covalent geometry    : angle       0.57984 ( 6330)
  hydrogen bonds       : bond        0.04271 (  347)
  hydrogen bonds       : angle       4.04746 (  990)
  Misc. bond           : bond        0.03520 (    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: 15
    poor density    : 59
  time to evaluate  : 0.185 
Fit side-chains
REVERT: B   90 GLU cc_start: 0.6747 (tp30) cc_final: 0.6466 (mm-30)
REVERT: B   95 LYS cc_start: 0.7663 (tmtt) cc_final: 0.7182 (mptt)
REVERT: B  101 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7824 (tp30)
REVERT: B  104 ARG cc_start: 0.7672 (ttp80) cc_final: 0.7036 (mtt90)
REVERT: C    8 THR cc_start: 0.6888 (m) cc_final: 0.6406 (p)
REVERT: D   90 GLU cc_start: 0.7193 (tt0) cc_final: 0.6267 (mm-30)
REVERT: D   95 LYS cc_start: 0.7697 (tmtt) cc_final: 0.7139 (mptt)
REVERT: D  101 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7927 (tp30)
REVERT: D  104 ARG cc_start: 0.7689 (ttp-170) cc_final: 0.6952 (mtt90)
REVERT: D  120 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.7113 (mptp)
  outliers start: 15
  outliers final: 6
  residues processed: 68
  average time/residue: 0.7403
  time to fit residues: 51.7960
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  : 0.174 
-------------------------------------------------------------------------------
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    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 43 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0470
   chunk 4 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.5478

-------------------------------------------------------------------------------
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 = 0.154179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.125757 restraints weight = 4069.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.45
r_work: 0.3219 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.1243

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= 0.127
  Angle     :  0.564   7.135   6330  Z= 0.262
  Chirality :  0.040   0.162    692
  Planarity :  0.005   0.047    790
  Dihedral  : 10.099  85.559    622
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.52 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.75 (0.36), residues: 558
  helix:  2.12 (0.25), residues: 450
  sheet:  None (None), residues: 0
  loop :  0.68 (0.63), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  92 
 TYR   0.007   0.001   TYR B  35 
 PHE   0.010   0.001   PHE D 118 
 TRP   0.011   0.001   TRP C  14 
 HIS   0.003   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4610)
  covalent geometry    : angle       0.56357 ( 6330)
  hydrogen bonds       : bond        0.03926 (  347)
  hydrogen bonds       : angle       3.99816 (  990)
  Misc. bond           : bond        0.02329 (    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
  67 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
REVERT: B   26 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7294 (tt0)
REVERT: B   90 GLU cc_start: 0.6704 (tp30) cc_final: 0.6450 (mm-30)
REVERT: B   95 LYS cc_start: 0.7648 (tmtt) cc_final: 0.7175 (mptt)
REVERT: B  101 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7886 (tp30)
REVERT: B  104 ARG cc_start: 0.7633 (ttp80) cc_final: 0.7014 (mtt90)
REVERT: C    8 THR cc_start: 0.6830 (m) cc_final: 0.6351 (p)
REVERT: D   90 GLU cc_start: 0.7167 (tt0) cc_final: 0.6227 (mm-30)
REVERT: D   95 LYS cc_start: 0.7712 (tmtt) cc_final: 0.7175 (mptt)
REVERT: D  101 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7903 (tp30)
REVERT: D  120 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7054 (mptp)
  outliers start: 11
  outliers final: 4
  residues processed: 62
  average time/residue: 0.7921
  time to fit residues: 50.4193
Evaluate side-chains
  63 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
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   14 LEU
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  120 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 55 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0570
   chunk 46 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.5698

-------------------------------------------------------------------------------
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 = 0.3637 r_free = 0.3637 target = 0.154602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.126734 restraints weight = 4029.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 1.41
r_work: 0.3239 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.1262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4614  Z= 0.130
  Angle     :  0.565   7.015   6330  Z= 0.264
  Chirality :  0.040   0.164    692
  Planarity :  0.005   0.047    790
  Dihedral  : 10.120  86.198    622
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 17.62 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.71 (0.36), residues: 558
  helix:  2.09 (0.25), residues: 450
  sheet:  None (None), residues: 0
  loop :  0.67 (0.63), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  92 
 TYR   0.007   0.001   TYR B  35 
 PHE   0.010   0.001   PHE D 118 
 TRP   0.011   0.001   TRP C  14 
 HIS   0.003   0.001   HIS C  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 4610)
  covalent geometry    : angle       0.56547 ( 6330)
  hydrogen bonds       : bond        0.03985 (  347)
  hydrogen bonds       : angle       4.00164 (  990)
  Misc. bond           : bond        0.02620 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1778.99 seconds
wall clock time: 31 minutes 7.17 seconds (1867.17 seconds total)