Starting phenix.real_space_refine
on Wed Jun  4 23:13:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqp_45818/06_2025/9cqp_45818.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqp_45818/06_2025/9cqp_45818.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cqp_45818/06_2025/9cqp_45818.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqp_45818/06_2025/9cqp_45818.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqp_45818/06_2025/9cqp_45818.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqp_45818/06_2025/9cqp_45818.cif"
  }
  resolution = 2.78
  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=   0.023
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 17 residue(s): 0.02s

  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: 3.34, per 1000 atoms: 0.75
  Number of scatterers: 4470
  At special positions: 0
  Unit cell: (77.175, 71.295, 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: 1.29
  Conformation dependent library (CDL) restraints added in 845.4 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
      88.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  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: 3.591A  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
      removed outlier: 3.535A  pdb=" N   LYS B  17 " --> pdb=" O   ALA B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 35
      removed outlier: 4.581A  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 55
    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: 3.969A  pdb=" N   PHE B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.520A  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: 3.582A  pdb=" N   PHE C  98 " --> pdb=" O   ASP C  94 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 137
    Processing helix  chain 'D' and resid 4 through 17
      removed outlier: 3.553A  pdb=" N   LYS D  17 " --> pdb=" O   ALA D  13 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 19 through 35
      removed outlier: 4.452A  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: 3.931A  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: 3.951A  pdb=" N   PHE D 103 " --> pdb=" O   ASP D  99 " (cutoff:3.500A)
      removed outlier: 3.527A  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

    343 hydrogen bonds defined for protein.
    978 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: 1.31

  Time building geometry restraints manager: 1.56 seconds

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

  Histogram of bond lengths:
        1.21 -     1.38: 1645
        1.38 -     1.55: 2923
        1.55 -     1.72: 8
        1.72 -     1.89: 18
        1.89 -     2.06: 16
  Bond restraints: 4610
  Sorted by residual:
  bond pdb=" CA  PRO D 124 "
       pdb=" C   PRO D 124 "
    ideal  model  delta    sigma   weight residual
    1.517  1.547 -0.030 9.30e-03 1.16e+04 1.02e+01
  bond pdb=" N   PHE B  42 "
       pdb=" CA  PHE B  42 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.038 1.18e-02 7.18e+03 1.01e+01
  bond pdb=" N   VAL B  11 "
       pdb=" CA  VAL B  11 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.17e-02 7.31e+03 9.06e+00
  bond pdb=" N   VAL D  11 "
       pdb=" CA  VAL D  11 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.17e-02 7.31e+03 8.88e+00
  bond pdb=" N   PHE D 118 "
       pdb=" CA  PHE D 118 "
    ideal  model  delta    sigma   weight residual
    1.455  1.493 -0.038 1.29e-02 6.01e+03 8.60e+00
  ... (remaining 4605 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 6015
        1.99 -     3.97: 276
        3.97 -     5.96: 35
        5.96 -     7.95: 2
        7.95 -     9.94: 2
  Bond angle restraints: 6330
  Sorted by residual:
  angle pdb=" C   THR C 118 "
        pdb=" CA  THR C 118 "
        pdb=" CB  THR C 118 "
      ideal   model   delta    sigma   weight residual
     109.45  119.39   -9.94 1.81e+00 3.05e-01 3.01e+01
  angle pdb=" C   THR A 118 "
        pdb=" CA  THR A 118 "
        pdb=" CB  THR A 118 "
      ideal   model   delta    sigma   weight residual
     109.45  119.11   -9.66 1.81e+00 3.05e-01 2.85e+01
  angle pdb=" CA  PRO D 124 "
        pdb=" C   PRO D 124 "
        pdb=" N   PRO D 125 "
      ideal   model   delta    sigma   weight residual
     117.93  124.25   -6.32 1.20e+00 6.94e-01 2.78e+01
  angle pdb=" C   GLY B  46 "
        pdb=" N   ASP B  47 "
        pdb=" CA  ASP B  47 "
      ideal   model   delta    sigma   weight residual
     121.24  114.68    6.56 1.44e+00 4.82e-01 2.07e+01
  angle pdb=" N   PRO D 124 "
        pdb=" CA  PRO D 124 "
        pdb=" C   PRO D 124 "
      ideal   model   delta    sigma   weight residual
     110.70  116.19   -5.49 1.22e+00 6.72e-01 2.03e+01
  ... (remaining 6325 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.65: 2360
       16.65 -    33.30: 170
       33.30 -    49.94: 51
       49.94 -    66.59: 25
       66.59 -    83.24: 8
  Dihedral angle restraints: 2614
    sinusoidal: 990
      harmonic: 1624
  Sorted by residual:
  dihedral pdb=" CG  ARG A  92 "
           pdb=" CD  ARG A  92 "
           pdb=" NE  ARG A  92 "
           pdb=" CZ  ARG A  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -39.93  -50.07     2      1.50e+01 4.44e-03 1.25e+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  -80.62   80.62     2      2.00e+01 2.50e-03 1.17e+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  -80.59   80.59     2      2.00e+01 2.50e-03 1.17e+01
  ... (remaining 2611 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 508
       0.048 -    0.095: 136
       0.095 -    0.143: 33
       0.143 -    0.190: 12
       0.190 -    0.238: 3
  Chirality restraints: 692
  Sorted by residual:
  chirality pdb=" CB  VAL D 134 "
            pdb=" CA  VAL D 134 "
            pdb=" CG1 VAL D 134 "
            pdb=" CG2 VAL D 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CB  VAL B  67 "
            pdb=" CA  VAL B  67 "
            pdb=" CG1 VAL B  67 "
            pdb=" CG2 VAL B  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CB  VAL D 133 "
            pdb=" CA  VAL D 133 "
            pdb=" CG1 VAL D 133 "
            pdb=" CG2 VAL D 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.95e-01
  ... (remaining 689 not shown)

  Planarity restraints: 790
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A   3 "    0.032 5.00e-02 4.00e+02   4.85e-02 3.76e+00
        pdb=" N   PRO A   4 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A   4 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A   4 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 129 "    0.010 2.00e-02 2.50e+03   1.91e-02 3.64e+00
        pdb=" C   LEU A 129 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   LEU A 129 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ALA A 130 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 135 "   -0.009 2.00e-02 2.50e+03   1.83e-02 3.35e+00
        pdb=" C   VAL C 135 "    0.032 2.00e-02 2.50e+03
        pdb=" O   VAL C 135 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   LEU C 136 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 787 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 723
        2.77 -     3.30: 4355
        3.30 -     3.83: 7857
        3.83 -     4.37: 9243
        4.37 -     4.90: 15632
  Nonbonded interactions: 37810
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU C  27 "
            pdb=" NE2 HIS C 112 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" OE1 GLU A  27 "
            pdb=" NE2 HIS A 112 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" O   PRO A  77 "
            pdb=" OH  TYR A 140 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OE1 GLU D  26 "
            pdb=" NE2 HIS D 117 "
     model   vdw
     2.439 3.120
  nonbonded pdb=" OE2 GLU C  27 "
            pdb=" NE  ARG C  31 "
     model   vdw
     2.449 3.120
  ... (remaining 37805 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:             3.120
  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:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.710
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:18.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
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   0.072   4614  Z= 0.369
  Angle     :  0.868   9.937   6330  Z= 0.596
  Chirality :  0.051   0.238    692
  Planarity :  0.006   0.048    790
  Dihedral  : 15.268  83.240   1562
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 11.01 %
    Favored  : 86.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.75 (0.36), residues: 558
  helix:  2.24 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.40 (0.62), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP D  15 
 HIS   0.005   0.001   HIS D  77 
 PHE   0.016   0.002   PHE B  42 
 TYR   0.010   0.001   TYR D 130 
 ARG   0.011   0.001   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11420 (  343)
  hydrogen bonds       : angle       5.02983 (  978)
  covalent geometry    : bond        0.00530 ( 4610)
  covalent geometry    : angle       0.86826 ( 6330)
  Misc. bond           : bond        0.05297 (    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
  68 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.492 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6864 (mmt) cc_final: 0.6654 (mtt)
REVERT: A   99 LYS cc_start: 0.8155 (mttm) cc_final: 0.7870 (mtmt)
REVERT: A  118 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7876 (p)
REVERT: B   22 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6622 (mm-30)
REVERT: B   43 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6638 (mp0)
REVERT: B   66 LYS cc_start: 0.7939 (mmmm) cc_final: 0.7470 (mttt)
REVERT: B   68 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7398 (mp)
REVERT: B   95 LYS cc_start: 0.7978 (tmtt) cc_final: 0.7192 (mptt)
REVERT: B  104 ARG cc_start: 0.7438 (ttp80) cc_final: 0.6381 (mpt180)
REVERT: C   61 LYS cc_start: 0.8194 (mttt) cc_final: 0.7712 (mttp)
REVERT: C   99 LYS cc_start: 0.8182 (mttp) cc_final: 0.7920 (mtmt)
REVERT: D   66 LYS cc_start: 0.7870 (mmmm) cc_final: 0.7571 (mtmt)
REVERT: D   95 LYS cc_start: 0.8112 (tttt) cc_final: 0.7307 (mptt)
REVERT: D  104 ARG cc_start: 0.7460 (ttp80) cc_final: 0.6343 (mpt180)
REVERT: D  120 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6821 (tptp)
  outliers start: 13
  outliers final: 4
  residues processed: 65
  average time/residue: 1.8146
  time to fit residues: 121.8278
Evaluate side-chains
  60 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   43 GLU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain C residue  118 THR
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   68 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:    0.0870
   chunk 42 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 22 optimal weight:    0.5980
   chunk 43 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  89 HIS
D  77 HIS
D 131 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.177728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.152303 restraints weight = 3866.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 1.13
r_work: 0.3467 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.1066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080   4614  Z= 0.129
  Angle     :  0.576   6.687   6330  Z= 0.271
  Chirality :  0.039   0.130    692
  Planarity :  0.005   0.044    790
  Dihedral  : 10.784  80.825    633
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 11.23 %
    Favored  : 86.12 %
  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:  2.74 (0.36), residues: 558
  helix:  2.23 (0.25), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.33 (0.61), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  14 
 HIS   0.003   0.001   HIS A  58 
 PHE   0.007   0.001   PHE B  42 
 TYR   0.006   0.001   TYR B 130 
 ARG   0.002   0.001   ARG D  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03671 (  343)
  hydrogen bonds       : angle       4.17697 (  978)
  covalent geometry    : bond        0.00333 ( 4610)
  covalent geometry    : angle       0.57555 ( 6330)
  Misc. bond           : bond        0.07163 (    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
  63 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 0.506 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.6388 (mtt)
REVERT: A   99 LYS cc_start: 0.8087 (mttm) cc_final: 0.7761 (mtmt)
REVERT: B   22 GLU cc_start: 0.6708 (mt-10) cc_final: 0.6281 (tp30)
REVERT: B   66 LYS cc_start: 0.7617 (mmmm) cc_final: 0.7124 (mttt)
REVERT: B   95 LYS cc_start: 0.7878 (tmtt) cc_final: 0.7137 (mptt)
REVERT: B  104 ARG cc_start: 0.7358 (ttp80) cc_final: 0.6177 (mpt180)
REVERT: C   61 LYS cc_start: 0.8129 (mttt) cc_final: 0.7608 (mtpt)
REVERT: C   76 MET cc_start: 0.6837 (mtt) cc_final: 0.6261 (mtt)
REVERT: C   99 LYS cc_start: 0.8142 (mttp) cc_final: 0.7821 (mtmt)
REVERT: D   22 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6699 (mp0)
REVERT: D   66 LYS cc_start: 0.7631 (mmmm) cc_final: 0.7163 (mttt)
REVERT: D   95 LYS cc_start: 0.7967 (tttt) cc_final: 0.7150 (mptt)
REVERT: D  104 ARG cc_start: 0.7339 (ttp80) cc_final: 0.6117 (mpt180)
REVERT: D  120 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6913 (tttm)
  outliers start: 12
  outliers final: 2
  residues processed: 61
  average time/residue: 2.6792
  time to fit residues: 169.5808
Evaluate side-chains
  52 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain D residue   14 LEU
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:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 42 optimal weight:    0.4980
   chunk 15 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 28 optimal weight:    0.2980
   chunk 31 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  89 HIS
D 131 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.174970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.150080 restraints weight = 3878.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 1.11
r_work: 0.3440 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093   4614  Z= 0.137
  Angle     :  0.578   6.423   6330  Z= 0.271
  Chirality :  0.039   0.125    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.590  78.814    622
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.33 %
    Favored  : 85.68 %
  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:  2.21 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.35 (0.58), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  14 
 HIS   0.003   0.001   HIS C 112 
 PHE   0.009   0.001   PHE D 118 
 TYR   0.006   0.001   TYR D  35 
 ARG   0.003   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03774 (  343)
  hydrogen bonds       : angle       4.09893 (  978)
  covalent geometry    : bond        0.00359 ( 4610)
  covalent geometry    : angle       0.57753 ( 6330)
  Misc. bond           : bond        0.08802 (    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
  59 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.497 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6511 (mtt)
REVERT: A   99 LYS cc_start: 0.8155 (mttm) cc_final: 0.7847 (mtmt)
REVERT: B   66 LYS cc_start: 0.7691 (mmmm) cc_final: 0.7201 (mttt)
REVERT: B   95 LYS cc_start: 0.7918 (tmtt) cc_final: 0.7248 (mptt)
REVERT: B  104 ARG cc_start: 0.7463 (ttp80) cc_final: 0.6280 (mpt180)
REVERT: C   61 LYS cc_start: 0.8144 (mttt) cc_final: 0.7660 (mtpt)
REVERT: C   76 MET cc_start: 0.7017 (mtt) cc_final: 0.6808 (mtt)
REVERT: C   99 LYS cc_start: 0.8161 (mttp) cc_final: 0.7885 (mtmt)
REVERT: C  127 LYS cc_start: 0.7437 (mtmt) cc_final: 0.7057 (mttt)
REVERT: D   66 LYS cc_start: 0.7745 (mmmm) cc_final: 0.7080 (mttt)
REVERT: D   95 LYS cc_start: 0.7982 (tttt) cc_final: 0.7263 (mptt)
REVERT: D  104 ARG cc_start: 0.7445 (ttp80) cc_final: 0.6221 (mpt180)
REVERT: D  120 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6879 (tttp)
  outliers start: 9
  outliers final: 3
  residues processed: 56
  average time/residue: 2.1571
  time to fit residues: 124.8650
Evaluate side-chains
  53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  120 LYS
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 31 optimal weight:    0.3980
   chunk 49 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  89 HIS
D 131 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.171041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.146462 restraints weight = 3932.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 1.09
r_work: 0.3400 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3241 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.139   4614  Z= 0.190
  Angle     :  0.643   7.250   6330  Z= 0.303
  Chirality :  0.043   0.131    692
  Planarity :  0.006   0.050    790
  Dihedral  :  9.615  75.303    622
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 12.56 %
    Favored  : 85.68 %
  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:  2.17 (0.35), residues: 558
  helix:  1.84 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.12 (0.56), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  14 
 HIS   0.004   0.001   HIS C 112 
 PHE   0.015   0.002   PHE B  85 
 TYR   0.005   0.001   TYR D  35 
 ARG   0.002   0.001   ARG A  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04590 (  343)
  hydrogen bonds       : angle       4.30270 (  978)
  covalent geometry    : bond        0.00494 ( 4610)
  covalent geometry    : angle       0.64339 ( 6330)
  Misc. bond           : bond        0.12705 (    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
  61 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.808 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6511 (mtt)
REVERT: A   99 LYS cc_start: 0.8200 (mttm) cc_final: 0.7878 (mtmt)
REVERT: B   66 LYS cc_start: 0.7772 (mmmm) cc_final: 0.7156 (mttt)
REVERT: B   95 LYS cc_start: 0.7964 (tmtt) cc_final: 0.7289 (mptt)
REVERT: B  104 ARG cc_start: 0.7568 (ttp80) cc_final: 0.6320 (mpt180)
REVERT: B  132 LYS cc_start: 0.8172 (ptmt) cc_final: 0.7710 (ptpt)
REVERT: C   61 LYS cc_start: 0.8182 (mttt) cc_final: 0.7702 (mtpt)
REVERT: C   76 MET cc_start: 0.7071 (mtt) cc_final: 0.6723 (mtt)
REVERT: C   99 LYS cc_start: 0.8213 (mttp) cc_final: 0.7933 (mtmt)
REVERT: D   66 LYS cc_start: 0.7815 (mmmm) cc_final: 0.7127 (mttt)
REVERT: D   95 LYS cc_start: 0.8027 (tttt) cc_final: 0.7341 (mptt)
REVERT: D  104 ARG cc_start: 0.7540 (ttp80) cc_final: 0.6255 (mpt180)
REVERT: D  120 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6905 (tttp)
  outliers start: 8
  outliers final: 3
  residues processed: 58
  average time/residue: 2.4530
  time to fit residues: 146.8010
Evaluate side-chains
  55 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  120 LYS
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:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 54 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0870
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  89 HIS
D 131 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.173565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.148007 restraints weight = 3970.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 1.15
r_work: 0.3424 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093   4614  Z= 0.128
  Angle     :  0.575   6.662   6330  Z= 0.266
  Chirality :  0.039   0.121    692
  Planarity :  0.005   0.048    790
  Dihedral  :  9.261  75.497    622
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 12.78 %
    Favored  : 85.02 %
  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:  2.55 (0.36), residues: 558
  helix:  2.15 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.09 (0.56), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  14 
 HIS   0.003   0.001   HIS D 117 
 PHE   0.012   0.001   PHE D 118 
 TYR   0.005   0.001   TYR D 130 
 ARG   0.002   0.000   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03533 (  343)
  hydrogen bonds       : angle       4.02685 (  978)
  covalent geometry    : bond        0.00336 ( 4610)
  covalent geometry    : angle       0.57479 ( 6330)
  Misc. bond           : bond        0.07712 (    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
  60 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.472 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6540 (mtt)
REVERT: A   99 LYS cc_start: 0.8151 (mttm) cc_final: 0.7826 (mtmt)
REVERT: B   66 LYS cc_start: 0.7694 (mmmm) cc_final: 0.7175 (mttt)
REVERT: B   95 LYS cc_start: 0.7942 (tmtt) cc_final: 0.7293 (mptt)
REVERT: B  104 ARG cc_start: 0.7498 (ttp80) cc_final: 0.6256 (mpt180)
REVERT: B  121 GLU cc_start: 0.7561 (pm20) cc_final: 0.7282 (pm20)
REVERT: C   61 LYS cc_start: 0.8108 (mttt) cc_final: 0.7637 (mtpt)
REVERT: C   76 MET cc_start: 0.7080 (mtt) cc_final: 0.6755 (mtt)
REVERT: C   99 LYS cc_start: 0.8141 (mttp) cc_final: 0.7854 (mtmt)
REVERT: D   66 LYS cc_start: 0.7727 (mmmm) cc_final: 0.7232 (mttt)
REVERT: D   95 LYS cc_start: 0.7925 (tttt) cc_final: 0.7266 (mptt)
REVERT: D  104 ARG cc_start: 0.7456 (ttp80) cc_final: 0.6184 (mpt180)
REVERT: D  120 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6919 (tttp)
  outliers start: 10
  outliers final: 2
  residues processed: 57
  average time/residue: 2.5073
  time to fit residues: 146.9509
Evaluate side-chains
  51 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  120 LYS
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 4 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0870
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  89 HIS
D 131 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.173103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.147471 restraints weight = 3917.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 1.15
r_work: 0.3435 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3276 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.109   4614  Z= 0.136
  Angle     :  0.582   6.507   6330  Z= 0.270
  Chirality :  0.039   0.130    692
  Planarity :  0.005   0.048    790
  Dihedral  :  9.191  75.051    622
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 12.56 %
    Favored  : 85.68 %
  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:  2.56 (0.36), residues: 558
  helix:  2.17 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.04 (0.56), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  14 
 HIS   0.004   0.001   HIS D 117 
 PHE   0.013   0.001   PHE D 118 
 TYR   0.005   0.001   TYR D 130 
 ARG   0.002   0.001   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03696 (  343)
  hydrogen bonds       : angle       4.03451 (  978)
  covalent geometry    : bond        0.00355 ( 4610)
  covalent geometry    : angle       0.58158 ( 6330)
  Misc. bond           : bond        0.09127 (    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
  61 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.488 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6582 (mtt)
REVERT: A   99 LYS cc_start: 0.8129 (mttm) cc_final: 0.7796 (mtmt)
REVERT: B   66 LYS cc_start: 0.7667 (mmmm) cc_final: 0.7143 (mttt)
REVERT: B   95 LYS cc_start: 0.7937 (tmtt) cc_final: 0.7308 (mptt)
REVERT: B  104 ARG cc_start: 0.7472 (ttp80) cc_final: 0.6211 (mpt180)
REVERT: B  121 GLU cc_start: 0.7578 (pm20) cc_final: 0.7349 (pm20)
REVERT: C   61 LYS cc_start: 0.8067 (mttt) cc_final: 0.7595 (mtpt)
REVERT: C   76 MET cc_start: 0.7126 (mtt) cc_final: 0.6825 (mtt)
REVERT: C   99 LYS cc_start: 0.8109 (mttp) cc_final: 0.7819 (mtmt)
REVERT: D   66 LYS cc_start: 0.7715 (mmmm) cc_final: 0.7008 (mttt)
REVERT: D   95 LYS cc_start: 0.7940 (tttt) cc_final: 0.7285 (mptt)
REVERT: D  104 ARG cc_start: 0.7443 (ttp80) cc_final: 0.6156 (mpt180)
REVERT: D  120 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6949 (tttp)
  outliers start: 8
  outliers final: 4
  residues processed: 58
  average time/residue: 1.4931
  time to fit residues: 89.4443
Evaluate side-chains
  56 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  120 LYS
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 21 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C  89 HIS
D 131 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.174107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.154424 restraints weight = 3930.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 0.92
r_work: 0.3459 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3323 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.126   4614  Z= 0.160
  Angle     :  0.608   6.515   6330  Z= 0.284
  Chirality :  0.041   0.125    692
  Planarity :  0.006   0.049    790
  Dihedral  :  9.197  72.600    622
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.00 %
    Favored  : 84.80 %
  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:  2.32 (0.35), residues: 558
  helix:  1.98 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.04 (0.56), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  14 
 HIS   0.004   0.001   HIS D 117 
 PHE   0.012   0.001   PHE D 118 
 TYR   0.005   0.001   TYR D 130 
 ARG   0.002   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04083 (  343)
  hydrogen bonds       : angle       4.14606 (  978)
  covalent geometry    : bond        0.00420 ( 4610)
  covalent geometry    : angle       0.60823 ( 6330)
  Misc. bond           : bond        0.11506 (    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
  63 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.605 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6604 (mtt)
REVERT: A   99 LYS cc_start: 0.8225 (mttm) cc_final: 0.8003 (mtmt)
REVERT: B   66 LYS cc_start: 0.7912 (mmmm) cc_final: 0.7522 (mttt)
REVERT: B   95 LYS cc_start: 0.8019 (tmtt) cc_final: 0.7515 (mptt)
REVERT: B  104 ARG cc_start: 0.7593 (ttp80) cc_final: 0.6546 (mpt180)
REVERT: C   61 LYS cc_start: 0.8228 (mttt) cc_final: 0.7837 (mtpt)
REVERT: C   76 MET cc_start: 0.7225 (mtt) cc_final: 0.6917 (mtt)
REVERT: D   66 LYS cc_start: 0.7928 (mmmm) cc_final: 0.7385 (mttt)
REVERT: D   95 LYS cc_start: 0.7994 (tttt) cc_final: 0.7510 (mptt)
REVERT: D  104 ARG cc_start: 0.7584 (ttp80) cc_final: 0.6500 (mpt180)
REVERT: D  120 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.7127 (tptp)
  outliers start: 10
  outliers final: 4
  residues processed: 59
  average time/residue: 1.6087
  time to fit residues: 97.8022
Evaluate side-chains
  55 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  120 LYS
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 41 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C  89 HIS
D 131 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.173754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.154196 restraints weight = 3893.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 0.92
r_work: 0.3465 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.122   4614  Z= 0.160
  Angle     :  0.611   6.441   6330  Z= 0.285
  Chirality :  0.041   0.125    692
  Planarity :  0.006   0.049    790
  Dihedral  :  9.188  71.777    622
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 14.32 %
    Favored  : 83.92 %
  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:  2.32 (0.35), residues: 558
  helix:  1.98 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.03 (0.55), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  14 
 HIS   0.004   0.001   HIS D 117 
 PHE   0.012   0.001   PHE D 118 
 TYR   0.005   0.001   TYR B  35 
 ARG   0.002   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04032 (  343)
  hydrogen bonds       : angle       4.13890 (  978)
  covalent geometry    : bond        0.00422 ( 4610)
  covalent geometry    : angle       0.61149 ( 6330)
  Misc. bond           : bond        0.10934 (    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
  57 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.428 
Fit side-chains
REVERT: A   99 LYS cc_start: 0.8214 (mttm) cc_final: 0.7998 (mtmt)
REVERT: B   66 LYS cc_start: 0.7892 (mmmm) cc_final: 0.7504 (mttt)
REVERT: B   95 LYS cc_start: 0.7986 (tmtt) cc_final: 0.7516 (mptt)
REVERT: B  104 ARG cc_start: 0.7587 (ttp80) cc_final: 0.6542 (mpt180)
REVERT: B  132 LYS cc_start: 0.8268 (ptmt) cc_final: 0.7701 (ptpt)
REVERT: C   61 LYS cc_start: 0.8212 (mttt) cc_final: 0.7822 (mtpt)
REVERT: C   76 MET cc_start: 0.7250 (mtt) cc_final: 0.6956 (mtt)
REVERT: D   66 LYS cc_start: 0.7940 (mmmm) cc_final: 0.7395 (mttt)
REVERT: D   68 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7426 (mp)
REVERT: D   95 LYS cc_start: 0.7993 (tttt) cc_final: 0.7520 (mptt)
REVERT: D  104 ARG cc_start: 0.7572 (ttp80) cc_final: 0.6514 (mpt180)
REVERT: D  120 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.7126 (tptp)
  outliers start: 8
  outliers final: 4
  residues processed: 54
  average time/residue: 1.5944
  time to fit residues: 88.8177
Evaluate side-chains
  54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue  120 LYS
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 41 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 47 optimal weight:    0.3980
   chunk 33 optimal weight:    0.6980
   chunk 31 optimal weight:    0.4980
   chunk 19 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 36 optimal weight:    0.4980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
C  89 HIS
D 131 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.191278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.168521 restraints weight = 3521.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3746 rms_B_bonded: 1.06
r_work: 0.3619 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3468 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.104   4614  Z= 0.129
  Angle     :  0.575   6.746   6330  Z= 0.265
  Chirality :  0.039   0.119    692
  Planarity :  0.005   0.048    790
  Dihedral  :  9.094  73.735    622
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 14.10 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.60 (0.36), residues: 558
  helix:  2.21 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.00 (0.55), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  14 
 HIS   0.003   0.001   HIS C  89 
 PHE   0.010   0.001   PHE D 118 
 TYR   0.005   0.001   TYR D 130 
 ARG   0.002   0.000   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03467 (  343)
  hydrogen bonds       : angle       3.97848 (  978)
  covalent geometry    : bond        0.00338 ( 4610)
  covalent geometry    : angle       0.57509 ( 6330)
  Misc. bond           : bond        0.08280 (    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
  59 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.498 
Fit side-chains
REVERT: A   99 LYS cc_start: 0.8089 (mttm) cc_final: 0.7780 (mtmt)
REVERT: B   66 LYS cc_start: 0.7711 (mmmm) cc_final: 0.7195 (mttt)
REVERT: B   95 LYS cc_start: 0.7950 (tmtt) cc_final: 0.7421 (mptt)
REVERT: B  104 ARG cc_start: 0.7486 (ttp80) cc_final: 0.6299 (mpt180)
REVERT: C   61 LYS cc_start: 0.8067 (mttt) cc_final: 0.7604 (mtpt)
REVERT: C   76 MET cc_start: 0.7205 (mtt) cc_final: 0.6986 (mtt)
REVERT: D   66 LYS cc_start: 0.7745 (mmmm) cc_final: 0.7272 (mtmt)
REVERT: D   68 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7229 (mp)
REVERT: D   95 LYS cc_start: 0.7951 (tttt) cc_final: 0.7382 (mptt)
REVERT: D  104 ARG cc_start: 0.7471 (ttp80) cc_final: 0.6269 (mpt180)
REVERT: D  120 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6938 (tptp)
  outliers start: 8
  outliers final: 3
  residues processed: 57
  average time/residue: 1.5543
  time to fit residues: 91.4408
Evaluate side-chains
  53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue  120 LYS
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0470
   chunk 33 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0570
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
C  89 HIS
D 131 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.187432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.168045 restraints weight = 3582.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3759 rms_B_bonded: 0.91
r_work: 0.3626 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3478 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.107   4614  Z= 0.125
  Angle     :  0.572   6.955   6330  Z= 0.264
  Chirality :  0.039   0.119    692
  Planarity :  0.005   0.048    790
  Dihedral  :  9.085  74.217    622
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 14.32 %
    Favored  : 84.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.68 (0.36), residues: 558
  helix:  2.28 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop : -0.02 (0.55), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  14 
 HIS   0.003   0.001   HIS C  89 
 PHE   0.011   0.001   PHE D 118 
 TYR   0.006   0.001   TYR D 130 
 ARG   0.002   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03444 (  343)
  hydrogen bonds       : angle       3.95342 (  978)
  covalent geometry    : bond        0.00327 ( 4610)
  covalent geometry    : angle       0.57237 ( 6330)
  Misc. bond           : bond        0.08538 (    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
  58 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.436 
Fit side-chains
REVERT: A   99 LYS cc_start: 0.8137 (mttm) cc_final: 0.7889 (mtmt)
REVERT: B   66 LYS cc_start: 0.7828 (mmmm) cc_final: 0.7367 (mttt)
REVERT: B   95 LYS cc_start: 0.8011 (tmtt) cc_final: 0.7518 (mptt)
REVERT: B  104 ARG cc_start: 0.7541 (ttp80) cc_final: 0.6472 (mpt180)
REVERT: C   61 LYS cc_start: 0.8143 (mttt) cc_final: 0.7735 (mtpt)
REVERT: C   76 MET cc_start: 0.7269 (mtt) cc_final: 0.7045 (mtt)
REVERT: D   66 LYS cc_start: 0.7851 (mmmm) cc_final: 0.7440 (mtmt)
REVERT: D   68 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7393 (mp)
REVERT: D   95 LYS cc_start: 0.7986 (tttt) cc_final: 0.7499 (mptt)
REVERT: D  104 ARG cc_start: 0.7507 (ttp80) cc_final: 0.6433 (mpt180)
REVERT: D  120 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7020 (tptp)
  outliers start: 6
  outliers final: 3
  residues processed: 57
  average time/residue: 1.5580
  time to fit residues: 91.5519
Evaluate side-chains
  54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue  120 LYS
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 41 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 42 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:
C  89 HIS
D 131 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.175103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.153637 restraints weight = 3768.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3857 rms_B_bonded: 0.98
r_work: 0.3721 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3571 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.126   4614  Z= 0.150
  Angle     :  0.602   6.970   6330  Z= 0.280
  Chirality :  0.040   0.124    692
  Planarity :  0.005   0.048    790
  Dihedral  :  9.153  72.408    622
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 13.88 %
    Favored  : 84.58 %
  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:  2.47 (0.35), residues: 558
  helix:  2.13 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop : -0.09 (0.55), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  14 
 HIS   0.004   0.001   HIS C  89 
 PHE   0.012   0.001   PHE D 118 
 TYR   0.006   0.001   TYR D 130 
 ARG   0.002   0.001   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03903 (  343)
  hydrogen bonds       : angle       4.08160 (  978)
  covalent geometry    : bond        0.00395 ( 4610)
  covalent geometry    : angle       0.60153 ( 6330)
  Misc. bond           : bond        0.11116 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3887.08 seconds
wall clock time: 69 minutes 0.78 seconds (4140.78 seconds total)